| anno_start anno_end anno_text entity_type sentence section | |
| 24 34 Coenzyme A chemical The Structural Basis of Coenzyme A Recycling in a Bacterial Organelle TITLE | |
| 50 59 Bacterial taxonomy_domain The Structural Basis of Coenzyme A Recycling in a Bacterial Organelle TITLE | |
| 0 9 Bacterial taxonomy_domain Bacterial Microcompartments (BMCs) are proteinaceous organelles that encapsulate critical segments of autotrophic and heterotrophic metabolic pathways; they are functionally diverse and are found across 23 different phyla. ABSTRACT | |
| 10 27 Microcompartments complex_assembly Bacterial Microcompartments (BMCs) are proteinaceous organelles that encapsulate critical segments of autotrophic and heterotrophic metabolic pathways; they are functionally diverse and are found across 23 different phyla. ABSTRACT | |
| 29 33 BMCs complex_assembly Bacterial Microcompartments (BMCs) are proteinaceous organelles that encapsulate critical segments of autotrophic and heterotrophic metabolic pathways; they are functionally diverse and are found across 23 different phyla. ABSTRACT | |
| 16 25 catabolic protein_state The majority of catabolic BMCs (metabolosomes) compartmentalize a common core of enzymes to metabolize compounds via a toxic and/or volatile aldehyde intermediate. ABSTRACT | |
| 26 30 BMCs complex_assembly The majority of catabolic BMCs (metabolosomes) compartmentalize a common core of enzymes to metabolize compounds via a toxic and/or volatile aldehyde intermediate. ABSTRACT | |
| 32 45 metabolosomes complex_assembly The majority of catabolic BMCs (metabolosomes) compartmentalize a common core of enzymes to metabolize compounds via a toxic and/or volatile aldehyde intermediate. ABSTRACT | |
| 141 149 aldehyde chemical The majority of catabolic BMCs (metabolosomes) compartmentalize a common core of enzymes to metabolize compounds via a toxic and/or volatile aldehyde intermediate. ABSTRACT | |
| 16 35 phosphotransacylase protein_type The core enzyme phosphotransacylase (PTAC) recycles Coenzyme A and generates an acyl phosphate that can serve as an energy source. ABSTRACT | |
| 37 41 PTAC protein_type The core enzyme phosphotransacylase (PTAC) recycles Coenzyme A and generates an acyl phosphate that can serve as an energy source. ABSTRACT | |
| 52 62 Coenzyme A chemical The core enzyme phosphotransacylase (PTAC) recycles Coenzyme A and generates an acyl phosphate that can serve as an energy source. ABSTRACT | |
| 80 94 acyl phosphate chemical The core enzyme phosphotransacylase (PTAC) recycles Coenzyme A and generates an acyl phosphate that can serve as an energy source. ABSTRACT | |
| 4 8 PTAC protein_type The PTAC predominantly associated with metabolosomes (PduL) has no sequence homology to the PTAC ubiquitous among fermentative bacteria (Pta). ABSTRACT | |
| 39 52 metabolosomes complex_assembly The PTAC predominantly associated with metabolosomes (PduL) has no sequence homology to the PTAC ubiquitous among fermentative bacteria (Pta). ABSTRACT | |
| 54 58 PduL protein_type The PTAC predominantly associated with metabolosomes (PduL) has no sequence homology to the PTAC ubiquitous among fermentative bacteria (Pta). ABSTRACT | |
| 92 96 PTAC protein_type The PTAC predominantly associated with metabolosomes (PduL) has no sequence homology to the PTAC ubiquitous among fermentative bacteria (Pta). ABSTRACT | |
| 114 135 fermentative bacteria taxonomy_domain The PTAC predominantly associated with metabolosomes (PduL) has no sequence homology to the PTAC ubiquitous among fermentative bacteria (Pta). ABSTRACT | |
| 137 140 Pta protein_type The PTAC predominantly associated with metabolosomes (PduL) has no sequence homology to the PTAC ubiquitous among fermentative bacteria (Pta). ABSTRACT | |
| 36 40 PduL protein_type Here, we report two high-resolution PduL crystal structures with bound substrates. ABSTRACT | |
| 41 59 crystal structures evidence Here, we report two high-resolution PduL crystal structures with bound substrates. ABSTRACT | |
| 60 81 with bound substrates protein_state Here, we report two high-resolution PduL crystal structures with bound substrates. ABSTRACT | |
| 4 8 PduL protein_type The PduL fold is unrelated to that of Pta; it contains a dimetal active site involved in a catalytic mechanism distinct from that of the housekeeping PTAC. ABSTRACT | |
| 9 13 fold structure_element The PduL fold is unrelated to that of Pta; it contains a dimetal active site involved in a catalytic mechanism distinct from that of the housekeeping PTAC. ABSTRACT | |
| 30 34 that structure_element The PduL fold is unrelated to that of Pta; it contains a dimetal active site involved in a catalytic mechanism distinct from that of the housekeeping PTAC. ABSTRACT | |
| 38 41 Pta protein_type The PduL fold is unrelated to that of Pta; it contains a dimetal active site involved in a catalytic mechanism distinct from that of the housekeeping PTAC. ABSTRACT | |
| 57 76 dimetal active site site The PduL fold is unrelated to that of Pta; it contains a dimetal active site involved in a catalytic mechanism distinct from that of the housekeeping PTAC. ABSTRACT | |
| 137 149 housekeeping protein_state The PduL fold is unrelated to that of Pta; it contains a dimetal active site involved in a catalytic mechanism distinct from that of the housekeeping PTAC. ABSTRACT | |
| 150 154 PTAC protein_type The PduL fold is unrelated to that of Pta; it contains a dimetal active site involved in a catalytic mechanism distinct from that of the housekeeping PTAC. ABSTRACT | |
| 13 17 PduL protein_type Accordingly, PduL and Pta exemplify functional, but not structural, convergent evolution. ABSTRACT | |
| 22 25 Pta protein_type Accordingly, PduL and Pta exemplify functional, but not structural, convergent evolution. ABSTRACT | |
| 4 8 PduL protein_type The PduL structure, in the context of the catalytic core, completes our understanding of the structural basis of cofactor recycling in the metabolosome lumen. ABSTRACT | |
| 9 18 structure evidence The PduL structure, in the context of the catalytic core, completes our understanding of the structural basis of cofactor recycling in the metabolosome lumen. ABSTRACT | |
| 139 151 metabolosome complex_assembly The PduL structure, in the context of the catalytic core, completes our understanding of the structural basis of cofactor recycling in the metabolosome lumen. ABSTRACT | |
| 25 34 structure evidence This study describes the structure of a novel phosphotransacylase enzyme that facilitates the recycling of the essential cofactor acetyl-CoA within a bacterial organelle and discusses the properties of the enzyme's active site and how it is packaged into the organelle. ABSTRACT | |
| 46 65 phosphotransacylase protein_type This study describes the structure of a novel phosphotransacylase enzyme that facilitates the recycling of the essential cofactor acetyl-CoA within a bacterial organelle and discusses the properties of the enzyme's active site and how it is packaged into the organelle. ABSTRACT | |
| 130 140 acetyl-CoA chemical This study describes the structure of a novel phosphotransacylase enzyme that facilitates the recycling of the essential cofactor acetyl-CoA within a bacterial organelle and discusses the properties of the enzyme's active site and how it is packaged into the organelle. ABSTRACT | |
| 150 159 bacterial taxonomy_domain This study describes the structure of a novel phosphotransacylase enzyme that facilitates the recycling of the essential cofactor acetyl-CoA within a bacterial organelle and discusses the properties of the enzyme's active site and how it is packaged into the organelle. ABSTRACT | |
| 215 226 active site site This study describes the structure of a novel phosphotransacylase enzyme that facilitates the recycling of the essential cofactor acetyl-CoA within a bacterial organelle and discusses the properties of the enzyme's active site and how it is packaged into the organelle. ABSTRACT | |
| 57 60 ATP chemical In metabolism, molecules with “high-energy” bonds (e.g., ATP and Acetyl~CoA) are critical for both catabolic and anabolic processes. ABSTRACT | |
| 65 75 Acetyl~CoA chemical In metabolism, molecules with “high-energy” bonds (e.g., ATP and Acetyl~CoA) are critical for both catabolic and anabolic processes. ABSTRACT | |
| 4 23 phosphotransacylase protein_type The phosphotransacylase (Pta) enzyme catalyzes the conversion between acyl-CoA and acyl-phosphate. ABSTRACT | |
| 25 28 Pta protein_type The phosphotransacylase (Pta) enzyme catalyzes the conversion between acyl-CoA and acyl-phosphate. ABSTRACT | |
| 70 78 acyl-CoA chemical The phosphotransacylase (Pta) enzyme catalyzes the conversion between acyl-CoA and acyl-phosphate. ABSTRACT | |
| 83 97 acyl-phosphate chemical The phosphotransacylase (Pta) enzyme catalyzes the conversion between acyl-CoA and acyl-phosphate. ABSTRACT | |
| 32 40 acyl-CoA chemical This reaction directly links an acyl-CoA with ATP generation via substrate-level phosphorylation, producing short-chain fatty acids (e.g., acetate), and also provides a path for short-chain fatty acids to enter central metabolism. ABSTRACT | |
| 46 49 ATP chemical This reaction directly links an acyl-CoA with ATP generation via substrate-level phosphorylation, producing short-chain fatty acids (e.g., acetate), and also provides a path for short-chain fatty acids to enter central metabolism. ABSTRACT | |
| 108 131 short-chain fatty acids chemical This reaction directly links an acyl-CoA with ATP generation via substrate-level phosphorylation, producing short-chain fatty acids (e.g., acetate), and also provides a path for short-chain fatty acids to enter central metabolism. ABSTRACT | |
| 139 146 acetate chemical This reaction directly links an acyl-CoA with ATP generation via substrate-level phosphorylation, producing short-chain fatty acids (e.g., acetate), and also provides a path for short-chain fatty acids to enter central metabolism. ABSTRACT | |
| 178 201 short-chain fatty acids chemical This reaction directly links an acyl-CoA with ATP generation via substrate-level phosphorylation, producing short-chain fatty acids (e.g., acetate), and also provides a path for short-chain fatty acids to enter central metabolism. ABSTRACT | |
| 33 42 conserved protein_state Due to this key function, Pta is conserved across the bacterial kingdom. ABSTRACT | |
| 54 71 bacterial kingdom taxonomy_domain Due to this key function, Pta is conserved across the bacterial kingdom. ABSTRACT | |
| 24 43 phosphotransacylase protein_type Recently, a new type of phosphotransacylase was described that shares no evolutionary relation to Pta. ABSTRACT | |
| 98 101 Pta protein_type Recently, a new type of phosphotransacylase was described that shares no evolutionary relation to Pta. ABSTRACT | |
| 13 17 PduL protein_type This enzyme, PduL, is exclusively associated with organelles called bacterial microcompartments, which are used to catabolize various compounds. ABSTRACT | |
| 22 33 exclusively protein_state This enzyme, PduL, is exclusively associated with organelles called bacterial microcompartments, which are used to catabolize various compounds. ABSTRACT | |
| 68 77 bacterial taxonomy_domain This enzyme, PduL, is exclusively associated with organelles called bacterial microcompartments, which are used to catabolize various compounds. ABSTRACT | |
| 78 95 microcompartments complex_assembly This enzyme, PduL, is exclusively associated with organelles called bacterial microcompartments, which are used to catabolize various compounds. ABSTRACT | |
| 14 18 PduL protein_type Not only does PduL facilitate substrate level phosphorylation, but it also is critical for cofactor recycling within, and product efflux from, the organelle. ABSTRACT | |
| 3 9 solved experimental_method We solved the structure of this convergent phosphotransacylase and show that it is completely structurally different from Pta, including its active site architecture. ABSTRACT | |
| 14 23 structure evidence We solved the structure of this convergent phosphotransacylase and show that it is completely structurally different from Pta, including its active site architecture. ABSTRACT | |
| 32 42 convergent protein_state We solved the structure of this convergent phosphotransacylase and show that it is completely structurally different from Pta, including its active site architecture. ABSTRACT | |
| 43 62 phosphotransacylase protein_type We solved the structure of this convergent phosphotransacylase and show that it is completely structurally different from Pta, including its active site architecture. ABSTRACT | |
| 122 125 Pta protein_type We solved the structure of this convergent phosphotransacylase and show that it is completely structurally different from Pta, including its active site architecture. ABSTRACT | |
| 141 152 active site site We solved the structure of this convergent phosphotransacylase and show that it is completely structurally different from Pta, including its active site architecture. ABSTRACT | |
| 0 9 Bacterial taxonomy_domain Bacterial Microcompartments (BMCs) are organelles that encapsulate enzymes for sequential biochemical reactions within a protein shell. INTRO | |
| 10 27 Microcompartments complex_assembly Bacterial Microcompartments (BMCs) are organelles that encapsulate enzymes for sequential biochemical reactions within a protein shell. INTRO | |
| 29 33 BMCs complex_assembly Bacterial Microcompartments (BMCs) are organelles that encapsulate enzymes for sequential biochemical reactions within a protein shell. INTRO | |
| 129 134 shell structure_element Bacterial Microcompartments (BMCs) are organelles that encapsulate enzymes for sequential biochemical reactions within a protein shell. INTRO | |
| 4 9 shell structure_element The shell is typically composed of three types of protein subunits, which form either hexagonal (BMC-H and BMC-T) or pentagonal (BMC-P) tiles that assemble into a polyhedral shell. INTRO | |
| 86 95 hexagonal protein_state The shell is typically composed of three types of protein subunits, which form either hexagonal (BMC-H and BMC-T) or pentagonal (BMC-P) tiles that assemble into a polyhedral shell. INTRO | |
| 97 102 BMC-H complex_assembly The shell is typically composed of three types of protein subunits, which form either hexagonal (BMC-H and BMC-T) or pentagonal (BMC-P) tiles that assemble into a polyhedral shell. INTRO | |
| 107 112 BMC-T complex_assembly The shell is typically composed of three types of protein subunits, which form either hexagonal (BMC-H and BMC-T) or pentagonal (BMC-P) tiles that assemble into a polyhedral shell. INTRO | |
| 117 127 pentagonal protein_state The shell is typically composed of three types of protein subunits, which form either hexagonal (BMC-H and BMC-T) or pentagonal (BMC-P) tiles that assemble into a polyhedral shell. INTRO | |
| 129 134 BMC-P complex_assembly The shell is typically composed of three types of protein subunits, which form either hexagonal (BMC-H and BMC-T) or pentagonal (BMC-P) tiles that assemble into a polyhedral shell. INTRO | |
| 163 173 polyhedral protein_state The shell is typically composed of three types of protein subunits, which form either hexagonal (BMC-H and BMC-T) or pentagonal (BMC-P) tiles that assemble into a polyhedral shell. INTRO | |
| 174 179 shell structure_element The shell is typically composed of three types of protein subunits, which form either hexagonal (BMC-H and BMC-T) or pentagonal (BMC-P) tiles that assemble into a polyhedral shell. INTRO | |
| 18 23 shell structure_element The facets of the shell are composed primarily of hexamers that are typically perforated by pores lined with highly conserved, polar residues that presumably function as the conduits for metabolites into and out of the shell. INTRO | |
| 50 58 hexamers oligomeric_state The facets of the shell are composed primarily of hexamers that are typically perforated by pores lined with highly conserved, polar residues that presumably function as the conduits for metabolites into and out of the shell. INTRO | |
| 92 97 pores site The facets of the shell are composed primarily of hexamers that are typically perforated by pores lined with highly conserved, polar residues that presumably function as the conduits for metabolites into and out of the shell. INTRO | |
| 109 125 highly conserved protein_state The facets of the shell are composed primarily of hexamers that are typically perforated by pores lined with highly conserved, polar residues that presumably function as the conduits for metabolites into and out of the shell. INTRO | |
| 127 132 polar protein_state The facets of the shell are composed primarily of hexamers that are typically perforated by pores lined with highly conserved, polar residues that presumably function as the conduits for metabolites into and out of the shell. INTRO | |
| 133 141 residues structure_element The facets of the shell are composed primarily of hexamers that are typically perforated by pores lined with highly conserved, polar residues that presumably function as the conduits for metabolites into and out of the shell. INTRO | |
| 219 224 shell structure_element The facets of the shell are composed primarily of hexamers that are typically perforated by pores lined with highly conserved, polar residues that presumably function as the conduits for metabolites into and out of the shell. INTRO | |
| 4 57 vitamin B12-dependent propanediol-utilizing (PDU) BMC complex_assembly The vitamin B12-dependent propanediol-utilizing (PDU) BMC was one of the first functionally characterized catabolic BMCs; subsequently, other types have been implicated in the degradation of ethanolamine, choline, fucose, rhamnose, and ethanol, all of which produce different aldehyde intermediates (Table 1). INTRO | |
| 106 115 catabolic protein_state The vitamin B12-dependent propanediol-utilizing (PDU) BMC was one of the first functionally characterized catabolic BMCs; subsequently, other types have been implicated in the degradation of ethanolamine, choline, fucose, rhamnose, and ethanol, all of which produce different aldehyde intermediates (Table 1). INTRO | |
| 116 120 BMCs complex_assembly The vitamin B12-dependent propanediol-utilizing (PDU) BMC was one of the first functionally characterized catabolic BMCs; subsequently, other types have been implicated in the degradation of ethanolamine, choline, fucose, rhamnose, and ethanol, all of which produce different aldehyde intermediates (Table 1). INTRO | |
| 191 203 ethanolamine chemical The vitamin B12-dependent propanediol-utilizing (PDU) BMC was one of the first functionally characterized catabolic BMCs; subsequently, other types have been implicated in the degradation of ethanolamine, choline, fucose, rhamnose, and ethanol, all of which produce different aldehyde intermediates (Table 1). INTRO | |
| 205 212 choline chemical The vitamin B12-dependent propanediol-utilizing (PDU) BMC was one of the first functionally characterized catabolic BMCs; subsequently, other types have been implicated in the degradation of ethanolamine, choline, fucose, rhamnose, and ethanol, all of which produce different aldehyde intermediates (Table 1). INTRO | |
| 214 220 fucose chemical The vitamin B12-dependent propanediol-utilizing (PDU) BMC was one of the first functionally characterized catabolic BMCs; subsequently, other types have been implicated in the degradation of ethanolamine, choline, fucose, rhamnose, and ethanol, all of which produce different aldehyde intermediates (Table 1). INTRO | |
| 222 230 rhamnose chemical The vitamin B12-dependent propanediol-utilizing (PDU) BMC was one of the first functionally characterized catabolic BMCs; subsequently, other types have been implicated in the degradation of ethanolamine, choline, fucose, rhamnose, and ethanol, all of which produce different aldehyde intermediates (Table 1). INTRO | |
| 236 243 ethanol chemical The vitamin B12-dependent propanediol-utilizing (PDU) BMC was one of the first functionally characterized catabolic BMCs; subsequently, other types have been implicated in the degradation of ethanolamine, choline, fucose, rhamnose, and ethanol, all of which produce different aldehyde intermediates (Table 1). INTRO | |
| 276 284 aldehyde chemical The vitamin B12-dependent propanediol-utilizing (PDU) BMC was one of the first functionally characterized catabolic BMCs; subsequently, other types have been implicated in the degradation of ethanolamine, choline, fucose, rhamnose, and ethanol, all of which produce different aldehyde intermediates (Table 1). INTRO | |
| 15 36 bioinformatic studies experimental_method More recently, bioinformatic studies have demonstrated the widespread distribution of BMCs among diverse bacterial phyla and grouped them into 23 different functional types. INTRO | |
| 86 90 BMCs complex_assembly More recently, bioinformatic studies have demonstrated the widespread distribution of BMCs among diverse bacterial phyla and grouped them into 23 different functional types. INTRO | |
| 105 120 bacterial phyla taxonomy_domain More recently, bioinformatic studies have demonstrated the widespread distribution of BMCs among diverse bacterial phyla and grouped them into 23 different functional types. INTRO | |
| 45 54 catabolic protein_state The reactions carried out in the majority of catabolic BMCs (also known as metabolosomes) fit a generalized biochemical paradigm for the oxidation of aldehydes (Fig 1). INTRO | |
| 55 59 BMCs complex_assembly The reactions carried out in the majority of catabolic BMCs (also known as metabolosomes) fit a generalized biochemical paradigm for the oxidation of aldehydes (Fig 1). INTRO | |
| 75 88 metabolosomes complex_assembly The reactions carried out in the majority of catabolic BMCs (also known as metabolosomes) fit a generalized biochemical paradigm for the oxidation of aldehydes (Fig 1). INTRO | |
| 150 159 aldehydes chemical The reactions carried out in the majority of catabolic BMCs (also known as metabolosomes) fit a generalized biochemical paradigm for the oxidation of aldehydes (Fig 1). INTRO | |
| 16 19 BMC complex_assembly This involves a BMC-encapsulated signature enzyme that generates a toxic and/or volatile aldehyde that the BMC shell sequesters from the cytosol. INTRO | |
| 89 97 aldehyde chemical This involves a BMC-encapsulated signature enzyme that generates a toxic and/or volatile aldehyde that the BMC shell sequesters from the cytosol. INTRO | |
| 107 110 BMC complex_assembly This involves a BMC-encapsulated signature enzyme that generates a toxic and/or volatile aldehyde that the BMC shell sequesters from the cytosol. INTRO | |
| 111 116 shell structure_element This involves a BMC-encapsulated signature enzyme that generates a toxic and/or volatile aldehyde that the BMC shell sequesters from the cytosol. INTRO | |
| 4 12 aldehyde chemical The aldehyde is subsequently converted into an acyl-CoA by aldehyde dehydrogenase, which uses NAD+ and CoA as cofactors. INTRO | |
| 47 55 acyl-CoA chemical The aldehyde is subsequently converted into an acyl-CoA by aldehyde dehydrogenase, which uses NAD+ and CoA as cofactors. INTRO | |
| 59 81 aldehyde dehydrogenase protein_type The aldehyde is subsequently converted into an acyl-CoA by aldehyde dehydrogenase, which uses NAD+ and CoA as cofactors. INTRO | |
| 94 98 NAD+ chemical The aldehyde is subsequently converted into an acyl-CoA by aldehyde dehydrogenase, which uses NAD+ and CoA as cofactors. INTRO | |
| 103 106 CoA chemical The aldehyde is subsequently converted into an acyl-CoA by aldehyde dehydrogenase, which uses NAD+ and CoA as cofactors. INTRO | |
| 73 86 protein shell structure_element These two cofactors are relatively large, and their diffusion across the protein shell is thought to be restricted, necessitating their regeneration within the BMC lumen. INTRO | |
| 160 163 BMC complex_assembly These two cofactors are relatively large, and their diffusion across the protein shell is thought to be restricted, necessitating their regeneration within the BMC lumen. INTRO | |
| 0 4 NAD+ chemical NAD+ is recycled via alcohol dehydrogenase, and CoA is recycled via phosphotransacetylase (PTAC) (Fig 1). INTRO | |
| 21 42 alcohol dehydrogenase protein_type NAD+ is recycled via alcohol dehydrogenase, and CoA is recycled via phosphotransacetylase (PTAC) (Fig 1). INTRO | |
| 48 51 CoA chemical NAD+ is recycled via alcohol dehydrogenase, and CoA is recycled via phosphotransacetylase (PTAC) (Fig 1). INTRO | |
| 68 89 phosphotransacetylase protein_type NAD+ is recycled via alcohol dehydrogenase, and CoA is recycled via phosphotransacetylase (PTAC) (Fig 1). INTRO | |
| 91 95 PTAC protein_type NAD+ is recycled via alcohol dehydrogenase, and CoA is recycled via phosphotransacetylase (PTAC) (Fig 1). INTRO | |
| 25 28 BMC complex_assembly The final product of the BMC, an acyl-phosphate, can then be used to generate ATP via acyl kinase, or revert back to acyl-CoA by Pta for biosynthesis. INTRO | |
| 33 47 acyl-phosphate chemical The final product of the BMC, an acyl-phosphate, can then be used to generate ATP via acyl kinase, or revert back to acyl-CoA by Pta for biosynthesis. INTRO | |
| 78 81 ATP chemical The final product of the BMC, an acyl-phosphate, can then be used to generate ATP via acyl kinase, or revert back to acyl-CoA by Pta for biosynthesis. INTRO | |
| 86 97 acyl kinase protein_type The final product of the BMC, an acyl-phosphate, can then be used to generate ATP via acyl kinase, or revert back to acyl-CoA by Pta for biosynthesis. INTRO | |
| 117 125 acyl-CoA chemical The final product of the BMC, an acyl-phosphate, can then be used to generate ATP via acyl kinase, or revert back to acyl-CoA by Pta for biosynthesis. INTRO | |
| 129 132 Pta protein_type The final product of the BMC, an acyl-phosphate, can then be used to generate ATP via acyl kinase, or revert back to acyl-CoA by Pta for biosynthesis. INTRO | |
| 18 53 aldehyde and alcohol dehydrogenases protein_type Collectively, the aldehyde and alcohol dehydrogenases, as well as the PTAC, constitute the common metabolosome core. INTRO | |
| 70 74 PTAC protein_type Collectively, the aldehyde and alcohol dehydrogenases, as well as the PTAC, constitute the common metabolosome core. INTRO | |
| 98 110 metabolosome complex_assembly Collectively, the aldehyde and alcohol dehydrogenases, as well as the PTAC, constitute the common metabolosome core. INTRO | |
| 29 47 aldehyde-degrading protein_state General biochemical model of aldehyde-degrading BMCs (metabolosomes) illustrating the common metabolosome core enzymes and reactions. FIG | |
| 48 52 BMCs complex_assembly General biochemical model of aldehyde-degrading BMCs (metabolosomes) illustrating the common metabolosome core enzymes and reactions. FIG | |
| 54 67 metabolosomes complex_assembly General biochemical model of aldehyde-degrading BMCs (metabolosomes) illustrating the common metabolosome core enzymes and reactions. FIG | |
| 93 105 metabolosome complex_assembly General biochemical model of aldehyde-degrading BMCs (metabolosomes) illustrating the common metabolosome core enzymes and reactions. FIG | |
| 39 43 PTAC protein_type Substrates and cofactors involving the PTAC reaction are shown in red; other substrates and enzymes are shown in black, and other cofactors are shown in gray. FIG | |
| 28 37 catabolic protein_state Characterized and predicted catabolic BMC (metabolosome) types that represent the aldehyde-degrading paradigm (for definition of types see Kerfeld and Erbilgin). TABLE | |
| 38 41 BMC complex_assembly Characterized and predicted catabolic BMC (metabolosome) types that represent the aldehyde-degrading paradigm (for definition of types see Kerfeld and Erbilgin). TABLE | |
| 43 55 metabolosome complex_assembly Characterized and predicted catabolic BMC (metabolosome) types that represent the aldehyde-degrading paradigm (for definition of types see Kerfeld and Erbilgin). TABLE | |
| 82 90 aldehyde chemical Characterized and predicted catabolic BMC (metabolosome) types that represent the aldehyde-degrading paradigm (for definition of types see Kerfeld and Erbilgin). TABLE | |
| 5 9 PTAC protein_type "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 27 35 Aldehyde chemical "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 38 41 PDU complex_assembly "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 43 47 PduL protein_type "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 48 63 propionaldehyde chemical "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 66 70 EUT1 complex_assembly "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 71 78 PTA_PTB protein_type "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 79 91 acetaldehyde chemical "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 94 98 EUT2 complex_assembly "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 99 103 PduL protein_type "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 104 116 acetaldehyde chemical "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 119 122 ETU complex_assembly "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 128 140 acetaldehyde chemical "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 143 151 GRM1/CUT complex_assembly "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 152 156 PduL protein_type "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 157 169 acetaldehyde chemical "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 172 176 GRM2 complex_assembly "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 177 181 PduL protein_type "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 182 194 acetaldehyde chemical "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 197 204 GRM3*,4 complex_assembly "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 205 209 PduL protein_type "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 210 225 propionaldehyde chemical "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 228 236 GRM5/GRP complex_assembly "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 237 241 PduL protein_type "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 242 257 propionaldehyde chemical "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 260 263 PVM complex_assembly "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 265 269 PduL protein_type "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 270 282 lactaldehyde chemical "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 285 291 RMM1,2 complex_assembly "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 307 310 SPU complex_assembly "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 311 315 PduL protein_type "Name PTAC Type Sequestered Aldehyde PDU* PduL propionaldehyde EUT1 PTA_PTB acetaldehyde EUT2 PduL acetaldehyde ETU None acetaldehyde GRM1/CUT PduL acetaldehyde GRM2 PduL acetaldehyde GRM3*,4 PduL propionaldehyde GRM5/GRP PduL propionaldehyde PVM* PduL lactaldehyde RMM1,2 None unknown SPU PduL unknown " TABLE | |
| 2 6 PduL protein_type * PduL from these functional types of metabolosomes were purified in this study. TABLE | |
| 38 51 metabolosomes complex_assembly * PduL from these functional types of metabolosomes were purified in this study. TABLE | |
| 51 54 BMC complex_assembly The activities of core enzymes are not confined to BMC-associated functions: aldehyde and alcohol dehydrogenases are utilized in diverse metabolic reactions, and PTAC catalyzes a key biochemical reaction in the process of obtaining energy during fermentation. INTRO | |
| 77 112 aldehyde and alcohol dehydrogenases protein_type The activities of core enzymes are not confined to BMC-associated functions: aldehyde and alcohol dehydrogenases are utilized in diverse metabolic reactions, and PTAC catalyzes a key biochemical reaction in the process of obtaining energy during fermentation. INTRO | |
| 162 166 PTAC protein_type The activities of core enzymes are not confined to BMC-associated functions: aldehyde and alcohol dehydrogenases are utilized in diverse metabolic reactions, and PTAC catalyzes a key biochemical reaction in the process of obtaining energy during fermentation. INTRO | |
| 31 35 PTAC protein_type The concerted functioning of a PTAC and an acetate kinase (Ack) is crucial for ATP generation in the fermentation of pyruvate to acetate (see Reactions 1 and 2). INTRO | |
| 43 57 acetate kinase protein_type The concerted functioning of a PTAC and an acetate kinase (Ack) is crucial for ATP generation in the fermentation of pyruvate to acetate (see Reactions 1 and 2). INTRO | |
| 59 62 Ack protein_type The concerted functioning of a PTAC and an acetate kinase (Ack) is crucial for ATP generation in the fermentation of pyruvate to acetate (see Reactions 1 and 2). INTRO | |
| 79 82 ATP chemical The concerted functioning of a PTAC and an acetate kinase (Ack) is crucial for ATP generation in the fermentation of pyruvate to acetate (see Reactions 1 and 2). INTRO | |
| 117 125 pyruvate chemical The concerted functioning of a PTAC and an acetate kinase (Ack) is crucial for ATP generation in the fermentation of pyruvate to acetate (see Reactions 1 and 2). INTRO | |
| 129 136 acetate chemical The concerted functioning of a PTAC and an acetate kinase (Ack) is crucial for ATP generation in the fermentation of pyruvate to acetate (see Reactions 1 and 2). INTRO | |
| 45 67 fermentative organisms taxonomy_domain Both enzymes are, however, not restricted to fermentative organisms. INTRO | |
| 56 63 acetate chemical They can also work in the reverse direction to activate acetate to the CoA-thioester. INTRO | |
| 71 84 CoA-thioester chemical They can also work in the reverse direction to activate acetate to the CoA-thioester. INTRO | |
| 68 76 archaeal taxonomy_domain This occurs, for example, during acetoclastic methanogenesis in the archaeal Methanosarcina species. INTRO | |
| 77 99 Methanosarcina species taxonomy_domain This occurs, for example, during acetoclastic methanogenesis in the archaeal Methanosarcina species. INTRO | |
| 13 25 acetyl-S-CoA chemical Reaction 1: acetyl-S-CoA + Pi ←→ acetyl phosphate + CoA-SH (PTAC) INTRO | |
| 28 30 Pi chemical Reaction 1: acetyl-S-CoA + Pi ←→ acetyl phosphate + CoA-SH (PTAC) INTRO | |
| 34 50 acetyl phosphate chemical Reaction 1: acetyl-S-CoA + Pi ←→ acetyl phosphate + CoA-SH (PTAC) INTRO | |
| 53 59 CoA-SH chemical Reaction 1: acetyl-S-CoA + Pi ←→ acetyl phosphate + CoA-SH (PTAC) INTRO | |
| 61 65 PTAC protein_type Reaction 1: acetyl-S-CoA + Pi ←→ acetyl phosphate + CoA-SH (PTAC) INTRO | |
| 13 29 acetyl phosphate chemical Reaction 2: acetyl phosphate + ADP ←→ acetate + ATP (Ack) INTRO | |
| 32 35 ADP chemical Reaction 2: acetyl phosphate + ADP ←→ acetate + ATP (Ack) INTRO | |
| 39 46 acetate chemical Reaction 2: acetyl phosphate + ADP ←→ acetate + ATP (Ack) INTRO | |
| 49 52 ATP chemical Reaction 2: acetyl phosphate + ADP ←→ acetate + ATP (Ack) INTRO | |
| 54 57 Ack protein_type Reaction 2: acetyl phosphate + ADP ←→ acetate + ATP (Ack) INTRO | |
| 14 18 PTAC protein_type The canonical PTAC, Pta, is an ancient enzyme found in some eukaryotes and archaea, and widespread among the bacteria; 90% of the bacterial genomes in the Integrated Microbial Genomes database contain a gene encoding the PTA_PTB phosphotransacylase (Pfam domain PF01515). INTRO | |
| 20 23 Pta protein_type The canonical PTAC, Pta, is an ancient enzyme found in some eukaryotes and archaea, and widespread among the bacteria; 90% of the bacterial genomes in the Integrated Microbial Genomes database contain a gene encoding the PTA_PTB phosphotransacylase (Pfam domain PF01515). INTRO | |
| 60 70 eukaryotes taxonomy_domain The canonical PTAC, Pta, is an ancient enzyme found in some eukaryotes and archaea, and widespread among the bacteria; 90% of the bacterial genomes in the Integrated Microbial Genomes database contain a gene encoding the PTA_PTB phosphotransacylase (Pfam domain PF01515). INTRO | |
| 75 82 archaea taxonomy_domain The canonical PTAC, Pta, is an ancient enzyme found in some eukaryotes and archaea, and widespread among the bacteria; 90% of the bacterial genomes in the Integrated Microbial Genomes database contain a gene encoding the PTA_PTB phosphotransacylase (Pfam domain PF01515). INTRO | |
| 109 117 bacteria taxonomy_domain The canonical PTAC, Pta, is an ancient enzyme found in some eukaryotes and archaea, and widespread among the bacteria; 90% of the bacterial genomes in the Integrated Microbial Genomes database contain a gene encoding the PTA_PTB phosphotransacylase (Pfam domain PF01515). INTRO | |
| 130 139 bacterial taxonomy_domain The canonical PTAC, Pta, is an ancient enzyme found in some eukaryotes and archaea, and widespread among the bacteria; 90% of the bacterial genomes in the Integrated Microbial Genomes database contain a gene encoding the PTA_PTB phosphotransacylase (Pfam domain PF01515). INTRO | |
| 221 248 PTA_PTB phosphotransacylase protein_type The canonical PTAC, Pta, is an ancient enzyme found in some eukaryotes and archaea, and widespread among the bacteria; 90% of the bacterial genomes in the Integrated Microbial Genomes database contain a gene encoding the PTA_PTB phosphotransacylase (Pfam domain PF01515). INTRO | |
| 262 269 PF01515 structure_element The canonical PTAC, Pta, is an ancient enzyme found in some eukaryotes and archaea, and widespread among the bacteria; 90% of the bacterial genomes in the Integrated Microbial Genomes database contain a gene encoding the PTA_PTB phosphotransacylase (Pfam domain PF01515). INTRO | |
| 0 3 Pta protein_type Pta has been extensively characterized due to its key role in fermentation. INTRO | |
| 32 36 PTAC protein_type More recently, a second type of PTAC without any sequence homology to Pta was identified. INTRO | |
| 70 73 Pta protein_type More recently, a second type of PTAC without any sequence homology to Pta was identified. INTRO | |
| 14 18 PduL protein_type This protein, PduL (Pfam domain PF06130), was shown to catalyze the conversion of propionyl-CoA to propionyl-phosphate and is associated with a BMC involved in propanediol utilization, the PDU BMC. INTRO | |
| 32 39 PF06130 structure_element This protein, PduL (Pfam domain PF06130), was shown to catalyze the conversion of propionyl-CoA to propionyl-phosphate and is associated with a BMC involved in propanediol utilization, the PDU BMC. INTRO | |
| 82 95 propionyl-CoA chemical This protein, PduL (Pfam domain PF06130), was shown to catalyze the conversion of propionyl-CoA to propionyl-phosphate and is associated with a BMC involved in propanediol utilization, the PDU BMC. INTRO | |
| 99 118 propionyl-phosphate chemical This protein, PduL (Pfam domain PF06130), was shown to catalyze the conversion of propionyl-CoA to propionyl-phosphate and is associated with a BMC involved in propanediol utilization, the PDU BMC. INTRO | |
| 144 147 BMC complex_assembly This protein, PduL (Pfam domain PF06130), was shown to catalyze the conversion of propionyl-CoA to propionyl-phosphate and is associated with a BMC involved in propanediol utilization, the PDU BMC. INTRO | |
| 189 196 PDU BMC complex_assembly This protein, PduL (Pfam domain PF06130), was shown to catalyze the conversion of propionyl-CoA to propionyl-phosphate and is associated with a BMC involved in propanediol utilization, the PDU BMC. INTRO | |
| 5 9 pduL gene Both pduL and pta genes can be found in genetic loci of functionally distinct BMCs, although the PduL type is much more prevalent, being found in all but one type of metabolosome locus: EUT1 (Table 1). INTRO | |
| 14 17 pta gene Both pduL and pta genes can be found in genetic loci of functionally distinct BMCs, although the PduL type is much more prevalent, being found in all but one type of metabolosome locus: EUT1 (Table 1). INTRO | |
| 78 82 BMCs complex_assembly Both pduL and pta genes can be found in genetic loci of functionally distinct BMCs, although the PduL type is much more prevalent, being found in all but one type of metabolosome locus: EUT1 (Table 1). INTRO | |
| 97 101 PduL protein_type Both pduL and pta genes can be found in genetic loci of functionally distinct BMCs, although the PduL type is much more prevalent, being found in all but one type of metabolosome locus: EUT1 (Table 1). INTRO | |
| 166 184 metabolosome locus gene Both pduL and pta genes can be found in genetic loci of functionally distinct BMCs, although the PduL type is much more prevalent, being found in all but one type of metabolosome locus: EUT1 (Table 1). INTRO | |
| 186 190 EUT1 gene Both pduL and pta genes can be found in genetic loci of functionally distinct BMCs, although the PduL type is much more prevalent, being found in all but one type of metabolosome locus: EUT1 (Table 1). INTRO | |
| 86 93 PF06130 structure_element Furthermore, in the Integrated Microbial Genomes Database, 91% of genomes that encode PF06130 also encode genes for shell proteins. INTRO | |
| 70 88 aldehyde-oxidizing protein_state As a member of the core biochemical machinery of functionally diverse aldehyde-oxidizing metabolosomes, PduL must have a certain level of substrate plasticity (see Table 1) that is not required of Pta, which has generally been observed to prefer acetyl-CoA. PduL from the PDU BMC of Salmonella enterica favors propionyl-CoA over acetyl-CoA, and it is likely that PduL orthologs in functionally diverse BMCs would have substrate preferences for other CoA derivatives. INTRO | |
| 89 102 metabolosomes complex_assembly As a member of the core biochemical machinery of functionally diverse aldehyde-oxidizing metabolosomes, PduL must have a certain level of substrate plasticity (see Table 1) that is not required of Pta, which has generally been observed to prefer acetyl-CoA. PduL from the PDU BMC of Salmonella enterica favors propionyl-CoA over acetyl-CoA, and it is likely that PduL orthologs in functionally diverse BMCs would have substrate preferences for other CoA derivatives. INTRO | |
| 104 108 PduL protein_type As a member of the core biochemical machinery of functionally diverse aldehyde-oxidizing metabolosomes, PduL must have a certain level of substrate plasticity (see Table 1) that is not required of Pta, which has generally been observed to prefer acetyl-CoA. PduL from the PDU BMC of Salmonella enterica favors propionyl-CoA over acetyl-CoA, and it is likely that PduL orthologs in functionally diverse BMCs would have substrate preferences for other CoA derivatives. INTRO | |
| 197 200 Pta protein_type As a member of the core biochemical machinery of functionally diverse aldehyde-oxidizing metabolosomes, PduL must have a certain level of substrate plasticity (see Table 1) that is not required of Pta, which has generally been observed to prefer acetyl-CoA. PduL from the PDU BMC of Salmonella enterica favors propionyl-CoA over acetyl-CoA, and it is likely that PduL orthologs in functionally diverse BMCs would have substrate preferences for other CoA derivatives. INTRO | |
| 246 256 acetyl-CoA chemical As a member of the core biochemical machinery of functionally diverse aldehyde-oxidizing metabolosomes, PduL must have a certain level of substrate plasticity (see Table 1) that is not required of Pta, which has generally been observed to prefer acetyl-CoA. PduL from the PDU BMC of Salmonella enterica favors propionyl-CoA over acetyl-CoA, and it is likely that PduL orthologs in functionally diverse BMCs would have substrate preferences for other CoA derivatives. INTRO | |
| 258 262 PduL protein_type As a member of the core biochemical machinery of functionally diverse aldehyde-oxidizing metabolosomes, PduL must have a certain level of substrate plasticity (see Table 1) that is not required of Pta, which has generally been observed to prefer acetyl-CoA. PduL from the PDU BMC of Salmonella enterica favors propionyl-CoA over acetyl-CoA, and it is likely that PduL orthologs in functionally diverse BMCs would have substrate preferences for other CoA derivatives. INTRO | |
| 272 279 PDU BMC complex_assembly As a member of the core biochemical machinery of functionally diverse aldehyde-oxidizing metabolosomes, PduL must have a certain level of substrate plasticity (see Table 1) that is not required of Pta, which has generally been observed to prefer acetyl-CoA. PduL from the PDU BMC of Salmonella enterica favors propionyl-CoA over acetyl-CoA, and it is likely that PduL orthologs in functionally diverse BMCs would have substrate preferences for other CoA derivatives. INTRO | |
| 283 302 Salmonella enterica species As a member of the core biochemical machinery of functionally diverse aldehyde-oxidizing metabolosomes, PduL must have a certain level of substrate plasticity (see Table 1) that is not required of Pta, which has generally been observed to prefer acetyl-CoA. PduL from the PDU BMC of Salmonella enterica favors propionyl-CoA over acetyl-CoA, and it is likely that PduL orthologs in functionally diverse BMCs would have substrate preferences for other CoA derivatives. INTRO | |
| 310 323 propionyl-CoA chemical As a member of the core biochemical machinery of functionally diverse aldehyde-oxidizing metabolosomes, PduL must have a certain level of substrate plasticity (see Table 1) that is not required of Pta, which has generally been observed to prefer acetyl-CoA. PduL from the PDU BMC of Salmonella enterica favors propionyl-CoA over acetyl-CoA, and it is likely that PduL orthologs in functionally diverse BMCs would have substrate preferences for other CoA derivatives. INTRO | |
| 329 339 acetyl-CoA chemical As a member of the core biochemical machinery of functionally diverse aldehyde-oxidizing metabolosomes, PduL must have a certain level of substrate plasticity (see Table 1) that is not required of Pta, which has generally been observed to prefer acetyl-CoA. PduL from the PDU BMC of Salmonella enterica favors propionyl-CoA over acetyl-CoA, and it is likely that PduL orthologs in functionally diverse BMCs would have substrate preferences for other CoA derivatives. INTRO | |
| 363 367 PduL protein_type As a member of the core biochemical machinery of functionally diverse aldehyde-oxidizing metabolosomes, PduL must have a certain level of substrate plasticity (see Table 1) that is not required of Pta, which has generally been observed to prefer acetyl-CoA. PduL from the PDU BMC of Salmonella enterica favors propionyl-CoA over acetyl-CoA, and it is likely that PduL orthologs in functionally diverse BMCs would have substrate preferences for other CoA derivatives. INTRO | |
| 402 406 BMCs complex_assembly As a member of the core biochemical machinery of functionally diverse aldehyde-oxidizing metabolosomes, PduL must have a certain level of substrate plasticity (see Table 1) that is not required of Pta, which has generally been observed to prefer acetyl-CoA. PduL from the PDU BMC of Salmonella enterica favors propionyl-CoA over acetyl-CoA, and it is likely that PduL orthologs in functionally diverse BMCs would have substrate preferences for other CoA derivatives. INTRO | |
| 450 453 CoA chemical As a member of the core biochemical machinery of functionally diverse aldehyde-oxidizing metabolosomes, PduL must have a certain level of substrate plasticity (see Table 1) that is not required of Pta, which has generally been observed to prefer acetyl-CoA. PduL from the PDU BMC of Salmonella enterica favors propionyl-CoA over acetyl-CoA, and it is likely that PduL orthologs in functionally diverse BMCs would have substrate preferences for other CoA derivatives. INTRO | |
| 31 45 BMC-associated protein_state Another distinctive feature of BMC-associated PduL homologs is an N-terminal encapsulation peptide (EP) that is thought to “target” proteins for encapsulation by the BMC shell. INTRO | |
| 46 50 PduL protein_type Another distinctive feature of BMC-associated PduL homologs is an N-terminal encapsulation peptide (EP) that is thought to “target” proteins for encapsulation by the BMC shell. INTRO | |
| 77 98 encapsulation peptide structure_element Another distinctive feature of BMC-associated PduL homologs is an N-terminal encapsulation peptide (EP) that is thought to “target” proteins for encapsulation by the BMC shell. INTRO | |
| 100 102 EP structure_element Another distinctive feature of BMC-associated PduL homologs is an N-terminal encapsulation peptide (EP) that is thought to “target” proteins for encapsulation by the BMC shell. INTRO | |
| 166 169 BMC complex_assembly Another distinctive feature of BMC-associated PduL homologs is an N-terminal encapsulation peptide (EP) that is thought to “target” proteins for encapsulation by the BMC shell. INTRO | |
| 170 175 shell structure_element Another distinctive feature of BMC-associated PduL homologs is an N-terminal encapsulation peptide (EP) that is thought to “target” proteins for encapsulation by the BMC shell. INTRO | |
| 0 3 EPs structure_element EPs are frequently found on BMC-associated proteins and have been shown to interact with shell proteins. INTRO | |
| 28 51 BMC-associated proteins protein_type EPs are frequently found on BMC-associated proteins and have been shown to interact with shell proteins. INTRO | |
| 0 3 EPs structure_element EPs have also been observed to cause proteins to aggregate, and this has recently been suggested to be functionally relevant as an initial step in metabolosome assembly, in which a multifunctional protein core is formed, around which the shell assembles. INTRO | |
| 147 159 metabolosome complex_assembly EPs have also been observed to cause proteins to aggregate, and this has recently been suggested to be functionally relevant as an initial step in metabolosome assembly, in which a multifunctional protein core is formed, around which the shell assembles. INTRO | |
| 238 243 shell structure_element EPs have also been observed to cause proteins to aggregate, and this has recently been suggested to be functionally relevant as an initial step in metabolosome assembly, in which a multifunctional protein core is formed, around which the shell assembles. INTRO | |
| 20 32 metabolosome complex_assembly Of the three common metabolosome core enzymes, crystal structures are available for both the alcohol and aldehyde dehydrogenases. INTRO | |
| 47 65 crystal structures evidence Of the three common metabolosome core enzymes, crystal structures are available for both the alcohol and aldehyde dehydrogenases. INTRO | |
| 93 128 alcohol and aldehyde dehydrogenases protein_type Of the three common metabolosome core enzymes, crystal structures are available for both the alcohol and aldehyde dehydrogenases. INTRO | |
| 17 26 structure evidence In contrast, the structure of PduL, the PTAC found in the vast majority of catabolic BMCs, has not been determined. INTRO | |
| 30 34 PduL protein_type In contrast, the structure of PduL, the PTAC found in the vast majority of catabolic BMCs, has not been determined. INTRO | |
| 40 44 PTAC protein_type In contrast, the structure of PduL, the PTAC found in the vast majority of catabolic BMCs, has not been determined. INTRO | |
| 75 84 catabolic protein_state In contrast, the structure of PduL, the PTAC found in the vast majority of catabolic BMCs, has not been determined. INTRO | |
| 85 89 BMCs complex_assembly In contrast, the structure of PduL, the PTAC found in the vast majority of catabolic BMCs, has not been determined. INTRO | |
| 44 56 metabolosome complex_assembly This is a major gap in our understanding of metabolosome-encapsulated biochemistry and cofactor recycling. INTRO | |
| 66 69 BMC complex_assembly Moreover, it will be useful for guiding efforts to engineer novel BMC cores for biotechnological applications. INTRO | |
| 25 29 PduL protein_type The primary structure of PduL homologs is subdivided into two PF06130 domains, each roughly 80 residues in length. INTRO | |
| 62 69 PF06130 structure_element The primary structure of PduL homologs is subdivided into two PF06130 domains, each roughly 80 residues in length. INTRO | |
| 92 113 80 residues in length residue_range The primary structure of PduL homologs is subdivided into two PF06130 domains, each roughly 80 residues in length. INTRO | |
| 44 51 PF06130 structure_element No available protein structures contain the PF06130 domain, and homology searches using the primary structure of PduL do not return any significant results that would allow prediction of the structure. INTRO | |
| 64 81 homology searches experimental_method No available protein structures contain the PF06130 domain, and homology searches using the primary structure of PduL do not return any significant results that would allow prediction of the structure. INTRO | |
| 113 117 PduL protein_type No available protein structures contain the PF06130 domain, and homology searches using the primary structure of PduL do not return any significant results that would allow prediction of the structure. INTRO | |
| 191 200 structure evidence No available protein structures contain the PF06130 domain, and homology searches using the primary structure of PduL do not return any significant results that would allow prediction of the structure. INTRO | |
| 33 37 PduL protein_type Moreover, the evident novelty of PduL makes its structure interesting in the context of convergent evolution of PTAC function; to-date, only the Pta active site and catalytic mechanism is known. INTRO | |
| 48 57 structure evidence Moreover, the evident novelty of PduL makes its structure interesting in the context of convergent evolution of PTAC function; to-date, only the Pta active site and catalytic mechanism is known. INTRO | |
| 112 116 PTAC protein_type Moreover, the evident novelty of PduL makes its structure interesting in the context of convergent evolution of PTAC function; to-date, only the Pta active site and catalytic mechanism is known. INTRO | |
| 145 148 Pta protein_type Moreover, the evident novelty of PduL makes its structure interesting in the context of convergent evolution of PTAC function; to-date, only the Pta active site and catalytic mechanism is known. INTRO | |
| 149 160 active site site Moreover, the evident novelty of PduL makes its structure interesting in the context of convergent evolution of PTAC function; to-date, only the Pta active site and catalytic mechanism is known. INTRO | |
| 31 49 crystal structures evidence Here we report high-resolution crystal structures of a PduL-type PTAC in both CoA- and phosphate-bound forms, completing our understanding of the structural basis of catalysis by the metabolosome common core enzymes. INTRO | |
| 55 69 PduL-type PTAC protein_type Here we report high-resolution crystal structures of a PduL-type PTAC in both CoA- and phosphate-bound forms, completing our understanding of the structural basis of catalysis by the metabolosome common core enzymes. INTRO | |
| 78 82 CoA- protein_state Here we report high-resolution crystal structures of a PduL-type PTAC in both CoA- and phosphate-bound forms, completing our understanding of the structural basis of catalysis by the metabolosome common core enzymes. INTRO | |
| 87 102 phosphate-bound protein_state Here we report high-resolution crystal structures of a PduL-type PTAC in both CoA- and phosphate-bound forms, completing our understanding of the structural basis of catalysis by the metabolosome common core enzymes. INTRO | |
| 183 195 metabolosome complex_assembly Here we report high-resolution crystal structures of a PduL-type PTAC in both CoA- and phosphate-bound forms, completing our understanding of the structural basis of catalysis by the metabolosome common core enzymes. INTRO | |
| 80 83 Pta protein_type We propose a catalytic mechanism analogous but yet distinct from the ubiquitous Pta enzyme, highlighting the functional convergence of two enzymes with completely different structures and metal requirements. INTRO | |
| 65 69 PduL protein_type We also investigate the quaternary structures of three different PduL homologs and situate our findings in the context of organelle biogenesis in functionally diverse BMCs. INTRO | |
| 167 171 BMCs complex_assembly We also investigate the quaternary structures of three different PduL homologs and situate our findings in the context of organelle biogenesis in functionally diverse BMCs. INTRO | |
| 0 23 Structure Determination experimental_method Structure Determination of PduL RESULTS | |
| 27 31 PduL protein_type Structure Determination of PduL RESULTS | |
| 3 34 cloned, expressed, and purified experimental_method We cloned, expressed, and purified three different PduL homologs from functionally distinct BMCs (Table 1): from the well-studied pdu locus in S. enterica Typhimurium LT2 (sPduL), from the recently characterized pvm locus in Planctomyces limnophilus (pPduL), and from the grm3 locus in Rhodopseudomonas palustris BisB18 (rPduL). RESULTS | |
| 51 55 PduL protein_type We cloned, expressed, and purified three different PduL homologs from functionally distinct BMCs (Table 1): from the well-studied pdu locus in S. enterica Typhimurium LT2 (sPduL), from the recently characterized pvm locus in Planctomyces limnophilus (pPduL), and from the grm3 locus in Rhodopseudomonas palustris BisB18 (rPduL). RESULTS | |
| 92 96 BMCs complex_assembly We cloned, expressed, and purified three different PduL homologs from functionally distinct BMCs (Table 1): from the well-studied pdu locus in S. enterica Typhimurium LT2 (sPduL), from the recently characterized pvm locus in Planctomyces limnophilus (pPduL), and from the grm3 locus in Rhodopseudomonas palustris BisB18 (rPduL). RESULTS | |
| 130 139 pdu locus gene We cloned, expressed, and purified three different PduL homologs from functionally distinct BMCs (Table 1): from the well-studied pdu locus in S. enterica Typhimurium LT2 (sPduL), from the recently characterized pvm locus in Planctomyces limnophilus (pPduL), and from the grm3 locus in Rhodopseudomonas palustris BisB18 (rPduL). RESULTS | |
| 143 170 S. enterica Typhimurium LT2 species We cloned, expressed, and purified three different PduL homologs from functionally distinct BMCs (Table 1): from the well-studied pdu locus in S. enterica Typhimurium LT2 (sPduL), from the recently characterized pvm locus in Planctomyces limnophilus (pPduL), and from the grm3 locus in Rhodopseudomonas palustris BisB18 (rPduL). RESULTS | |
| 172 177 sPduL protein We cloned, expressed, and purified three different PduL homologs from functionally distinct BMCs (Table 1): from the well-studied pdu locus in S. enterica Typhimurium LT2 (sPduL), from the recently characterized pvm locus in Planctomyces limnophilus (pPduL), and from the grm3 locus in Rhodopseudomonas palustris BisB18 (rPduL). RESULTS | |
| 212 221 pvm locus gene We cloned, expressed, and purified three different PduL homologs from functionally distinct BMCs (Table 1): from the well-studied pdu locus in S. enterica Typhimurium LT2 (sPduL), from the recently characterized pvm locus in Planctomyces limnophilus (pPduL), and from the grm3 locus in Rhodopseudomonas palustris BisB18 (rPduL). RESULTS | |
| 225 249 Planctomyces limnophilus species We cloned, expressed, and purified three different PduL homologs from functionally distinct BMCs (Table 1): from the well-studied pdu locus in S. enterica Typhimurium LT2 (sPduL), from the recently characterized pvm locus in Planctomyces limnophilus (pPduL), and from the grm3 locus in Rhodopseudomonas palustris BisB18 (rPduL). RESULTS | |
| 251 256 pPduL protein We cloned, expressed, and purified three different PduL homologs from functionally distinct BMCs (Table 1): from the well-studied pdu locus in S. enterica Typhimurium LT2 (sPduL), from the recently characterized pvm locus in Planctomyces limnophilus (pPduL), and from the grm3 locus in Rhodopseudomonas palustris BisB18 (rPduL). RESULTS | |
| 272 282 grm3 locus gene We cloned, expressed, and purified three different PduL homologs from functionally distinct BMCs (Table 1): from the well-studied pdu locus in S. enterica Typhimurium LT2 (sPduL), from the recently characterized pvm locus in Planctomyces limnophilus (pPduL), and from the grm3 locus in Rhodopseudomonas palustris BisB18 (rPduL). RESULTS | |
| 286 319 Rhodopseudomonas palustris BisB18 species We cloned, expressed, and purified three different PduL homologs from functionally distinct BMCs (Table 1): from the well-studied pdu locus in S. enterica Typhimurium LT2 (sPduL), from the recently characterized pvm locus in Planctomyces limnophilus (pPduL), and from the grm3 locus in Rhodopseudomonas palustris BisB18 (rPduL). RESULTS | |
| 321 326 rPduL protein We cloned, expressed, and purified three different PduL homologs from functionally distinct BMCs (Table 1): from the well-studied pdu locus in S. enterica Typhimurium LT2 (sPduL), from the recently characterized pvm locus in Planctomyces limnophilus (pPduL), and from the grm3 locus in Rhodopseudomonas palustris BisB18 (rPduL). RESULTS | |
| 16 27 full-length protein_state While purifying full-length sPduL, we observed a tendency to aggregation as described previously, with a large fraction of the expressed protein found in the insoluble fraction in a white, cake-like pellet. RESULTS | |
| 28 33 sPduL protein While purifying full-length sPduL, we observed a tendency to aggregation as described previously, with a large fraction of the expressed protein found in the insoluble fraction in a white, cake-like pellet. RESULTS | |
| 18 26 removing experimental_method Remarkably, after removing the N-terminal putative EP (27 amino acids), most of the sPduLΔEP protein was in the soluble fraction upon cell lysis. RESULTS | |
| 51 53 EP structure_element Remarkably, after removing the N-terminal putative EP (27 amino acids), most of the sPduLΔEP protein was in the soluble fraction upon cell lysis. RESULTS | |
| 55 69 27 amino acids residue_range Remarkably, after removing the N-terminal putative EP (27 amino acids), most of the sPduLΔEP protein was in the soluble fraction upon cell lysis. RESULTS | |
| 84 92 sPduLΔEP mutant Remarkably, after removing the N-terminal putative EP (27 amino acids), most of the sPduLΔEP protein was in the soluble fraction upon cell lysis. RESULTS | |
| 52 57 pPduL protein Similar differences in solubility were observed for pPduL and rPduL when comparing EP-truncated forms to the full-length protein, but none were quite as dramatic as for sPduL. We confirmed that all homologs were active (S1a and S1b Fig). RESULTS | |
| 62 67 rPduL protein Similar differences in solubility were observed for pPduL and rPduL when comparing EP-truncated forms to the full-length protein, but none were quite as dramatic as for sPduL. We confirmed that all homologs were active (S1a and S1b Fig). RESULTS | |
| 83 95 EP-truncated protein_state Similar differences in solubility were observed for pPduL and rPduL when comparing EP-truncated forms to the full-length protein, but none were quite as dramatic as for sPduL. We confirmed that all homologs were active (S1a and S1b Fig). RESULTS | |
| 109 120 full-length protein_state Similar differences in solubility were observed for pPduL and rPduL when comparing EP-truncated forms to the full-length protein, but none were quite as dramatic as for sPduL. We confirmed that all homologs were active (S1a and S1b Fig). RESULTS | |
| 169 174 sPduL protein Similar differences in solubility were observed for pPduL and rPduL when comparing EP-truncated forms to the full-length protein, but none were quite as dramatic as for sPduL. We confirmed that all homologs were active (S1a and S1b Fig). RESULTS | |
| 212 218 active protein_state Similar differences in solubility were observed for pPduL and rPduL when comparing EP-truncated forms to the full-length protein, but none were quite as dramatic as for sPduL. We confirmed that all homologs were active (S1a and S1b Fig). RESULTS | |
| 41 69 diffraction-quality crystals evidence Among these, we were only able to obtain diffraction-quality crystals of rPduL after removing the N-terminal putative EP (33 amino acids, also see Fig 2a) (rPduLΔEP). RESULTS | |
| 73 78 rPduL protein Among these, we were only able to obtain diffraction-quality crystals of rPduL after removing the N-terminal putative EP (33 amino acids, also see Fig 2a) (rPduLΔEP). RESULTS | |
| 85 93 removing experimental_method Among these, we were only able to obtain diffraction-quality crystals of rPduL after removing the N-terminal putative EP (33 amino acids, also see Fig 2a) (rPduLΔEP). RESULTS | |
| 118 120 EP structure_element Among these, we were only able to obtain diffraction-quality crystals of rPduL after removing the N-terminal putative EP (33 amino acids, also see Fig 2a) (rPduLΔEP). RESULTS | |
| 122 136 33 amino acids residue_range Among these, we were only able to obtain diffraction-quality crystals of rPduL after removing the N-terminal putative EP (33 amino acids, also see Fig 2a) (rPduLΔEP). RESULTS | |
| 156 164 rPduLΔEP mutant Among these, we were only able to obtain diffraction-quality crystals of rPduL after removing the N-terminal putative EP (33 amino acids, also see Fig 2a) (rPduLΔEP). RESULTS | |
| 0 9 Truncated protein_state Truncated rPduLΔEP had comparable enzymatic activity to the full-length enzyme (S1a Fig). RESULTS | |
| 10 18 rPduLΔEP mutant Truncated rPduLΔEP had comparable enzymatic activity to the full-length enzyme (S1a Fig). RESULTS | |
| 60 71 full-length protein_state Truncated rPduLΔEP had comparable enzymatic activity to the full-length enzyme (S1a Fig). RESULTS | |
| 23 35 R. palustris species Structural overview of R. palustris PduL from the grm3 locus. FIG | |
| 36 40 PduL protein_type Structural overview of R. palustris PduL from the grm3 locus. FIG | |
| 50 60 grm3 locus gene Structural overview of R. palustris PduL from the grm3 locus. FIG | |
| 39 44 rPduL protein (a) Primary and secondary structure of rPduL (tubes represent α-helices, arrows β-sheets and dashed line residues disordered in the structure. FIG | |
| 62 71 α-helices structure_element (a) Primary and secondary structure of rPduL (tubes represent α-helices, arrows β-sheets and dashed line residues disordered in the structure. FIG | |
| 80 88 β-sheets structure_element (a) Primary and secondary structure of rPduL (tubes represent α-helices, arrows β-sheets and dashed line residues disordered in the structure. FIG | |
| 132 141 structure evidence (a) Primary and secondary structure of rPduL (tubes represent α-helices, arrows β-sheets and dashed line residues disordered in the structure. FIG | |
| 4 24 first 33 amino acids residue_range The first 33 amino acids are present only in the wildtype construct and contains the predicted EP alpha helix, α0); the truncated rPduLΔEP that was crystallized begins with M-G-V. Coloring is according to structural domains (domain 1 D36-N46/Q155-C224, blue; loop insertion G61-E81, grey; domain 2 R47-F60/E82-A154, red). FIG | |
| 95 97 EP structure_element The first 33 amino acids are present only in the wildtype construct and contains the predicted EP alpha helix, α0); the truncated rPduLΔEP that was crystallized begins with M-G-V. Coloring is according to structural domains (domain 1 D36-N46/Q155-C224, blue; loop insertion G61-E81, grey; domain 2 R47-F60/E82-A154, red). FIG | |
| 98 109 alpha helix structure_element The first 33 amino acids are present only in the wildtype construct and contains the predicted EP alpha helix, α0); the truncated rPduLΔEP that was crystallized begins with M-G-V. Coloring is according to structural domains (domain 1 D36-N46/Q155-C224, blue; loop insertion G61-E81, grey; domain 2 R47-F60/E82-A154, red). FIG | |
| 111 113 α0 structure_element The first 33 amino acids are present only in the wildtype construct and contains the predicted EP alpha helix, α0); the truncated rPduLΔEP that was crystallized begins with M-G-V. Coloring is according to structural domains (domain 1 D36-N46/Q155-C224, blue; loop insertion G61-E81, grey; domain 2 R47-F60/E82-A154, red). FIG | |
| 120 129 truncated protein_state The first 33 amino acids are present only in the wildtype construct and contains the predicted EP alpha helix, α0); the truncated rPduLΔEP that was crystallized begins with M-G-V. Coloring is according to structural domains (domain 1 D36-N46/Q155-C224, blue; loop insertion G61-E81, grey; domain 2 R47-F60/E82-A154, red). FIG | |
| 130 138 rPduLΔEP mutant The first 33 amino acids are present only in the wildtype construct and contains the predicted EP alpha helix, α0); the truncated rPduLΔEP that was crystallized begins with M-G-V. Coloring is according to structural domains (domain 1 D36-N46/Q155-C224, blue; loop insertion G61-E81, grey; domain 2 R47-F60/E82-A154, red). FIG | |
| 148 160 crystallized experimental_method The first 33 amino acids are present only in the wildtype construct and contains the predicted EP alpha helix, α0); the truncated rPduLΔEP that was crystallized begins with M-G-V. Coloring is according to structural domains (domain 1 D36-N46/Q155-C224, blue; loop insertion G61-E81, grey; domain 2 R47-F60/E82-A154, red). FIG | |
| 173 174 M residue_name The first 33 amino acids are present only in the wildtype construct and contains the predicted EP alpha helix, α0); the truncated rPduLΔEP that was crystallized begins with M-G-V. Coloring is according to structural domains (domain 1 D36-N46/Q155-C224, blue; loop insertion G61-E81, grey; domain 2 R47-F60/E82-A154, red). FIG | |
| 175 176 G residue_name The first 33 amino acids are present only in the wildtype construct and contains the predicted EP alpha helix, α0); the truncated rPduLΔEP that was crystallized begins with M-G-V. Coloring is according to structural domains (domain 1 D36-N46/Q155-C224, blue; loop insertion G61-E81, grey; domain 2 R47-F60/E82-A154, red). FIG | |
| 177 178 V residue_name The first 33 amino acids are present only in the wildtype construct and contains the predicted EP alpha helix, α0); the truncated rPduLΔEP that was crystallized begins with M-G-V. Coloring is according to structural domains (domain 1 D36-N46/Q155-C224, blue; loop insertion G61-E81, grey; domain 2 R47-F60/E82-A154, red). FIG | |
| 225 233 domain 1 structure_element The first 33 amino acids are present only in the wildtype construct and contains the predicted EP alpha helix, α0); the truncated rPduLΔEP that was crystallized begins with M-G-V. Coloring is according to structural domains (domain 1 D36-N46/Q155-C224, blue; loop insertion G61-E81, grey; domain 2 R47-F60/E82-A154, red). FIG | |
| 234 241 D36-N46 residue_range The first 33 amino acids are present only in the wildtype construct and contains the predicted EP alpha helix, α0); the truncated rPduLΔEP that was crystallized begins with M-G-V. Coloring is according to structural domains (domain 1 D36-N46/Q155-C224, blue; loop insertion G61-E81, grey; domain 2 R47-F60/E82-A154, red). FIG | |
| 242 251 Q155-C224 residue_range The first 33 amino acids are present only in the wildtype construct and contains the predicted EP alpha helix, α0); the truncated rPduLΔEP that was crystallized begins with M-G-V. Coloring is according to structural domains (domain 1 D36-N46/Q155-C224, blue; loop insertion G61-E81, grey; domain 2 R47-F60/E82-A154, red). FIG | |
| 259 273 loop insertion structure_element The first 33 amino acids are present only in the wildtype construct and contains the predicted EP alpha helix, α0); the truncated rPduLΔEP that was crystallized begins with M-G-V. Coloring is according to structural domains (domain 1 D36-N46/Q155-C224, blue; loop insertion G61-E81, grey; domain 2 R47-F60/E82-A154, red). FIG | |
| 274 281 G61-E81 residue_range The first 33 amino acids are present only in the wildtype construct and contains the predicted EP alpha helix, α0); the truncated rPduLΔEP that was crystallized begins with M-G-V. Coloring is according to structural domains (domain 1 D36-N46/Q155-C224, blue; loop insertion G61-E81, grey; domain 2 R47-F60/E82-A154, red). FIG | |
| 289 297 domain 2 structure_element The first 33 amino acids are present only in the wildtype construct and contains the predicted EP alpha helix, α0); the truncated rPduLΔEP that was crystallized begins with M-G-V. Coloring is according to structural domains (domain 1 D36-N46/Q155-C224, blue; loop insertion G61-E81, grey; domain 2 R47-F60/E82-A154, red). FIG | |
| 298 305 R47-F60 residue_range The first 33 amino acids are present only in the wildtype construct and contains the predicted EP alpha helix, α0); the truncated rPduLΔEP that was crystallized begins with M-G-V. Coloring is according to structural domains (domain 1 D36-N46/Q155-C224, blue; loop insertion G61-E81, grey; domain 2 R47-F60/E82-A154, red). FIG | |
| 306 314 E82-A154 residue_range The first 33 amino acids are present only in the wildtype construct and contains the predicted EP alpha helix, α0); the truncated rPduLΔEP that was crystallized begins with M-G-V. Coloring is according to structural domains (domain 1 D36-N46/Q155-C224, blue; loop insertion G61-E81, grey; domain 2 R47-F60/E82-A154, red). FIG | |
| 0 27 Metal coordination residues site Metal coordination residues are highlighted in light blue and CoA contacting residues in magenta, residues contacting the CoA of the other chain are also outlined. FIG | |
| 62 85 CoA contacting residues site Metal coordination residues are highlighted in light blue and CoA contacting residues in magenta, residues contacting the CoA of the other chain are also outlined. FIG | |
| 122 125 CoA chemical Metal coordination residues are highlighted in light blue and CoA contacting residues in magenta, residues contacting the CoA of the other chain are also outlined. FIG | |
| 34 43 structure evidence (b) Cartoon representation of the structure colored by domains and including secondary structure numbering. FIG | |
| 87 96 structure evidence (b) Cartoon representation of the structure colored by domains and including secondary structure numbering. FIG | |
| 0 10 Coenzyme A chemical Coenzyme A is shown in magenta sticks and Zinc (grey) as spheres. FIG | |
| 42 46 Zinc chemical Coenzyme A is shown in magenta sticks and Zinc (grey) as spheres. FIG | |
| 3 29 collected a native dataset experimental_method We collected a native dataset from rPduLΔEP crystals diffracting to a resolution of 1.54 Å (Table 2). RESULTS | |
| 35 43 rPduLΔEP mutant We collected a native dataset from rPduLΔEP crystals diffracting to a resolution of 1.54 Å (Table 2). RESULTS | |
| 44 52 crystals evidence We collected a native dataset from rPduLΔEP crystals diffracting to a resolution of 1.54 Å (Table 2). RESULTS | |
| 8 34 mercury-derivative crystal experimental_method Using a mercury-derivative crystal form diffracting to 1.99 Å (Table 2), we obtained high quality electron density for model building and used the initial model to refine against the native data to Rwork/Rfree values of 18.9/22.1%. RESULTS | |
| 98 114 electron density evidence Using a mercury-derivative crystal form diffracting to 1.99 Å (Table 2), we obtained high quality electron density for model building and used the initial model to refine against the native data to Rwork/Rfree values of 18.9/22.1%. RESULTS | |
| 198 203 Rwork evidence Using a mercury-derivative crystal form diffracting to 1.99 Å (Table 2), we obtained high quality electron density for model building and used the initial model to refine against the native data to Rwork/Rfree values of 18.9/22.1%. RESULTS | |
| 204 209 Rfree evidence Using a mercury-derivative crystal form diffracting to 1.99 Å (Table 2), we obtained high quality electron density for model building and used the initial model to refine against the native data to Rwork/Rfree values of 18.9/22.1%. RESULTS | |
| 14 18 PduL protein_type There are two PduL molecules in the asymmetric unit of the P212121 unit cell. RESULTS | |
| 52 59 PduLΔEP mutant We were able to fit all of the primary structure of PduLΔEP into the electron density with the exception of three amino acids at the N-terminus and two amino acids at the C-terminus (Fig 2a); the model is of excellent quality (Table 2). RESULTS | |
| 69 85 electron density evidence We were able to fit all of the primary structure of PduLΔEP into the electron density with the exception of three amino acids at the N-terminus and two amino acids at the C-terminus (Fig 2a); the model is of excellent quality (Table 2). RESULTS | |
| 2 5 CoA chemical A CoA cofactor as well as two metal ions are clearly resolved in the density (for omit maps of CoA see S2 Fig). RESULTS | |
| 69 76 density evidence A CoA cofactor as well as two metal ions are clearly resolved in the density (for omit maps of CoA see S2 Fig). RESULTS | |
| 82 91 omit maps evidence A CoA cofactor as well as two metal ions are clearly resolved in the density (for omit maps of CoA see S2 Fig). RESULTS | |
| 95 98 CoA chemical A CoA cofactor as well as two metal ions are clearly resolved in the density (for omit maps of CoA see S2 Fig). RESULTS | |
| 14 18 PduL protein_type Structurally, PduL consists of two domains (Fig 2, blue/red), each a beta-barrel that is capped on both ends by short α-helices. RESULTS | |
| 35 42 domains structure_element Structurally, PduL consists of two domains (Fig 2, blue/red), each a beta-barrel that is capped on both ends by short α-helices. RESULTS | |
| 69 80 beta-barrel structure_element Structurally, PduL consists of two domains (Fig 2, blue/red), each a beta-barrel that is capped on both ends by short α-helices. RESULTS | |
| 118 127 α-helices structure_element Structurally, PduL consists of two domains (Fig 2, blue/red), each a beta-barrel that is capped on both ends by short α-helices. RESULTS | |
| 0 10 β-Barrel 1 structure_element β-Barrel 1 consists of the N-terminal β strand and β strands from the C-terminal half of the polypeptide chain (β1, β10-β14; residues 37–46 and 155–224). RESULTS | |
| 38 46 β strand structure_element β-Barrel 1 consists of the N-terminal β strand and β strands from the C-terminal half of the polypeptide chain (β1, β10-β14; residues 37–46 and 155–224). RESULTS | |
| 51 60 β strands structure_element β-Barrel 1 consists of the N-terminal β strand and β strands from the C-terminal half of the polypeptide chain (β1, β10-β14; residues 37–46 and 155–224). RESULTS | |
| 70 85 C-terminal half structure_element β-Barrel 1 consists of the N-terminal β strand and β strands from the C-terminal half of the polypeptide chain (β1, β10-β14; residues 37–46 and 155–224). RESULTS | |
| 112 114 β1 structure_element β-Barrel 1 consists of the N-terminal β strand and β strands from the C-terminal half of the polypeptide chain (β1, β10-β14; residues 37–46 and 155–224). RESULTS | |
| 116 123 β10-β14 structure_element β-Barrel 1 consists of the N-terminal β strand and β strands from the C-terminal half of the polypeptide chain (β1, β10-β14; residues 37–46 and 155–224). RESULTS | |
| 134 139 37–46 residue_range β-Barrel 1 consists of the N-terminal β strand and β strands from the C-terminal half of the polypeptide chain (β1, β10-β14; residues 37–46 and 155–224). RESULTS | |
| 144 151 155–224 residue_range β-Barrel 1 consists of the N-terminal β strand and β strands from the C-terminal half of the polypeptide chain (β1, β10-β14; residues 37–46 and 155–224). RESULTS | |
| 0 10 β-Barrel 2 structure_element β-Barrel 2 consists mainly of the central segment of primary structure (β2, β5–β9; residues 47–60 and 82–154) (Fig 2, red), but is interrupted by a short two-strand beta sheet (β3-β4, residues 61–81). RESULTS | |
| 72 74 β2 structure_element β-Barrel 2 consists mainly of the central segment of primary structure (β2, β5–β9; residues 47–60 and 82–154) (Fig 2, red), but is interrupted by a short two-strand beta sheet (β3-β4, residues 61–81). RESULTS | |
| 76 81 β5–β9 structure_element β-Barrel 2 consists mainly of the central segment of primary structure (β2, β5–β9; residues 47–60 and 82–154) (Fig 2, red), but is interrupted by a short two-strand beta sheet (β3-β4, residues 61–81). RESULTS | |
| 92 97 47–60 residue_range β-Barrel 2 consists mainly of the central segment of primary structure (β2, β5–β9; residues 47–60 and 82–154) (Fig 2, red), but is interrupted by a short two-strand beta sheet (β3-β4, residues 61–81). RESULTS | |
| 102 108 82–154 residue_range β-Barrel 2 consists mainly of the central segment of primary structure (β2, β5–β9; residues 47–60 and 82–154) (Fig 2, red), but is interrupted by a short two-strand beta sheet (β3-β4, residues 61–81). RESULTS | |
| 148 175 short two-strand beta sheet structure_element β-Barrel 2 consists mainly of the central segment of primary structure (β2, β5–β9; residues 47–60 and 82–154) (Fig 2, red), but is interrupted by a short two-strand beta sheet (β3-β4, residues 61–81). RESULTS | |
| 177 182 β3-β4 structure_element β-Barrel 2 consists mainly of the central segment of primary structure (β2, β5–β9; residues 47–60 and 82–154) (Fig 2, red), but is interrupted by a short two-strand beta sheet (β3-β4, residues 61–81). RESULTS | |
| 193 198 61–81 residue_range β-Barrel 2 consists mainly of the central segment of primary structure (β2, β5–β9; residues 47–60 and 82–154) (Fig 2, red), but is interrupted by a short two-strand beta sheet (β3-β4, residues 61–81). RESULTS | |
| 5 12 β-sheet structure_element This β-sheet is involved in contacts between the two domains and forms a lid over the active site. RESULTS | |
| 86 97 active site site This β-sheet is involved in contacts between the two domains and forms a lid over the active site. RESULTS | |
| 25 30 Gln42 residue_name_number Residues in this region (Gln42, Pro43, Gly44), covering the active site, are strongly conserved (Fig 3). RESULTS | |
| 32 37 Pro43 residue_name_number Residues in this region (Gln42, Pro43, Gly44), covering the active site, are strongly conserved (Fig 3). RESULTS | |
| 39 44 Gly44 residue_name_number Residues in this region (Gln42, Pro43, Gly44), covering the active site, are strongly conserved (Fig 3). RESULTS | |
| 60 71 active site site Residues in this region (Gln42, Pro43, Gly44), covering the active site, are strongly conserved (Fig 3). RESULTS | |
| 77 95 strongly conserved protein_state Residues in this region (Gln42, Pro43, Gly44), covering the active site, are strongly conserved (Fig 3). RESULTS | |
| 82 85 Pta protein_type This structural arrangement is completely different from the functionally related Pta, which is composed of two domains, each consisting of a central flat beta sheet with alpha-helices on the top and bottom. RESULTS | |
| 112 119 domains structure_element This structural arrangement is completely different from the functionally related Pta, which is composed of two domains, each consisting of a central flat beta sheet with alpha-helices on the top and bottom. RESULTS | |
| 155 165 beta sheet structure_element This structural arrangement is completely different from the functionally related Pta, which is composed of two domains, each consisting of a central flat beta sheet with alpha-helices on the top and bottom. RESULTS | |
| 171 184 alpha-helices structure_element This structural arrangement is completely different from the functionally related Pta, which is composed of two domains, each consisting of a central flat beta sheet with alpha-helices on the top and bottom. RESULTS | |
| 38 42 PduL protein_type Primary structure conservation of the PduL protein family. FIG | |
| 34 61 multiple sequence alignment experimental_method Sequence logo calculated from the multiple sequence alignment of PduL homologs (see Materials and Methods), but not including putative EP sequences. FIG | |
| 65 69 PduL protein_type Sequence logo calculated from the multiple sequence alignment of PduL homologs (see Materials and Methods), but not including putative EP sequences. FIG | |
| 112 125 not including protein_state Sequence logo calculated from the multiple sequence alignment of PduL homologs (see Materials and Methods), but not including putative EP sequences. FIG | |
| 135 137 EP structure_element Sequence logo calculated from the multiple sequence alignment of PduL homologs (see Materials and Methods), but not including putative EP sequences. FIG | |
| 35 39 PduL protein_type Residues 100% conserved across all PduL homologs in our dataset are noted with an asterisk, and residues conserved in over 90% of sequences are noted with a colon. FIG | |
| 30 37 PF06130 structure_element The sequences aligning to the PF06130 domain (determined by BLAST) are highlighted in red and blue. FIG | |
| 66 71 rPduL protein The position numbers shown correspond to the residue numbering of rPduL; note that some positions in the logo represent gaps in the rPduL sequence. FIG | |
| 132 137 rPduL protein The position numbers shown correspond to the residue numbering of rPduL; note that some positions in the logo represent gaps in the rPduL sequence. FIG | |
| 14 18 PduL protein_type There are two PduL molecules in the asymmetric unit forming a butterfly-shaped dimer (Fig 4c). RESULTS | |
| 62 78 butterfly-shaped protein_state There are two PduL molecules in the asymmetric unit forming a butterfly-shaped dimer (Fig 4c). RESULTS | |
| 79 84 dimer oligomeric_state There are two PduL molecules in the asymmetric unit forming a butterfly-shaped dimer (Fig 4c). RESULTS | |
| 35 64 size exclusion chromatography experimental_method Consistent with this, results from size exclusion chromatography of rPduLΔEP suggest that it is a dimer in solution (Fig 5e). RESULTS | |
| 68 76 rPduLΔEP mutant Consistent with this, results from size exclusion chromatography of rPduLΔEP suggest that it is a dimer in solution (Fig 5e). RESULTS | |
| 98 103 dimer oligomeric_state Consistent with this, results from size exclusion chromatography of rPduLΔEP suggest that it is a dimer in solution (Fig 5e). RESULTS | |
| 4 13 interface site The interface between the two chains buries 882 Å2 per monomer and is mainly formed by α-helices 2 and 4 and parts of β-sheets 12 and 14, as well as a π–π stacking of the adenine moiety of CoA with Phe116 of the adjacent chain (Fig 4c). RESULTS | |
| 55 62 monomer oligomeric_state The interface between the two chains buries 882 Å2 per monomer and is mainly formed by α-helices 2 and 4 and parts of β-sheets 12 and 14, as well as a π–π stacking of the adenine moiety of CoA with Phe116 of the adjacent chain (Fig 4c). RESULTS | |
| 87 104 α-helices 2 and 4 structure_element The interface between the two chains buries 882 Å2 per monomer and is mainly formed by α-helices 2 and 4 and parts of β-sheets 12 and 14, as well as a π–π stacking of the adenine moiety of CoA with Phe116 of the adjacent chain (Fig 4c). RESULTS | |
| 118 136 β-sheets 12 and 14 structure_element The interface between the two chains buries 882 Å2 per monomer and is mainly formed by α-helices 2 and 4 and parts of β-sheets 12 and 14, as well as a π–π stacking of the adenine moiety of CoA with Phe116 of the adjacent chain (Fig 4c). RESULTS | |
| 171 178 adenine chemical The interface between the two chains buries 882 Å2 per monomer and is mainly formed by α-helices 2 and 4 and parts of β-sheets 12 and 14, as well as a π–π stacking of the adenine moiety of CoA with Phe116 of the adjacent chain (Fig 4c). RESULTS | |
| 189 192 CoA chemical The interface between the two chains buries 882 Å2 per monomer and is mainly formed by α-helices 2 and 4 and parts of β-sheets 12 and 14, as well as a π–π stacking of the adenine moiety of CoA with Phe116 of the adjacent chain (Fig 4c). RESULTS | |
| 198 204 Phe116 residue_name_number The interface between the two chains buries 882 Å2 per monomer and is mainly formed by α-helices 2 and 4 and parts of β-sheets 12 and 14, as well as a π–π stacking of the adenine moiety of CoA with Phe116 of the adjacent chain (Fig 4c). RESULTS | |
| 69 82 superimposing experimental_method The folds of the two chains in the asymmetric unit are very similar, superimposing with a rmsd of 0.16 Å over 2,306 aligned atom pairs. RESULTS | |
| 90 94 rmsd evidence The folds of the two chains in the asymmetric unit are very similar, superimposing with a rmsd of 0.16 Å over 2,306 aligned atom pairs. RESULTS | |
| 15 22 helices structure_element The peripheral helices and the short antiparallel β3–4 sheet mediate most of the crystal contacts. RESULTS | |
| 31 60 short antiparallel β3–4 sheet structure_element The peripheral helices and the short antiparallel β3–4 sheet mediate most of the crystal contacts. RESULTS | |
| 11 22 active site site Details of active site, dimeric assembly, and sequence conservation of PduL. FIG | |
| 24 31 dimeric oligomeric_state Details of active site, dimeric assembly, and sequence conservation of PduL. FIG | |
| 71 75 PduL protein_type Details of active site, dimeric assembly, and sequence conservation of PduL. FIG | |
| 15 26 active site site (a,b) Proposed active site of PduL with relevant residues shown as sticks in atom coloring (nitrogen blue, oxygen red, sulfur yellow), zinc as grey colored spheres and coordinating ordered water molecules in red. FIG | |
| 30 34 PduL protein_type (a,b) Proposed active site of PduL with relevant residues shown as sticks in atom coloring (nitrogen blue, oxygen red, sulfur yellow), zinc as grey colored spheres and coordinating ordered water molecules in red. FIG | |
| 92 100 nitrogen chemical (a,b) Proposed active site of PduL with relevant residues shown as sticks in atom coloring (nitrogen blue, oxygen red, sulfur yellow), zinc as grey colored spheres and coordinating ordered water molecules in red. FIG | |
| 107 113 oxygen chemical (a,b) Proposed active site of PduL with relevant residues shown as sticks in atom coloring (nitrogen blue, oxygen red, sulfur yellow), zinc as grey colored spheres and coordinating ordered water molecules in red. FIG | |
| 119 125 sulfur chemical (a,b) Proposed active site of PduL with relevant residues shown as sticks in atom coloring (nitrogen blue, oxygen red, sulfur yellow), zinc as grey colored spheres and coordinating ordered water molecules in red. FIG | |
| 135 139 zinc chemical (a,b) Proposed active site of PduL with relevant residues shown as sticks in atom coloring (nitrogen blue, oxygen red, sulfur yellow), zinc as grey colored spheres and coordinating ordered water molecules in red. FIG | |
| 189 194 water chemical (a,b) Proposed active site of PduL with relevant residues shown as sticks in atom coloring (nitrogen blue, oxygen red, sulfur yellow), zinc as grey colored spheres and coordinating ordered water molecules in red. FIG | |
| 55 65 Coenzyme A chemical Distances between atom centers are indicated in Å. (a) Coenzyme A containing, (b) phosphate-bound structure. FIG | |
| 82 97 phosphate-bound protein_state Distances between atom centers are indicated in Å. (a) Coenzyme A containing, (b) phosphate-bound structure. FIG | |
| 98 107 structure evidence Distances between atom centers are indicated in Å. (a) Coenzyme A containing, (b) phosphate-bound structure. FIG | |
| 16 21 dimer oligomeric_state (c) View of the dimer in the asymmetric unit from the side, domains 1 and 2 colored as in Fig 2 and the two chains differentiated by blue/red versus slate/firebrick. FIG | |
| 60 75 domains 1 and 2 structure_element (c) View of the dimer in the asymmetric unit from the side, domains 1 and 2 colored as in Fig 2 and the two chains differentiated by blue/red versus slate/firebrick. FIG | |
| 56 71 π–π interaction bond_interaction The asterisk and double arrow marks the location of the π–π interaction between F116 and the CoA base of the other dimer chain. FIG | |
| 80 84 F116 residue_name_number The asterisk and double arrow marks the location of the π–π interaction between F116 and the CoA base of the other dimer chain. FIG | |
| 93 96 CoA chemical The asterisk and double arrow marks the location of the π–π interaction between F116 and the CoA base of the other dimer chain. FIG | |
| 115 120 dimer oligomeric_state The asterisk and double arrow marks the location of the π–π interaction between F116 and the CoA base of the other dimer chain. FIG | |
| 34 43 structure evidence (d) Surface representation of the structure with indicated conservation (red: high, white: intermediate, yellow: low). FIG | |
| 0 29 Size exclusion chromatography experimental_method Size exclusion chromatography of PduL homologs. FIG | |
| 33 37 PduL protein_type Size exclusion chromatography of PduL homologs. FIG | |
| 9 22 Chromatograms evidence (a)–(c): Chromatograms of sPduL (a), rPduL (b), and pPduL (c) with (orange) or without (blue) the predicted EP, post-nickel affinity purification, applied over a preparative size exclusion column (see Materials and Methods). FIG | |
| 26 31 sPduL protein (a)–(c): Chromatograms of sPduL (a), rPduL (b), and pPduL (c) with (orange) or without (blue) the predicted EP, post-nickel affinity purification, applied over a preparative size exclusion column (see Materials and Methods). FIG | |
| 37 42 rPduL protein (a)–(c): Chromatograms of sPduL (a), rPduL (b), and pPduL (c) with (orange) or without (blue) the predicted EP, post-nickel affinity purification, applied over a preparative size exclusion column (see Materials and Methods). FIG | |
| 52 57 pPduL protein (a)–(c): Chromatograms of sPduL (a), rPduL (b), and pPduL (c) with (orange) or without (blue) the predicted EP, post-nickel affinity purification, applied over a preparative size exclusion column (see Materials and Methods). FIG | |
| 108 110 EP structure_element (a)–(c): Chromatograms of sPduL (a), rPduL (b), and pPduL (c) with (orange) or without (blue) the predicted EP, post-nickel affinity purification, applied over a preparative size exclusion column (see Materials and Methods). FIG | |
| 117 145 nickel affinity purification experimental_method (a)–(c): Chromatograms of sPduL (a), rPduL (b), and pPduL (c) with (orange) or without (blue) the predicted EP, post-nickel affinity purification, applied over a preparative size exclusion column (see Materials and Methods). FIG | |
| 9 22 Chromatograms evidence (d)–(f): Chromatograms of sPduL (d), rPduL (e), and pPduL (f) post-preparative size exclusion chromatography with different size fractions separated, applied over an analytical size exclusion column (see Materials and Methods). FIG | |
| 26 31 sPduL protein (d)–(f): Chromatograms of sPduL (d), rPduL (e), and pPduL (f) post-preparative size exclusion chromatography with different size fractions separated, applied over an analytical size exclusion column (see Materials and Methods). FIG | |
| 37 42 rPduL protein (d)–(f): Chromatograms of sPduL (d), rPduL (e), and pPduL (f) post-preparative size exclusion chromatography with different size fractions separated, applied over an analytical size exclusion column (see Materials and Methods). FIG | |
| 52 57 pPduL protein (d)–(f): Chromatograms of sPduL (d), rPduL (e), and pPduL (f) post-preparative size exclusion chromatography with different size fractions separated, applied over an analytical size exclusion column (see Materials and Methods). FIG | |
| 79 108 size exclusion chromatography experimental_method (d)–(f): Chromatograms of sPduL (d), rPduL (e), and pPduL (f) post-preparative size exclusion chromatography with different size fractions separated, applied over an analytical size exclusion column (see Materials and Methods). FIG | |
| 4 17 chromatograms evidence All chromatograms are cropped to show only the linear range of separation based on standard runs, shown in black squares with a dashed linear trend line. FIG | |
| 0 11 Active Site site Active Site Properties RESULTS | |
| 0 3 CoA chemical CoA and the metal ions bind between the two domains, presumably in the active site (Figs 2b and 4a). RESULTS | |
| 71 82 active site site CoA and the metal ions bind between the two domains, presumably in the active site (Figs 2b and 4a). RESULTS | |
| 46 69 X-ray fluorescence scan experimental_method To identify the bound metals, we performed an X-ray fluorescence scan on the crystals at various wavelengths (corresponding to the K-edges of Mn, Fe, Co, Ni, Cu, and Zn). RESULTS | |
| 77 85 crystals evidence To identify the bound metals, we performed an X-ray fluorescence scan on the crystals at various wavelengths (corresponding to the K-edges of Mn, Fe, Co, Ni, Cu, and Zn). RESULTS | |
| 142 144 Mn chemical To identify the bound metals, we performed an X-ray fluorescence scan on the crystals at various wavelengths (corresponding to the K-edges of Mn, Fe, Co, Ni, Cu, and Zn). RESULTS | |
| 146 148 Fe chemical To identify the bound metals, we performed an X-ray fluorescence scan on the crystals at various wavelengths (corresponding to the K-edges of Mn, Fe, Co, Ni, Cu, and Zn). RESULTS | |
| 150 152 Co chemical To identify the bound metals, we performed an X-ray fluorescence scan on the crystals at various wavelengths (corresponding to the K-edges of Mn, Fe, Co, Ni, Cu, and Zn). RESULTS | |
| 154 156 Ni chemical To identify the bound metals, we performed an X-ray fluorescence scan on the crystals at various wavelengths (corresponding to the K-edges of Mn, Fe, Co, Ni, Cu, and Zn). RESULTS | |
| 158 160 Cu chemical To identify the bound metals, we performed an X-ray fluorescence scan on the crystals at various wavelengths (corresponding to the K-edges of Mn, Fe, Co, Ni, Cu, and Zn). RESULTS | |
| 166 168 Zn chemical To identify the bound metals, we performed an X-ray fluorescence scan on the crystals at various wavelengths (corresponding to the K-edges of Mn, Fe, Co, Ni, Cu, and Zn). RESULTS | |
| 77 81 zinc chemical There was a large signal at the zinc edge, and we tested for the presence of zinc by collecting full data sets before and after the Zn K-edge (1.2861 and 1.2822 Å, respectively). RESULTS | |
| 85 162 collecting full data sets before and after the Zn K-edge (1.2861 and 1.2822 Å experimental_method There was a large signal at the zinc edge, and we tested for the presence of zinc by collecting full data sets before and after the Zn K-edge (1.2861 and 1.2822 Å, respectively). RESULTS | |
| 76 80 zinc chemical The large differences between the anomalous signals confirm the presence of zinc at both metal sites (S3 Fig). RESULTS | |
| 10 14 zinc chemical The first zinc ion (Zn1) is in a tetrahedral coordination state with His48, His50, Glu109, and the CoA sulfur (Fig 4a). RESULTS | |
| 20 23 Zn1 chemical The first zinc ion (Zn1) is in a tetrahedral coordination state with His48, His50, Glu109, and the CoA sulfur (Fig 4a). RESULTS | |
| 69 74 His48 residue_name_number The first zinc ion (Zn1) is in a tetrahedral coordination state with His48, His50, Glu109, and the CoA sulfur (Fig 4a). RESULTS | |
| 76 81 His50 residue_name_number The first zinc ion (Zn1) is in a tetrahedral coordination state with His48, His50, Glu109, and the CoA sulfur (Fig 4a). RESULTS | |
| 83 89 Glu109 residue_name_number The first zinc ion (Zn1) is in a tetrahedral coordination state with His48, His50, Glu109, and the CoA sulfur (Fig 4a). RESULTS | |
| 99 102 CoA chemical The first zinc ion (Zn1) is in a tetrahedral coordination state with His48, His50, Glu109, and the CoA sulfur (Fig 4a). RESULTS | |
| 103 109 sulfur chemical The first zinc ion (Zn1) is in a tetrahedral coordination state with His48, His50, Glu109, and the CoA sulfur (Fig 4a). RESULTS | |
| 12 15 Zn2 chemical The second (Zn2) is in octahedral coordination by three conserved histidine residues (His157, His159 and His204) as well as three water molecules (Fig 4a). RESULTS | |
| 56 65 conserved protein_state The second (Zn2) is in octahedral coordination by three conserved histidine residues (His157, His159 and His204) as well as three water molecules (Fig 4a). RESULTS | |
| 66 75 histidine residue_name The second (Zn2) is in octahedral coordination by three conserved histidine residues (His157, His159 and His204) as well as three water molecules (Fig 4a). RESULTS | |
| 86 92 His157 residue_name_number The second (Zn2) is in octahedral coordination by three conserved histidine residues (His157, His159 and His204) as well as three water molecules (Fig 4a). RESULTS | |
| 94 100 His159 residue_name_number The second (Zn2) is in octahedral coordination by three conserved histidine residues (His157, His159 and His204) as well as three water molecules (Fig 4a). RESULTS | |
| 105 111 His204 residue_name_number The second (Zn2) is in octahedral coordination by three conserved histidine residues (His157, His159 and His204) as well as three water molecules (Fig 4a). RESULTS | |
| 130 135 water chemical The second (Zn2) is in octahedral coordination by three conserved histidine residues (His157, His159 and His204) as well as three water molecules (Fig 4a). RESULTS | |
| 35 39 zinc chemical The nitrogen atom coordinating the zinc is the Nε in each histidine residue, as is typical for this interaction. RESULTS | |
| 58 67 histidine residue_name The nitrogen atom coordinating the zinc is the Nε in each histidine residue, as is typical for this interaction. RESULTS | |
| 9 29 crystals were soaked experimental_method When the crystals were soaked in a sodium phosphate solution for 2 d prior to data collection, the CoA dissociates, and density for a phosphate molecule is visible at the active site (Table 2, Fig 4b). RESULTS | |
| 35 51 sodium phosphate chemical When the crystals were soaked in a sodium phosphate solution for 2 d prior to data collection, the CoA dissociates, and density for a phosphate molecule is visible at the active site (Table 2, Fig 4b). RESULTS | |
| 99 102 CoA chemical When the crystals were soaked in a sodium phosphate solution for 2 d prior to data collection, the CoA dissociates, and density for a phosphate molecule is visible at the active site (Table 2, Fig 4b). RESULTS | |
| 120 127 density evidence When the crystals were soaked in a sodium phosphate solution for 2 d prior to data collection, the CoA dissociates, and density for a phosphate molecule is visible at the active site (Table 2, Fig 4b). RESULTS | |
| 134 143 phosphate chemical When the crystals were soaked in a sodium phosphate solution for 2 d prior to data collection, the CoA dissociates, and density for a phosphate molecule is visible at the active site (Table 2, Fig 4b). RESULTS | |
| 171 182 active site site When the crystals were soaked in a sodium phosphate solution for 2 d prior to data collection, the CoA dissociates, and density for a phosphate molecule is visible at the active site (Table 2, Fig 4b). RESULTS | |
| 4 19 phosphate-bound protein_state The phosphate-bound structure aligns well with the CoA-bound structure (0.43 Å rmsd over 2,361 atoms for the monomer, 0.83 Å over 5,259 aligned atoms for the dimer). RESULTS | |
| 20 29 structure evidence The phosphate-bound structure aligns well with the CoA-bound structure (0.43 Å rmsd over 2,361 atoms for the monomer, 0.83 Å over 5,259 aligned atoms for the dimer). RESULTS | |
| 30 36 aligns experimental_method The phosphate-bound structure aligns well with the CoA-bound structure (0.43 Å rmsd over 2,361 atoms for the monomer, 0.83 Å over 5,259 aligned atoms for the dimer). RESULTS | |
| 51 60 CoA-bound protein_state The phosphate-bound structure aligns well with the CoA-bound structure (0.43 Å rmsd over 2,361 atoms for the monomer, 0.83 Å over 5,259 aligned atoms for the dimer). RESULTS | |
| 61 70 structure evidence The phosphate-bound structure aligns well with the CoA-bound structure (0.43 Å rmsd over 2,361 atoms for the monomer, 0.83 Å over 5,259 aligned atoms for the dimer). RESULTS | |
| 79 83 rmsd evidence The phosphate-bound structure aligns well with the CoA-bound structure (0.43 Å rmsd over 2,361 atoms for the monomer, 0.83 Å over 5,259 aligned atoms for the dimer). RESULTS | |
| 109 116 monomer oligomeric_state The phosphate-bound structure aligns well with the CoA-bound structure (0.43 Å rmsd over 2,361 atoms for the monomer, 0.83 Å over 5,259 aligned atoms for the dimer). RESULTS | |
| 158 163 dimer oligomeric_state The phosphate-bound structure aligns well with the CoA-bound structure (0.43 Å rmsd over 2,361 atoms for the monomer, 0.83 Å over 5,259 aligned atoms for the dimer). RESULTS | |
| 4 13 phosphate chemical The phosphate contacts both zinc atoms (Fig 4b) and replaces the coordination by CoA at Zn1; the coordination for Zn2 changes from octahedral with three bound waters to tetrahedral with a phosphate ion as one of the ligands (Fig 4b). RESULTS | |
| 28 32 zinc chemical The phosphate contacts both zinc atoms (Fig 4b) and replaces the coordination by CoA at Zn1; the coordination for Zn2 changes from octahedral with three bound waters to tetrahedral with a phosphate ion as one of the ligands (Fig 4b). RESULTS | |
| 81 84 CoA chemical The phosphate contacts both zinc atoms (Fig 4b) and replaces the coordination by CoA at Zn1; the coordination for Zn2 changes from octahedral with three bound waters to tetrahedral with a phosphate ion as one of the ligands (Fig 4b). RESULTS | |
| 88 91 Zn1 chemical The phosphate contacts both zinc atoms (Fig 4b) and replaces the coordination by CoA at Zn1; the coordination for Zn2 changes from octahedral with three bound waters to tetrahedral with a phosphate ion as one of the ligands (Fig 4b). RESULTS | |
| 114 117 Zn2 chemical The phosphate contacts both zinc atoms (Fig 4b) and replaces the coordination by CoA at Zn1; the coordination for Zn2 changes from octahedral with three bound waters to tetrahedral with a phosphate ion as one of the ligands (Fig 4b). RESULTS | |
| 159 165 waters chemical The phosphate contacts both zinc atoms (Fig 4b) and replaces the coordination by CoA at Zn1; the coordination for Zn2 changes from octahedral with three bound waters to tetrahedral with a phosphate ion as one of the ligands (Fig 4b). RESULTS | |
| 188 197 phosphate chemical The phosphate contacts both zinc atoms (Fig 4b) and replaces the coordination by CoA at Zn1; the coordination for Zn2 changes from octahedral with three bound waters to tetrahedral with a phosphate ion as one of the ligands (Fig 4b). RESULTS | |
| 0 9 Conserved protein_state Conserved Arg103 seems to be involved in maintaining the phosphate in that position. RESULTS | |
| 10 16 Arg103 residue_name_number Conserved Arg103 seems to be involved in maintaining the phosphate in that position. RESULTS | |
| 57 66 phosphate chemical Conserved Arg103 seems to be involved in maintaining the phosphate in that position. RESULTS | |
| 8 12 zinc chemical The two zinc atoms are slightly closer together in the phosphate-bound form (5.8 Å vs 6.3 Å), possibly due to the bridging effect of the phosphate. RESULTS | |
| 55 70 phosphate-bound protein_state The two zinc atoms are slightly closer together in the phosphate-bound form (5.8 Å vs 6.3 Å), possibly due to the bridging effect of the phosphate. RESULTS | |
| 137 146 phosphate chemical The two zinc atoms are slightly closer together in the phosphate-bound form (5.8 Å vs 6.3 Å), possibly due to the bridging effect of the phosphate. RESULTS | |
| 14 23 phosphate chemical An additional phosphate molecule is bound at a crystal contact interface, perhaps accounting for the 14 Å shorter c-axis in the phosphate-bound crystal form (Table 2). RESULTS | |
| 128 143 phosphate-bound protein_state An additional phosphate molecule is bound at a crystal contact interface, perhaps accounting for the 14 Å shorter c-axis in the phosphate-bound crystal form (Table 2). RESULTS | |
| 21 25 PduL protein_type Oligomeric States of PduL Orthologs Are Influenced by the EP RESULTS | |
| 58 60 EP structure_element Oligomeric States of PduL Orthologs Are Influenced by the EP RESULTS | |
| 66 71 rPduL protein Interestingly, some of the residues important for dimerization of rPduL, particularly Phe116, are poorly conserved across PduL homologs associated with functionally diverse BMCs (Figs 4c and 3), suggesting that they may have alternative oligomeric states. RESULTS | |
| 86 92 Phe116 residue_name_number Interestingly, some of the residues important for dimerization of rPduL, particularly Phe116, are poorly conserved across PduL homologs associated with functionally diverse BMCs (Figs 4c and 3), suggesting that they may have alternative oligomeric states. RESULTS | |
| 98 114 poorly conserved protein_state Interestingly, some of the residues important for dimerization of rPduL, particularly Phe116, are poorly conserved across PduL homologs associated with functionally diverse BMCs (Figs 4c and 3), suggesting that they may have alternative oligomeric states. RESULTS | |
| 122 126 PduL protein_type Interestingly, some of the residues important for dimerization of rPduL, particularly Phe116, are poorly conserved across PduL homologs associated with functionally diverse BMCs (Figs 4c and 3), suggesting that they may have alternative oligomeric states. RESULTS | |
| 173 177 BMCs complex_assembly Interestingly, some of the residues important for dimerization of rPduL, particularly Phe116, are poorly conserved across PduL homologs associated with functionally diverse BMCs (Figs 4c and 3), suggesting that they may have alternative oligomeric states. RESULTS | |
| 40 69 size exclusion chromatography experimental_method We tested this hypothesis by performing size exclusion chromatography on both full-length and truncated variants (lacking the EP, ΔEP) of sPduL, rPduL, and pPduL. These three homologs are found in functionally distinct BMCs (Table 1). RESULTS | |
| 78 89 full-length protein_state We tested this hypothesis by performing size exclusion chromatography on both full-length and truncated variants (lacking the EP, ΔEP) of sPduL, rPduL, and pPduL. These three homologs are found in functionally distinct BMCs (Table 1). RESULTS | |
| 114 121 lacking protein_state We tested this hypothesis by performing size exclusion chromatography on both full-length and truncated variants (lacking the EP, ΔEP) of sPduL, rPduL, and pPduL. These three homologs are found in functionally distinct BMCs (Table 1). RESULTS | |
| 126 128 EP structure_element We tested this hypothesis by performing size exclusion chromatography on both full-length and truncated variants (lacking the EP, ΔEP) of sPduL, rPduL, and pPduL. These three homologs are found in functionally distinct BMCs (Table 1). RESULTS | |
| 130 133 ΔEP mutant We tested this hypothesis by performing size exclusion chromatography on both full-length and truncated variants (lacking the EP, ΔEP) of sPduL, rPduL, and pPduL. These three homologs are found in functionally distinct BMCs (Table 1). RESULTS | |
| 138 143 sPduL protein We tested this hypothesis by performing size exclusion chromatography on both full-length and truncated variants (lacking the EP, ΔEP) of sPduL, rPduL, and pPduL. These three homologs are found in functionally distinct BMCs (Table 1). RESULTS | |
| 145 150 rPduL protein We tested this hypothesis by performing size exclusion chromatography on both full-length and truncated variants (lacking the EP, ΔEP) of sPduL, rPduL, and pPduL. These three homologs are found in functionally distinct BMCs (Table 1). RESULTS | |
| 156 161 pPduL protein We tested this hypothesis by performing size exclusion chromatography on both full-length and truncated variants (lacking the EP, ΔEP) of sPduL, rPduL, and pPduL. These three homologs are found in functionally distinct BMCs (Table 1). RESULTS | |
| 219 223 BMCs complex_assembly We tested this hypothesis by performing size exclusion chromatography on both full-length and truncated variants (lacking the EP, ΔEP) of sPduL, rPduL, and pPduL. These three homologs are found in functionally distinct BMCs (Table 1). RESULTS | |
| 30 39 catabolic protein_state It has been proposed that the catabolic BMCs may assemble in a core-first manner, with the luminal enzymes (signature enzyme, aldehyde, and alcohol dehydrogenases and the BMC PTAC) forming an initial bolus, or prometabolosome, around which a shell assembles. RESULTS | |
| 40 44 BMCs complex_assembly It has been proposed that the catabolic BMCs may assemble in a core-first manner, with the luminal enzymes (signature enzyme, aldehyde, and alcohol dehydrogenases and the BMC PTAC) forming an initial bolus, or prometabolosome, around which a shell assembles. RESULTS | |
| 126 162 aldehyde, and alcohol dehydrogenases protein_type It has been proposed that the catabolic BMCs may assemble in a core-first manner, with the luminal enzymes (signature enzyme, aldehyde, and alcohol dehydrogenases and the BMC PTAC) forming an initial bolus, or prometabolosome, around which a shell assembles. RESULTS | |
| 171 174 BMC complex_assembly It has been proposed that the catabolic BMCs may assemble in a core-first manner, with the luminal enzymes (signature enzyme, aldehyde, and alcohol dehydrogenases and the BMC PTAC) forming an initial bolus, or prometabolosome, around which a shell assembles. RESULTS | |
| 175 179 PTAC protein_type It has been proposed that the catabolic BMCs may assemble in a core-first manner, with the luminal enzymes (signature enzyme, aldehyde, and alcohol dehydrogenases and the BMC PTAC) forming an initial bolus, or prometabolosome, around which a shell assembles. RESULTS | |
| 242 247 shell structure_element It has been proposed that the catabolic BMCs may assemble in a core-first manner, with the luminal enzymes (signature enzyme, aldehyde, and alcohol dehydrogenases and the BMC PTAC) forming an initial bolus, or prometabolosome, around which a shell assembles. RESULTS | |
| 73 77 PduL protein_type Given the diversity of signature enzymes (Table 1), it is plausible that PduL orthologs may adopt different oligomeric states that reflect the differences in the proteins being packaged with them in the organelle lumen. RESULTS | |
| 170 172 EP structure_element We found that not only did the different orthologs appear to assemble into different oligomeric states, but that quaternary structure was dependent on whether or not the EP was present. RESULTS | |
| 0 11 Full-length protein_state Full-length sPduL was unstable in solution—precipitating over time—and eluted throughout the entire volume of a size exclusion column, indicating it was nonspecifically aggregating. RESULTS | |
| 12 17 sPduL protein Full-length sPduL was unstable in solution—precipitating over time—and eluted throughout the entire volume of a size exclusion column, indicating it was nonspecifically aggregating. RESULTS | |
| 27 29 EP structure_element However, when the putative EP (residues 1–27) was removed (sPduL ΔEP), the truncated protein was stable and eluted as a single peak (Fig 5a) consistent with the size of a monomer (Fig 5d, blue curve). RESULTS | |
| 40 44 1–27 residue_range However, when the putative EP (residues 1–27) was removed (sPduL ΔEP), the truncated protein was stable and eluted as a single peak (Fig 5a) consistent with the size of a monomer (Fig 5d, blue curve). RESULTS | |
| 50 57 removed experimental_method However, when the putative EP (residues 1–27) was removed (sPduL ΔEP), the truncated protein was stable and eluted as a single peak (Fig 5a) consistent with the size of a monomer (Fig 5d, blue curve). RESULTS | |
| 59 68 sPduL ΔEP mutant However, when the putative EP (residues 1–27) was removed (sPduL ΔEP), the truncated protein was stable and eluted as a single peak (Fig 5a) consistent with the size of a monomer (Fig 5d, blue curve). RESULTS | |
| 75 84 truncated protein_state However, when the putative EP (residues 1–27) was removed (sPduL ΔEP), the truncated protein was stable and eluted as a single peak (Fig 5a) consistent with the size of a monomer (Fig 5d, blue curve). RESULTS | |
| 171 178 monomer oligomeric_state However, when the putative EP (residues 1–27) was removed (sPduL ΔEP), the truncated protein was stable and eluted as a single peak (Fig 5a) consistent with the size of a monomer (Fig 5d, blue curve). RESULTS | |
| 18 29 full-length protein_state In contrast, both full-length rPduL and pPduL appeared to exist in two distinct oligomeric states (Fig 5b and 5c respectively, orange curves), one form of the approximate size of a dimer and the second, a higher molecular weight oligomer (~150 kDa). RESULTS | |
| 30 35 rPduL protein In contrast, both full-length rPduL and pPduL appeared to exist in two distinct oligomeric states (Fig 5b and 5c respectively, orange curves), one form of the approximate size of a dimer and the second, a higher molecular weight oligomer (~150 kDa). RESULTS | |
| 40 45 pPduL protein In contrast, both full-length rPduL and pPduL appeared to exist in two distinct oligomeric states (Fig 5b and 5c respectively, orange curves), one form of the approximate size of a dimer and the second, a higher molecular weight oligomer (~150 kDa). RESULTS | |
| 181 186 dimer oligomeric_state In contrast, both full-length rPduL and pPduL appeared to exist in two distinct oligomeric states (Fig 5b and 5c respectively, orange curves), one form of the approximate size of a dimer and the second, a higher molecular weight oligomer (~150 kDa). RESULTS | |
| 229 237 oligomer oligomeric_state In contrast, both full-length rPduL and pPduL appeared to exist in two distinct oligomeric states (Fig 5b and 5c respectively, orange curves), one form of the approximate size of a dimer and the second, a higher molecular weight oligomer (~150 kDa). RESULTS | |
| 5 13 deletion experimental_method Upon deletion of the putative EP (residues 1–47 for rPduL, and 1–20 for pPduL), there was a distinct change in the elution profiles (Fig 5b and 5c respectively, blue curves). RESULTS | |
| 30 32 EP structure_element Upon deletion of the putative EP (residues 1–47 for rPduL, and 1–20 for pPduL), there was a distinct change in the elution profiles (Fig 5b and 5c respectively, blue curves). RESULTS | |
| 43 47 1–47 residue_range Upon deletion of the putative EP (residues 1–47 for rPduL, and 1–20 for pPduL), there was a distinct change in the elution profiles (Fig 5b and 5c respectively, blue curves). RESULTS | |
| 52 57 rPduL protein Upon deletion of the putative EP (residues 1–47 for rPduL, and 1–20 for pPduL), there was a distinct change in the elution profiles (Fig 5b and 5c respectively, blue curves). RESULTS | |
| 63 67 1–20 residue_range Upon deletion of the putative EP (residues 1–47 for rPduL, and 1–20 for pPduL), there was a distinct change in the elution profiles (Fig 5b and 5c respectively, blue curves). RESULTS | |
| 72 77 pPduL protein Upon deletion of the putative EP (residues 1–47 for rPduL, and 1–20 for pPduL), there was a distinct change in the elution profiles (Fig 5b and 5c respectively, blue curves). RESULTS | |
| 0 8 pPduLΔEP mutant pPduLΔEP eluted as two smaller forms, possibly corresponding to a trimer and a monomer. RESULTS | |
| 66 72 trimer oligomeric_state pPduLΔEP eluted as two smaller forms, possibly corresponding to a trimer and a monomer. RESULTS | |
| 79 86 monomer oligomeric_state pPduLΔEP eluted as two smaller forms, possibly corresponding to a trimer and a monomer. RESULTS | |
| 13 21 rPduLΔEP mutant In contrast, rPduLΔEP eluted as one smaller oligomer, possibly a dimer. RESULTS | |
| 65 70 dimer oligomeric_state In contrast, rPduLΔEP eluted as one smaller oligomer, possibly a dimer. RESULTS | |
| 26 31 rPduL protein We also analyzed purified rPduL and rPduLΔEP by size exclusion chromatography coupled with multiangle light scattering (SEC-MALS) for a complementary approach to assessing oligomeric state. RESULTS | |
| 36 44 rPduLΔEP mutant We also analyzed purified rPduL and rPduLΔEP by size exclusion chromatography coupled with multiangle light scattering (SEC-MALS) for a complementary approach to assessing oligomeric state. RESULTS | |
| 48 77 size exclusion chromatography experimental_method We also analyzed purified rPduL and rPduLΔEP by size exclusion chromatography coupled with multiangle light scattering (SEC-MALS) for a complementary approach to assessing oligomeric state. RESULTS | |
| 91 118 multiangle light scattering experimental_method We also analyzed purified rPduL and rPduLΔEP by size exclusion chromatography coupled with multiangle light scattering (SEC-MALS) for a complementary approach to assessing oligomeric state. RESULTS | |
| 120 128 SEC-MALS experimental_method We also analyzed purified rPduL and rPduLΔEP by size exclusion chromatography coupled with multiangle light scattering (SEC-MALS) for a complementary approach to assessing oligomeric state. RESULTS | |
| 0 8 SEC-MALS experimental_method SEC-MALS analysis of rPdulΔEP is consistent with a dimer (as observed in the crystal structure) with a weighted average (Mw) and number average (Mn) of the molar mass of 58.4 kDa +/− 11.2% and 58.8 kDa +/− 10.9%, respectively (S4a Fig). RESULTS | |
| 21 29 rPdulΔEP mutant SEC-MALS analysis of rPdulΔEP is consistent with a dimer (as observed in the crystal structure) with a weighted average (Mw) and number average (Mn) of the molar mass of 58.4 kDa +/− 11.2% and 58.8 kDa +/− 10.9%, respectively (S4a Fig). RESULTS | |
| 51 56 dimer oligomeric_state SEC-MALS analysis of rPdulΔEP is consistent with a dimer (as observed in the crystal structure) with a weighted average (Mw) and number average (Mn) of the molar mass of 58.4 kDa +/− 11.2% and 58.8 kDa +/− 10.9%, respectively (S4a Fig). RESULTS | |
| 77 94 crystal structure evidence SEC-MALS analysis of rPdulΔEP is consistent with a dimer (as observed in the crystal structure) with a weighted average (Mw) and number average (Mn) of the molar mass of 58.4 kDa +/− 11.2% and 58.8 kDa +/− 10.9%, respectively (S4a Fig). RESULTS | |
| 103 166 weighted average (Mw) and number average (Mn) of the molar mass evidence SEC-MALS analysis of rPdulΔEP is consistent with a dimer (as observed in the crystal structure) with a weighted average (Mw) and number average (Mn) of the molar mass of 58.4 kDa +/− 11.2% and 58.8 kDa +/− 10.9%, respectively (S4a Fig). RESULTS | |
| 0 5 rPduL protein rPduL full length runs as Mw = 140.3 kDa +/− 1.2% and Mn = 140.5 kDa +/− 1.2%. RESULTS | |
| 6 17 full length protein_state rPduL full length runs as Mw = 140.3 kDa +/− 1.2% and Mn = 140.5 kDa +/− 1.2%. RESULTS | |
| 26 28 Mw evidence rPduL full length runs as Mw = 140.3 kDa +/− 1.2% and Mn = 140.5 kDa +/− 1.2%. RESULTS | |
| 54 56 Mn evidence rPduL full length runs as Mw = 140.3 kDa +/− 1.2% and Mn = 140.5 kDa +/− 1.2%. RESULTS | |
| 43 55 six subunits oligomeric_state This corresponds to an oligomeric state of six subunits (calculated molecular weight of 144 kDa). RESULTS | |
| 68 84 molecular weight evidence This corresponds to an oligomeric state of six subunits (calculated molecular weight of 144 kDa). RESULTS | |
| 62 64 EP structure_element Collectively, these data strongly suggest that the N-terminal EP of PduL plays a role in defining the quaternary structure of the protein. RESULTS | |
| 68 72 PduL protein_type Collectively, these data strongly suggest that the N-terminal EP of PduL plays a role in defining the quaternary structure of the protein. RESULTS | |
| 4 7 BMC complex_assembly The BMC shell not only sequesters specific enzymes but also their cofactors, thereby establishing a private cofactor pool dedicated to the encapsulated reactions. DISCUSS | |
| 8 13 shell structure_element The BMC shell not only sequesters specific enzymes but also their cofactors, thereby establishing a private cofactor pool dedicated to the encapsulated reactions. DISCUSS | |
| 3 12 catabolic protein_state In catabolic BMCs, CoA and NAD+ must be continually recycled within the organelle (Fig 1). DISCUSS | |
| 13 17 BMCs complex_assembly In catabolic BMCs, CoA and NAD+ must be continually recycled within the organelle (Fig 1). DISCUSS | |
| 19 22 CoA chemical In catabolic BMCs, CoA and NAD+ must be continually recycled within the organelle (Fig 1). DISCUSS | |
| 27 31 NAD+ chemical In catabolic BMCs, CoA and NAD+ must be continually recycled within the organelle (Fig 1). DISCUSS | |
| 47 69 aldehyde dehydrogenase protein_type Homologs of the predominant cofactor utilizer (aldehyde dehydrogenase) and NAD+ regenerator (alcohol dehydrogenase) have been structurally characterized, but until now structural information was lacking for PduL, which recycles CoA in the organelle lumen. DISCUSS | |
| 75 79 NAD+ chemical Homologs of the predominant cofactor utilizer (aldehyde dehydrogenase) and NAD+ regenerator (alcohol dehydrogenase) have been structurally characterized, but until now structural information was lacking for PduL, which recycles CoA in the organelle lumen. DISCUSS | |
| 93 114 alcohol dehydrogenase protein_type Homologs of the predominant cofactor utilizer (aldehyde dehydrogenase) and NAD+ regenerator (alcohol dehydrogenase) have been structurally characterized, but until now structural information was lacking for PduL, which recycles CoA in the organelle lumen. DISCUSS | |
| 207 211 PduL protein_type Homologs of the predominant cofactor utilizer (aldehyde dehydrogenase) and NAD+ regenerator (alcohol dehydrogenase) have been structurally characterized, but until now structural information was lacking for PduL, which recycles CoA in the organelle lumen. DISCUSS | |
| 228 231 CoA chemical Homologs of the predominant cofactor utilizer (aldehyde dehydrogenase) and NAD+ regenerator (alcohol dehydrogenase) have been structurally characterized, but until now structural information was lacking for PduL, which recycles CoA in the organelle lumen. DISCUSS | |
| 21 33 housekeeping protein_state Curiously, while the housekeeping Pta could provide this function, and indeed does so in the case of one type of ethanolamine-utilizing (EUT) BMC, the evolutionarily unrelated PduL fulfills this function for the majority of metabolosomes using a novel structure and active site for convergent evolution of function. DISCUSS | |
| 34 37 Pta protein_type Curiously, while the housekeeping Pta could provide this function, and indeed does so in the case of one type of ethanolamine-utilizing (EUT) BMC, the evolutionarily unrelated PduL fulfills this function for the majority of metabolosomes using a novel structure and active site for convergent evolution of function. DISCUSS | |
| 113 145 ethanolamine-utilizing (EUT) BMC complex_assembly Curiously, while the housekeeping Pta could provide this function, and indeed does so in the case of one type of ethanolamine-utilizing (EUT) BMC, the evolutionarily unrelated PduL fulfills this function for the majority of metabolosomes using a novel structure and active site for convergent evolution of function. DISCUSS | |
| 176 180 PduL protein_type Curiously, while the housekeeping Pta could provide this function, and indeed does so in the case of one type of ethanolamine-utilizing (EUT) BMC, the evolutionarily unrelated PduL fulfills this function for the majority of metabolosomes using a novel structure and active site for convergent evolution of function. DISCUSS | |
| 224 237 metabolosomes complex_assembly Curiously, while the housekeeping Pta could provide this function, and indeed does so in the case of one type of ethanolamine-utilizing (EUT) BMC, the evolutionarily unrelated PduL fulfills this function for the majority of metabolosomes using a novel structure and active site for convergent evolution of function. DISCUSS | |
| 252 261 structure evidence Curiously, while the housekeeping Pta could provide this function, and indeed does so in the case of one type of ethanolamine-utilizing (EUT) BMC, the evolutionarily unrelated PduL fulfills this function for the majority of metabolosomes using a novel structure and active site for convergent evolution of function. DISCUSS | |
| 266 277 active site site Curiously, while the housekeeping Pta could provide this function, and indeed does so in the case of one type of ethanolamine-utilizing (EUT) BMC, the evolutionarily unrelated PduL fulfills this function for the majority of metabolosomes using a novel structure and active site for convergent evolution of function. DISCUSS | |
| 26 30 PduL protein_type The Tertiary Structure of PduL Is Formed by Discontinuous Segments of Primary Structure DISCUSS | |
| 4 13 structure evidence The structure of PduL consists of two β-barrel domains capped by short alpha helical segments (Fig 2b). DISCUSS | |
| 17 21 PduL protein_type The structure of PduL consists of two β-barrel domains capped by short alpha helical segments (Fig 2b). DISCUSS | |
| 34 54 two β-barrel domains structure_element The structure of PduL consists of two β-barrel domains capped by short alpha helical segments (Fig 2b). DISCUSS | |
| 65 93 short alpha helical segments structure_element The structure of PduL consists of two β-barrel domains capped by short alpha helical segments (Fig 2b). DISCUSS | |
| 47 60 superimposing experimental_method The two domains are structurally very similar (superimposing with a rmsd of 1.34 Å (over 123 out of 320/348 aligned backbone atoms, S5a Fig). DISCUSS | |
| 68 72 rmsd evidence The two domains are structurally very similar (superimposing with a rmsd of 1.34 Å (over 123 out of 320/348 aligned backbone atoms, S5a Fig). DISCUSS | |
| 88 98 RHxH motif structure_element However, the amino acid sequences of the two domains are only 16% identical (mainly the RHxH motif, β2 and β10), and 34% similar. DISCUSS | |
| 100 102 β2 structure_element However, the amino acid sequences of the two domains are only 16% identical (mainly the RHxH motif, β2 and β10), and 34% similar. DISCUSS | |
| 107 110 β10 structure_element However, the amino acid sequences of the two domains are only 16% identical (mainly the RHxH motif, β2 and β10), and 34% similar. DISCUSS | |
| 4 13 structure evidence Our structure reveals that the two assigned PF06130 domains (Fig 3) do not form structurally discrete units; this reduces the apparent sequence conservation at the level of primary structure. DISCUSS | |
| 44 51 PF06130 structure_element Our structure reveals that the two assigned PF06130 domains (Fig 3) do not form structurally discrete units; this reduces the apparent sequence conservation at the level of primary structure. DISCUSS | |
| 4 10 strand structure_element One strand of the domain 1 beta barrel (shown in blue in Fig 2) is contributed by the N-terminus, while the rest of the domain is formed by the residues from the C-terminal half of the protein. DISCUSS | |
| 18 26 domain 1 structure_element One strand of the domain 1 beta barrel (shown in blue in Fig 2) is contributed by the N-terminus, while the rest of the domain is formed by the residues from the C-terminal half of the protein. DISCUSS | |
| 27 38 beta barrel structure_element One strand of the domain 1 beta barrel (shown in blue in Fig 2) is contributed by the N-terminus, while the rest of the domain is formed by the residues from the C-terminal half of the protein. DISCUSS | |
| 162 177 C-terminal half structure_element One strand of the domain 1 beta barrel (shown in blue in Fig 2) is contributed by the N-terminus, while the rest of the domain is formed by the residues from the C-terminal half of the protein. DISCUSS | |
| 185 192 protein protein_type One strand of the domain 1 beta barrel (shown in blue in Fig 2) is contributed by the N-terminus, while the rest of the domain is formed by the residues from the C-terminal half of the protein. DISCUSS | |
| 5 12 aligned experimental_method When aligned by structure, the β1 strand of the first domain (Fig 2a and 2b, blue) corresponds to the final strand of the second domain (β9), effectively making the domains continuous if the first strand was transplanted to the C-terminus. DISCUSS | |
| 16 25 structure evidence When aligned by structure, the β1 strand of the first domain (Fig 2a and 2b, blue) corresponds to the final strand of the second domain (β9), effectively making the domains continuous if the first strand was transplanted to the C-terminus. DISCUSS | |
| 31 40 β1 strand structure_element When aligned by structure, the β1 strand of the first domain (Fig 2a and 2b, blue) corresponds to the final strand of the second domain (β9), effectively making the domains continuous if the first strand was transplanted to the C-terminus. DISCUSS | |
| 48 60 first domain structure_element When aligned by structure, the β1 strand of the first domain (Fig 2a and 2b, blue) corresponds to the final strand of the second domain (β9), effectively making the domains continuous if the first strand was transplanted to the C-terminus. DISCUSS | |
| 102 114 final strand structure_element When aligned by structure, the β1 strand of the first domain (Fig 2a and 2b, blue) corresponds to the final strand of the second domain (β9), effectively making the domains continuous if the first strand was transplanted to the C-terminus. DISCUSS | |
| 122 135 second domain structure_element When aligned by structure, the β1 strand of the first domain (Fig 2a and 2b, blue) corresponds to the final strand of the second domain (β9), effectively making the domains continuous if the first strand was transplanted to the C-terminus. DISCUSS | |
| 137 139 β9 structure_element When aligned by structure, the β1 strand of the first domain (Fig 2a and 2b, blue) corresponds to the final strand of the second domain (β9), effectively making the domains continuous if the first strand was transplanted to the C-terminus. DISCUSS | |
| 39 48 structure evidence Refined domain assignment based on our structure should be able to predict domains of PF06130 homologs much more accurately. DISCUSS | |
| 86 93 PF06130 structure_element Refined domain assignment based on our structure should be able to predict domains of PF06130 homologs much more accurately. DISCUSS | |
| 38 42 PduL protein_type The closest structural homolog of the PduL barrel domain is a subdomain of a multienzyme complex, the alpha subunit of ethylbenzene dehydrogenase (S5b Fig, rmsd of 2.26 Å over 226 aligned atoms consisting of one beta barrel and one capping helix). DISCUSS | |
| 43 56 barrel domain structure_element The closest structural homolog of the PduL barrel domain is a subdomain of a multienzyme complex, the alpha subunit of ethylbenzene dehydrogenase (S5b Fig, rmsd of 2.26 Å over 226 aligned atoms consisting of one beta barrel and one capping helix). DISCUSS | |
| 102 115 alpha subunit structure_element The closest structural homolog of the PduL barrel domain is a subdomain of a multienzyme complex, the alpha subunit of ethylbenzene dehydrogenase (S5b Fig, rmsd of 2.26 Å over 226 aligned atoms consisting of one beta barrel and one capping helix). DISCUSS | |
| 119 145 ethylbenzene dehydrogenase protein_type The closest structural homolog of the PduL barrel domain is a subdomain of a multienzyme complex, the alpha subunit of ethylbenzene dehydrogenase (S5b Fig, rmsd of 2.26 Å over 226 aligned atoms consisting of one beta barrel and one capping helix). DISCUSS | |
| 156 160 rmsd evidence The closest structural homolog of the PduL barrel domain is a subdomain of a multienzyme complex, the alpha subunit of ethylbenzene dehydrogenase (S5b Fig, rmsd of 2.26 Å over 226 aligned atoms consisting of one beta barrel and one capping helix). DISCUSS | |
| 212 223 beta barrel structure_element The closest structural homolog of the PduL barrel domain is a subdomain of a multienzyme complex, the alpha subunit of ethylbenzene dehydrogenase (S5b Fig, rmsd of 2.26 Å over 226 aligned atoms consisting of one beta barrel and one capping helix). DISCUSS | |
| 232 245 capping helix structure_element The closest structural homolog of the PduL barrel domain is a subdomain of a multienzyme complex, the alpha subunit of ethylbenzene dehydrogenase (S5b Fig, rmsd of 2.26 Å over 226 aligned atoms consisting of one beta barrel and one capping helix). DISCUSS | |
| 15 19 PduL protein_type In contrast to PduL, there is only one barrel present in ethylbenzene dehydrogenase, and there is no comparable active site arrangement. DISCUSS | |
| 39 45 barrel structure_element In contrast to PduL, there is only one barrel present in ethylbenzene dehydrogenase, and there is no comparable active site arrangement. DISCUSS | |
| 57 83 ethylbenzene dehydrogenase protein_type In contrast to PduL, there is only one barrel present in ethylbenzene dehydrogenase, and there is no comparable active site arrangement. DISCUSS | |
| 112 123 active site site In contrast to PduL, there is only one barrel present in ethylbenzene dehydrogenase, and there is no comparable active site arrangement. DISCUSS | |
| 4 8 PduL protein_type The PduL signature primary structure, two PF06130 domains, occurs in some multidomain proteins, most of them annotated as Acks, suggesting that PduL may also replace Pta in variants of the phosphotransacetylase-Ack pathway. DISCUSS | |
| 42 49 PF06130 structure_element The PduL signature primary structure, two PF06130 domains, occurs in some multidomain proteins, most of them annotated as Acks, suggesting that PduL may also replace Pta in variants of the phosphotransacetylase-Ack pathway. DISCUSS | |
| 122 126 Acks protein_type The PduL signature primary structure, two PF06130 domains, occurs in some multidomain proteins, most of them annotated as Acks, suggesting that PduL may also replace Pta in variants of the phosphotransacetylase-Ack pathway. DISCUSS | |
| 144 148 PduL protein_type The PduL signature primary structure, two PF06130 domains, occurs in some multidomain proteins, most of them annotated as Acks, suggesting that PduL may also replace Pta in variants of the phosphotransacetylase-Ack pathway. DISCUSS | |
| 166 169 Pta protein_type The PduL signature primary structure, two PF06130 domains, occurs in some multidomain proteins, most of them annotated as Acks, suggesting that PduL may also replace Pta in variants of the phosphotransacetylase-Ack pathway. DISCUSS | |
| 189 210 phosphotransacetylase protein_type The PduL signature primary structure, two PF06130 domains, occurs in some multidomain proteins, most of them annotated as Acks, suggesting that PduL may also replace Pta in variants of the phosphotransacetylase-Ack pathway. DISCUSS | |
| 211 214 Ack protein_type The PduL signature primary structure, two PF06130 domains, occurs in some multidomain proteins, most of them annotated as Acks, suggesting that PduL may also replace Pta in variants of the phosphotransacetylase-Ack pathway. DISCUSS | |
| 6 10 PduL protein_type These PduL homologs lack EPs, and their fusion to Ack may have evolved as a way to facilitate substrate channeling between the two enzymes. DISCUSS | |
| 20 24 lack protein_state These PduL homologs lack EPs, and their fusion to Ack may have evolved as a way to facilitate substrate channeling between the two enzymes. DISCUSS | |
| 25 28 EPs structure_element These PduL homologs lack EPs, and their fusion to Ack may have evolved as a way to facilitate substrate channeling between the two enzymes. DISCUSS | |
| 34 39 their protein_type These PduL homologs lack EPs, and their fusion to Ack may have evolved as a way to facilitate substrate channeling between the two enzymes. DISCUSS | |
| 50 53 Ack protein_type These PduL homologs lack EPs, and their fusion to Ack may have evolved as a way to facilitate substrate channeling between the two enzymes. DISCUSS | |
| 17 29 Metabolosome complex_assembly Implications for Metabolosome Core Assembly DISCUSS | |
| 4 7 BMC complex_assembly For BMC-encapsulated proteins to properly function together, they must be targeted to the lumen and assemble into an organization that facilitates substrate/product channeling among the different catalytic sites of the signature and core enzymes. DISCUSS | |
| 196 211 catalytic sites site For BMC-encapsulated proteins to properly function together, they must be targeted to the lumen and assemble into an organization that facilitates substrate/product channeling among the different catalytic sites of the signature and core enzymes. DISCUSS | |
| 4 24 N-terminal extension structure_element The N-terminal extension on PduL homologs may serve both of these functions. DISCUSS | |
| 28 32 PduL protein_type The N-terminal extension on PduL homologs may serve both of these functions. DISCUSS | |
| 0 13 The extension structure_element The extension shares many features with previously characterized EPs: it is present only in homologs associated with BMC loci, and it is predicted to form an amphipathic α-helix. DISCUSS | |
| 65 68 EPs structure_element The extension shares many features with previously characterized EPs: it is present only in homologs associated with BMC loci, and it is predicted to form an amphipathic α-helix. DISCUSS | |
| 117 125 BMC loci gene The extension shares many features with previously characterized EPs: it is present only in homologs associated with BMC loci, and it is predicted to form an amphipathic α-helix. DISCUSS | |
| 158 169 amphipathic protein_state The extension shares many features with previously characterized EPs: it is present only in homologs associated with BMC loci, and it is predicted to form an amphipathic α-helix. DISCUSS | |
| 170 177 α-helix structure_element The extension shares many features with previously characterized EPs: it is present only in homologs associated with BMC loci, and it is predicted to form an amphipathic α-helix. DISCUSS | |
| 14 21 removal experimental_method Moreover, its removal affects the oligomeric state of the protein. DISCUSS | |
| 0 2 EP structure_element EP-mediated oligomerization has been observed for the signature and core BMC enzymes; for example, full-length propanediol dehydratase and ethanolamine ammonia-lyase (signature enzymes for PDU and EUT BMCs) subunits are also insoluble, but become soluble upon removal of the predicted EP. DISCUSS | |
| 73 76 BMC complex_assembly EP-mediated oligomerization has been observed for the signature and core BMC enzymes; for example, full-length propanediol dehydratase and ethanolamine ammonia-lyase (signature enzymes for PDU and EUT BMCs) subunits are also insoluble, but become soluble upon removal of the predicted EP. DISCUSS | |
| 99 110 full-length protein_state EP-mediated oligomerization has been observed for the signature and core BMC enzymes; for example, full-length propanediol dehydratase and ethanolamine ammonia-lyase (signature enzymes for PDU and EUT BMCs) subunits are also insoluble, but become soluble upon removal of the predicted EP. DISCUSS | |
| 111 134 propanediol dehydratase protein_type EP-mediated oligomerization has been observed for the signature and core BMC enzymes; for example, full-length propanediol dehydratase and ethanolamine ammonia-lyase (signature enzymes for PDU and EUT BMCs) subunits are also insoluble, but become soluble upon removal of the predicted EP. DISCUSS | |
| 139 165 ethanolamine ammonia-lyase protein_type EP-mediated oligomerization has been observed for the signature and core BMC enzymes; for example, full-length propanediol dehydratase and ethanolamine ammonia-lyase (signature enzymes for PDU and EUT BMCs) subunits are also insoluble, but become soluble upon removal of the predicted EP. DISCUSS | |
| 189 192 PDU complex_assembly EP-mediated oligomerization has been observed for the signature and core BMC enzymes; for example, full-length propanediol dehydratase and ethanolamine ammonia-lyase (signature enzymes for PDU and EUT BMCs) subunits are also insoluble, but become soluble upon removal of the predicted EP. DISCUSS | |
| 197 205 EUT BMCs complex_assembly EP-mediated oligomerization has been observed for the signature and core BMC enzymes; for example, full-length propanediol dehydratase and ethanolamine ammonia-lyase (signature enzymes for PDU and EUT BMCs) subunits are also insoluble, but become soluble upon removal of the predicted EP. DISCUSS | |
| 285 287 EP structure_element EP-mediated oligomerization has been observed for the signature and core BMC enzymes; for example, full-length propanediol dehydratase and ethanolamine ammonia-lyase (signature enzymes for PDU and EUT BMCs) subunits are also insoluble, but become soluble upon removal of the predicted EP. DISCUSS | |
| 0 5 sPduL protein sPduL has also previously been reported to localize to inclusion bodies when overexpressed; we show here that this is dependent on the presence of the EP. DISCUSS | |
| 77 90 overexpressed experimental_method sPduL has also previously been reported to localize to inclusion bodies when overexpressed; we show here that this is dependent on the presence of the EP. DISCUSS | |
| 151 153 EP structure_element sPduL has also previously been reported to localize to inclusion bodies when overexpressed; we show here that this is dependent on the presence of the EP. DISCUSS | |
| 23 25 EP structure_element This propensity of the EP to cause proteins to form complexes (Fig 5) might not be a coincidence, but could be a necessary step in the assembly of BMCs. DISCUSS | |
| 147 151 BMCs complex_assembly This propensity of the EP to cause proteins to form complexes (Fig 5) might not be a coincidence, but could be a necessary step in the assembly of BMCs. DISCUSS | |
| 87 99 metabolosome complex_assembly Structured aggregation of the core enzymes has been proposed to be the initial step in metabolosome assembly and is known to be the first step of β-carboxysome biogenesis, where the core enzyme Ribulose Bisphosphate Carboxylase/Oxygenase (RuBisCO) is aggregated by the CcmM protein. DISCUSS | |
| 194 237 Ribulose Bisphosphate Carboxylase/Oxygenase protein_type Structured aggregation of the core enzymes has been proposed to be the initial step in metabolosome assembly and is known to be the first step of β-carboxysome biogenesis, where the core enzyme Ribulose Bisphosphate Carboxylase/Oxygenase (RuBisCO) is aggregated by the CcmM protein. DISCUSS | |
| 239 246 RuBisCO protein_type Structured aggregation of the core enzymes has been proposed to be the initial step in metabolosome assembly and is known to be the first step of β-carboxysome biogenesis, where the core enzyme Ribulose Bisphosphate Carboxylase/Oxygenase (RuBisCO) is aggregated by the CcmM protein. DISCUSS | |
| 269 273 CcmM protein_type Structured aggregation of the core enzymes has been proposed to be the initial step in metabolosome assembly and is known to be the first step of β-carboxysome biogenesis, where the core enzyme Ribulose Bisphosphate Carboxylase/Oxygenase (RuBisCO) is aggregated by the CcmM protein. DISCUSS | |
| 10 15 CsoS2 protein_type Likewise, CsoS2, a protein in the α-carboxysome core, also aggregates when purified and is proposed to facilitate the nucleation and encapsulation of RuBisCO molecules in the lumen of the organelle. DISCUSS | |
| 34 47 α-carboxysome complex_assembly Likewise, CsoS2, a protein in the α-carboxysome core, also aggregates when purified and is proposed to facilitate the nucleation and encapsulation of RuBisCO molecules in the lumen of the organelle. DISCUSS | |
| 150 157 RuBisCO protein_type Likewise, CsoS2, a protein in the α-carboxysome core, also aggregates when purified and is proposed to facilitate the nucleation and encapsulation of RuBisCO molecules in the lumen of the organelle. DISCUSS | |
| 14 17 EPs structure_element This role for EPs in BMC assembly is in addition to their interaction with shell proteins. DISCUSS | |
| 21 24 BMC complex_assembly This role for EPs in BMC assembly is in addition to their interaction with shell proteins. DISCUSS | |
| 14 18 PduL protein_type Moreover, the PduL crystal structures offer a clue as to how required cofactors enter the BMC lumen during assembly. DISCUSS | |
| 19 37 crystal structures evidence Moreover, the PduL crystal structures offer a clue as to how required cofactors enter the BMC lumen during assembly. DISCUSS | |
| 90 93 BMC complex_assembly Moreover, the PduL crystal structures offer a clue as to how required cofactors enter the BMC lumen during assembly. DISCUSS | |
| 5 8 CoA chemical Free CoA and NAD+/H could potentially be bound to the enzymes as the core assembles and is encapsulated. DISCUSS | |
| 13 17 NAD+ chemical Free CoA and NAD+/H could potentially be bound to the enzymes as the core assembles and is encapsulated. DISCUSS | |
| 18 19 H chemical Free CoA and NAD+/H could potentially be bound to the enzymes as the core assembles and is encapsulated. DISCUSS | |
| 4 8 PduL protein_type Our PduL crystals contained CoA that was captured from the Escherichia coli cytosol, indicating that the “ground state” of PduL is in the CoA-bound form; this could provide an elegantly simple means of guaranteeing a 1:1 ratio of CoA:PduL within the metabolosome lumen. DISCUSS | |
| 9 17 crystals evidence Our PduL crystals contained CoA that was captured from the Escherichia coli cytosol, indicating that the “ground state” of PduL is in the CoA-bound form; this could provide an elegantly simple means of guaranteeing a 1:1 ratio of CoA:PduL within the metabolosome lumen. DISCUSS | |
| 28 31 CoA chemical Our PduL crystals contained CoA that was captured from the Escherichia coli cytosol, indicating that the “ground state” of PduL is in the CoA-bound form; this could provide an elegantly simple means of guaranteeing a 1:1 ratio of CoA:PduL within the metabolosome lumen. DISCUSS | |
| 59 75 Escherichia coli species Our PduL crystals contained CoA that was captured from the Escherichia coli cytosol, indicating that the “ground state” of PduL is in the CoA-bound form; this could provide an elegantly simple means of guaranteeing a 1:1 ratio of CoA:PduL within the metabolosome lumen. DISCUSS | |
| 123 127 PduL protein_type Our PduL crystals contained CoA that was captured from the Escherichia coli cytosol, indicating that the “ground state” of PduL is in the CoA-bound form; this could provide an elegantly simple means of guaranteeing a 1:1 ratio of CoA:PduL within the metabolosome lumen. DISCUSS | |
| 138 147 CoA-bound protein_state Our PduL crystals contained CoA that was captured from the Escherichia coli cytosol, indicating that the “ground state” of PduL is in the CoA-bound form; this could provide an elegantly simple means of guaranteeing a 1:1 ratio of CoA:PduL within the metabolosome lumen. DISCUSS | |
| 230 238 CoA:PduL complex_assembly Our PduL crystals contained CoA that was captured from the Escherichia coli cytosol, indicating that the “ground state” of PduL is in the CoA-bound form; this could provide an elegantly simple means of guaranteeing a 1:1 ratio of CoA:PduL within the metabolosome lumen. DISCUSS | |
| 250 262 metabolosome complex_assembly Our PduL crystals contained CoA that was captured from the Escherichia coli cytosol, indicating that the “ground state” of PduL is in the CoA-bound form; this could provide an elegantly simple means of guaranteeing a 1:1 ratio of CoA:PduL within the metabolosome lumen. DISCUSS | |
| 0 11 Active Site site Active Site Identification and Structural Insights into Catalysis DISCUSS | |
| 4 15 active site site The active site of PduL is formed at the interface of the two structural domains (Fig 2b). DISCUSS | |
| 19 23 PduL protein_type The active site of PduL is formed at the interface of the two structural domains (Fig 2b). DISCUSS | |
| 41 50 interface site The active site of PduL is formed at the interface of the two structural domains (Fig 2b). DISCUSS | |
| 73 80 domains structure_element The active site of PduL is formed at the interface of the two structural domains (Fig 2b). DISCUSS | |
| 95 106 active site site As expected, the amino acid sequence conservation is highest in the region around the proposed active site (Fig 4d); highly conserved residues are also involved in CoA binding (Figs 2a and 3, residues Ser45, Lys70, Arg97, Leu99, His204, Asn211). DISCUSS | |
| 117 133 highly conserved protein_state As expected, the amino acid sequence conservation is highest in the region around the proposed active site (Fig 4d); highly conserved residues are also involved in CoA binding (Figs 2a and 3, residues Ser45, Lys70, Arg97, Leu99, His204, Asn211). DISCUSS | |
| 164 167 CoA chemical As expected, the amino acid sequence conservation is highest in the region around the proposed active site (Fig 4d); highly conserved residues are also involved in CoA binding (Figs 2a and 3, residues Ser45, Lys70, Arg97, Leu99, His204, Asn211). DISCUSS | |
| 201 206 Ser45 residue_name_number As expected, the amino acid sequence conservation is highest in the region around the proposed active site (Fig 4d); highly conserved residues are also involved in CoA binding (Figs 2a and 3, residues Ser45, Lys70, Arg97, Leu99, His204, Asn211). DISCUSS | |
| 208 213 Lys70 residue_name_number As expected, the amino acid sequence conservation is highest in the region around the proposed active site (Fig 4d); highly conserved residues are also involved in CoA binding (Figs 2a and 3, residues Ser45, Lys70, Arg97, Leu99, His204, Asn211). DISCUSS | |
| 215 220 Arg97 residue_name_number As expected, the amino acid sequence conservation is highest in the region around the proposed active site (Fig 4d); highly conserved residues are also involved in CoA binding (Figs 2a and 3, residues Ser45, Lys70, Arg97, Leu99, His204, Asn211). DISCUSS | |
| 222 227 Leu99 residue_name_number As expected, the amino acid sequence conservation is highest in the region around the proposed active site (Fig 4d); highly conserved residues are also involved in CoA binding (Figs 2a and 3, residues Ser45, Lys70, Arg97, Leu99, His204, Asn211). DISCUSS | |
| 229 235 His204 residue_name_number As expected, the amino acid sequence conservation is highest in the region around the proposed active site (Fig 4d); highly conserved residues are also involved in CoA binding (Figs 2a and 3, residues Ser45, Lys70, Arg97, Leu99, His204, Asn211). DISCUSS | |
| 237 243 Asn211 residue_name_number As expected, the amino acid sequence conservation is highest in the region around the proposed active site (Fig 4d); highly conserved residues are also involved in CoA binding (Figs 2a and 3, residues Ser45, Lys70, Arg97, Leu99, His204, Asn211). DISCUSS | |
| 11 38 metal-coordinating residues site All of the metal-coordinating residues (Fig 2a) are absolutely conserved, implicating them in catalysis or the correct spatial orientation of the substrates. DISCUSS | |
| 52 72 absolutely conserved protein_state All of the metal-coordinating residues (Fig 2a) are absolutely conserved, implicating them in catalysis or the correct spatial orientation of the substrates. DISCUSS | |
| 0 6 Arg103 residue_name_number Arg103, which contacts the phosphate (Fig 4b), is present in all PduL homologs. DISCUSS | |
| 27 36 phosphate chemical Arg103, which contacts the phosphate (Fig 4b), is present in all PduL homologs. DISCUSS | |
| 65 69 PduL protein_type Arg103, which contacts the phosphate (Fig 4b), is present in all PduL homologs. DISCUSS | |
| 53 56 CoA chemical The close resemblance between the structures binding CoA and phosphate likely indicates that no large changes in protein conformation are involved in catalysis, and that our crystal structures are representative of the active form. DISCUSS | |
| 61 70 phosphate chemical The close resemblance between the structures binding CoA and phosphate likely indicates that no large changes in protein conformation are involved in catalysis, and that our crystal structures are representative of the active form. DISCUSS | |
| 174 192 crystal structures evidence The close resemblance between the structures binding CoA and phosphate likely indicates that no large changes in protein conformation are involved in catalysis, and that our crystal structures are representative of the active form. DISCUSS | |
| 219 225 active protein_state The close resemblance between the structures binding CoA and phosphate likely indicates that no large changes in protein conformation are involved in catalysis, and that our crystal structures are representative of the active form. DISCUSS | |
| 49 54 rPduL protein The native substrate for the forward reaction of rPduL and pPduL, propionyl-CoA, most likely binds to the enzyme in the same way at the observed nucleotide and pantothenic acid moiety, but the propionyl group in the CoA-thioester might point in a different direction. DISCUSS | |
| 59 64 pPduL protein The native substrate for the forward reaction of rPduL and pPduL, propionyl-CoA, most likely binds to the enzyme in the same way at the observed nucleotide and pantothenic acid moiety, but the propionyl group in the CoA-thioester might point in a different direction. DISCUSS | |
| 66 79 propionyl-CoA chemical The native substrate for the forward reaction of rPduL and pPduL, propionyl-CoA, most likely binds to the enzyme in the same way at the observed nucleotide and pantothenic acid moiety, but the propionyl group in the CoA-thioester might point in a different direction. DISCUSS | |
| 145 155 nucleotide chemical The native substrate for the forward reaction of rPduL and pPduL, propionyl-CoA, most likely binds to the enzyme in the same way at the observed nucleotide and pantothenic acid moiety, but the propionyl group in the CoA-thioester might point in a different direction. DISCUSS | |
| 160 176 pantothenic acid chemical The native substrate for the forward reaction of rPduL and pPduL, propionyl-CoA, most likely binds to the enzyme in the same way at the observed nucleotide and pantothenic acid moiety, but the propionyl group in the CoA-thioester might point in a different direction. DISCUSS | |
| 216 229 CoA-thioester chemical The native substrate for the forward reaction of rPduL and pPduL, propionyl-CoA, most likely binds to the enzyme in the same way at the observed nucleotide and pantothenic acid moiety, but the propionyl group in the CoA-thioester might point in a different direction. DISCUSS | |
| 11 17 pocket site There is a pocket nearby the active site between the well-conserved residues Ser45 and Ala154, which could accommodate the propionyl group (S6 Fig). DISCUSS | |
| 29 40 active site site There is a pocket nearby the active site between the well-conserved residues Ser45 and Ala154, which could accommodate the propionyl group (S6 Fig). DISCUSS | |
| 53 67 well-conserved protein_state There is a pocket nearby the active site between the well-conserved residues Ser45 and Ala154, which could accommodate the propionyl group (S6 Fig). DISCUSS | |
| 77 82 Ser45 residue_name_number There is a pocket nearby the active site between the well-conserved residues Ser45 and Ala154, which could accommodate the propionyl group (S6 Fig). DISCUSS | |
| 87 93 Ala154 residue_name_number There is a pocket nearby the active site between the well-conserved residues Ser45 and Ala154, which could accommodate the propionyl group (S6 Fig). DISCUSS | |
| 2 16 homology model experimental_method A homology model of sPduL indicates that the residues making up this pocket and the surrounding active site region are identical to that of rPduL, which is not surprising, because these two homologs presumably have the same propionyl-CoA substrate. DISCUSS | |
| 20 25 sPduL protein A homology model of sPduL indicates that the residues making up this pocket and the surrounding active site region are identical to that of rPduL, which is not surprising, because these two homologs presumably have the same propionyl-CoA substrate. DISCUSS | |
| 69 75 pocket site A homology model of sPduL indicates that the residues making up this pocket and the surrounding active site region are identical to that of rPduL, which is not surprising, because these two homologs presumably have the same propionyl-CoA substrate. DISCUSS | |
| 96 107 active site site A homology model of sPduL indicates that the residues making up this pocket and the surrounding active site region are identical to that of rPduL, which is not surprising, because these two homologs presumably have the same propionyl-CoA substrate. DISCUSS | |
| 140 145 rPduL protein A homology model of sPduL indicates that the residues making up this pocket and the surrounding active site region are identical to that of rPduL, which is not surprising, because these two homologs presumably have the same propionyl-CoA substrate. DISCUSS | |
| 224 237 propionyl-CoA chemical A homology model of sPduL indicates that the residues making up this pocket and the surrounding active site region are identical to that of rPduL, which is not surprising, because these two homologs presumably have the same propionyl-CoA substrate. DISCUSS | |
| 4 18 homology model experimental_method The homology model of pPduL also has identical residues making up the pocket, but with a key difference in the vicinity of the active site: Gln77 of rPduL is replaced by a tyrosine (Tyr77) in pPduL. The physiological substrate of pPduL (Table 1) is thought to be lactyl-CoA, which contains an additional hydroxyl group relative to propionyl-CoA. The presence of an aromatic residue at this position may underlie the substrate preference of the PduL enzyme from the pvm locus. DISCUSS | |
| 22 27 pPduL protein The homology model of pPduL also has identical residues making up the pocket, but with a key difference in the vicinity of the active site: Gln77 of rPduL is replaced by a tyrosine (Tyr77) in pPduL. The physiological substrate of pPduL (Table 1) is thought to be lactyl-CoA, which contains an additional hydroxyl group relative to propionyl-CoA. The presence of an aromatic residue at this position may underlie the substrate preference of the PduL enzyme from the pvm locus. DISCUSS | |
| 70 76 pocket site The homology model of pPduL also has identical residues making up the pocket, but with a key difference in the vicinity of the active site: Gln77 of rPduL is replaced by a tyrosine (Tyr77) in pPduL. The physiological substrate of pPduL (Table 1) is thought to be lactyl-CoA, which contains an additional hydroxyl group relative to propionyl-CoA. The presence of an aromatic residue at this position may underlie the substrate preference of the PduL enzyme from the pvm locus. DISCUSS | |
| 127 138 active site site The homology model of pPduL also has identical residues making up the pocket, but with a key difference in the vicinity of the active site: Gln77 of rPduL is replaced by a tyrosine (Tyr77) in pPduL. The physiological substrate of pPduL (Table 1) is thought to be lactyl-CoA, which contains an additional hydroxyl group relative to propionyl-CoA. The presence of an aromatic residue at this position may underlie the substrate preference of the PduL enzyme from the pvm locus. DISCUSS | |
| 140 145 Gln77 residue_name_number The homology model of pPduL also has identical residues making up the pocket, but with a key difference in the vicinity of the active site: Gln77 of rPduL is replaced by a tyrosine (Tyr77) in pPduL. The physiological substrate of pPduL (Table 1) is thought to be lactyl-CoA, which contains an additional hydroxyl group relative to propionyl-CoA. The presence of an aromatic residue at this position may underlie the substrate preference of the PduL enzyme from the pvm locus. DISCUSS | |
| 149 154 rPduL protein The homology model of pPduL also has identical residues making up the pocket, but with a key difference in the vicinity of the active site: Gln77 of rPduL is replaced by a tyrosine (Tyr77) in pPduL. The physiological substrate of pPduL (Table 1) is thought to be lactyl-CoA, which contains an additional hydroxyl group relative to propionyl-CoA. The presence of an aromatic residue at this position may underlie the substrate preference of the PduL enzyme from the pvm locus. DISCUSS | |
| 172 180 tyrosine residue_name The homology model of pPduL also has identical residues making up the pocket, but with a key difference in the vicinity of the active site: Gln77 of rPduL is replaced by a tyrosine (Tyr77) in pPduL. The physiological substrate of pPduL (Table 1) is thought to be lactyl-CoA, which contains an additional hydroxyl group relative to propionyl-CoA. The presence of an aromatic residue at this position may underlie the substrate preference of the PduL enzyme from the pvm locus. DISCUSS | |
| 182 187 Tyr77 residue_name_number The homology model of pPduL also has identical residues making up the pocket, but with a key difference in the vicinity of the active site: Gln77 of rPduL is replaced by a tyrosine (Tyr77) in pPduL. The physiological substrate of pPduL (Table 1) is thought to be lactyl-CoA, which contains an additional hydroxyl group relative to propionyl-CoA. The presence of an aromatic residue at this position may underlie the substrate preference of the PduL enzyme from the pvm locus. DISCUSS | |
| 192 197 pPduL protein The homology model of pPduL also has identical residues making up the pocket, but with a key difference in the vicinity of the active site: Gln77 of rPduL is replaced by a tyrosine (Tyr77) in pPduL. The physiological substrate of pPduL (Table 1) is thought to be lactyl-CoA, which contains an additional hydroxyl group relative to propionyl-CoA. The presence of an aromatic residue at this position may underlie the substrate preference of the PduL enzyme from the pvm locus. DISCUSS | |
| 230 235 pPduL protein The homology model of pPduL also has identical residues making up the pocket, but with a key difference in the vicinity of the active site: Gln77 of rPduL is replaced by a tyrosine (Tyr77) in pPduL. The physiological substrate of pPduL (Table 1) is thought to be lactyl-CoA, which contains an additional hydroxyl group relative to propionyl-CoA. The presence of an aromatic residue at this position may underlie the substrate preference of the PduL enzyme from the pvm locus. DISCUSS | |
| 263 273 lactyl-CoA chemical The homology model of pPduL also has identical residues making up the pocket, but with a key difference in the vicinity of the active site: Gln77 of rPduL is replaced by a tyrosine (Tyr77) in pPduL. The physiological substrate of pPduL (Table 1) is thought to be lactyl-CoA, which contains an additional hydroxyl group relative to propionyl-CoA. The presence of an aromatic residue at this position may underlie the substrate preference of the PduL enzyme from the pvm locus. DISCUSS | |
| 331 344 propionyl-CoA chemical The homology model of pPduL also has identical residues making up the pocket, but with a key difference in the vicinity of the active site: Gln77 of rPduL is replaced by a tyrosine (Tyr77) in pPduL. The physiological substrate of pPduL (Table 1) is thought to be lactyl-CoA, which contains an additional hydroxyl group relative to propionyl-CoA. The presence of an aromatic residue at this position may underlie the substrate preference of the PduL enzyme from the pvm locus. DISCUSS | |
| 365 373 aromatic protein_state The homology model of pPduL also has identical residues making up the pocket, but with a key difference in the vicinity of the active site: Gln77 of rPduL is replaced by a tyrosine (Tyr77) in pPduL. The physiological substrate of pPduL (Table 1) is thought to be lactyl-CoA, which contains an additional hydroxyl group relative to propionyl-CoA. The presence of an aromatic residue at this position may underlie the substrate preference of the PduL enzyme from the pvm locus. DISCUSS | |
| 374 381 residue structure_element The homology model of pPduL also has identical residues making up the pocket, but with a key difference in the vicinity of the active site: Gln77 of rPduL is replaced by a tyrosine (Tyr77) in pPduL. The physiological substrate of pPduL (Table 1) is thought to be lactyl-CoA, which contains an additional hydroxyl group relative to propionyl-CoA. The presence of an aromatic residue at this position may underlie the substrate preference of the PduL enzyme from the pvm locus. DISCUSS | |
| 444 448 PduL protein_type The homology model of pPduL also has identical residues making up the pocket, but with a key difference in the vicinity of the active site: Gln77 of rPduL is replaced by a tyrosine (Tyr77) in pPduL. The physiological substrate of pPduL (Table 1) is thought to be lactyl-CoA, which contains an additional hydroxyl group relative to propionyl-CoA. The presence of an aromatic residue at this position may underlie the substrate preference of the PduL enzyme from the pvm locus. DISCUSS | |
| 465 474 pvm locus gene The homology model of pPduL also has identical residues making up the pocket, but with a key difference in the vicinity of the active site: Gln77 of rPduL is replaced by a tyrosine (Tyr77) in pPduL. The physiological substrate of pPduL (Table 1) is thought to be lactyl-CoA, which contains an additional hydroxyl group relative to propionyl-CoA. The presence of an aromatic residue at this position may underlie the substrate preference of the PduL enzyme from the pvm locus. DISCUSS | |
| 27 32 PduLs protein_type Indeed, in the majority of PduLs encoded in pvm loci, Gln77 is substituted by either a Tyr or Phe, whereas it is typically a Gln or Glu in PduLs in all other BMC types that degrade acetyl- or propionyl-CoA. A comparison of the PduL active site to that of the functionally identical Pta suggests that the two enzymes have distinctly different mechanisms. DISCUSS | |
| 44 52 pvm loci gene Indeed, in the majority of PduLs encoded in pvm loci, Gln77 is substituted by either a Tyr or Phe, whereas it is typically a Gln or Glu in PduLs in all other BMC types that degrade acetyl- or propionyl-CoA. A comparison of the PduL active site to that of the functionally identical Pta suggests that the two enzymes have distinctly different mechanisms. DISCUSS | |
| 54 59 Gln77 residue_name_number Indeed, in the majority of PduLs encoded in pvm loci, Gln77 is substituted by either a Tyr or Phe, whereas it is typically a Gln or Glu in PduLs in all other BMC types that degrade acetyl- or propionyl-CoA. A comparison of the PduL active site to that of the functionally identical Pta suggests that the two enzymes have distinctly different mechanisms. DISCUSS | |
| 87 90 Tyr residue_name Indeed, in the majority of PduLs encoded in pvm loci, Gln77 is substituted by either a Tyr or Phe, whereas it is typically a Gln or Glu in PduLs in all other BMC types that degrade acetyl- or propionyl-CoA. A comparison of the PduL active site to that of the functionally identical Pta suggests that the two enzymes have distinctly different mechanisms. DISCUSS | |
| 94 97 Phe residue_name Indeed, in the majority of PduLs encoded in pvm loci, Gln77 is substituted by either a Tyr or Phe, whereas it is typically a Gln or Glu in PduLs in all other BMC types that degrade acetyl- or propionyl-CoA. A comparison of the PduL active site to that of the functionally identical Pta suggests that the two enzymes have distinctly different mechanisms. DISCUSS | |
| 125 128 Gln residue_name Indeed, in the majority of PduLs encoded in pvm loci, Gln77 is substituted by either a Tyr or Phe, whereas it is typically a Gln or Glu in PduLs in all other BMC types that degrade acetyl- or propionyl-CoA. A comparison of the PduL active site to that of the functionally identical Pta suggests that the two enzymes have distinctly different mechanisms. DISCUSS | |
| 132 135 Glu residue_name Indeed, in the majority of PduLs encoded in pvm loci, Gln77 is substituted by either a Tyr or Phe, whereas it is typically a Gln or Glu in PduLs in all other BMC types that degrade acetyl- or propionyl-CoA. A comparison of the PduL active site to that of the functionally identical Pta suggests that the two enzymes have distinctly different mechanisms. DISCUSS | |
| 139 144 PduLs protein_type Indeed, in the majority of PduLs encoded in pvm loci, Gln77 is substituted by either a Tyr or Phe, whereas it is typically a Gln or Glu in PduLs in all other BMC types that degrade acetyl- or propionyl-CoA. A comparison of the PduL active site to that of the functionally identical Pta suggests that the two enzymes have distinctly different mechanisms. DISCUSS | |
| 158 161 BMC complex_assembly Indeed, in the majority of PduLs encoded in pvm loci, Gln77 is substituted by either a Tyr or Phe, whereas it is typically a Gln or Glu in PduLs in all other BMC types that degrade acetyl- or propionyl-CoA. A comparison of the PduL active site to that of the functionally identical Pta suggests that the two enzymes have distinctly different mechanisms. DISCUSS | |
| 181 188 acetyl- chemical Indeed, in the majority of PduLs encoded in pvm loci, Gln77 is substituted by either a Tyr or Phe, whereas it is typically a Gln or Glu in PduLs in all other BMC types that degrade acetyl- or propionyl-CoA. A comparison of the PduL active site to that of the functionally identical Pta suggests that the two enzymes have distinctly different mechanisms. DISCUSS | |
| 192 205 propionyl-CoA chemical Indeed, in the majority of PduLs encoded in pvm loci, Gln77 is substituted by either a Tyr or Phe, whereas it is typically a Gln or Glu in PduLs in all other BMC types that degrade acetyl- or propionyl-CoA. A comparison of the PduL active site to that of the functionally identical Pta suggests that the two enzymes have distinctly different mechanisms. DISCUSS | |
| 209 219 comparison experimental_method Indeed, in the majority of PduLs encoded in pvm loci, Gln77 is substituted by either a Tyr or Phe, whereas it is typically a Gln or Glu in PduLs in all other BMC types that degrade acetyl- or propionyl-CoA. A comparison of the PduL active site to that of the functionally identical Pta suggests that the two enzymes have distinctly different mechanisms. DISCUSS | |
| 227 231 PduL protein_type Indeed, in the majority of PduLs encoded in pvm loci, Gln77 is substituted by either a Tyr or Phe, whereas it is typically a Gln or Glu in PduLs in all other BMC types that degrade acetyl- or propionyl-CoA. A comparison of the PduL active site to that of the functionally identical Pta suggests that the two enzymes have distinctly different mechanisms. DISCUSS | |
| 232 243 active site site Indeed, in the majority of PduLs encoded in pvm loci, Gln77 is substituted by either a Tyr or Phe, whereas it is typically a Gln or Glu in PduLs in all other BMC types that degrade acetyl- or propionyl-CoA. A comparison of the PduL active site to that of the functionally identical Pta suggests that the two enzymes have distinctly different mechanisms. DISCUSS | |
| 282 285 Pta protein_type Indeed, in the majority of PduLs encoded in pvm loci, Gln77 is substituted by either a Tyr or Phe, whereas it is typically a Gln or Glu in PduLs in all other BMC types that degrade acetyl- or propionyl-CoA. A comparison of the PduL active site to that of the functionally identical Pta suggests that the two enzymes have distinctly different mechanisms. DISCUSS | |
| 27 30 Pta protein_type The catalytic mechanism of Pta involves the abstraction of a thiol hydrogen by an aspartate residue, resulting in the nucleophilic attack of thiolate upon the carbonyl carbon of acetyl-phosphate, oriented by an arginine and stabilized by a serine —there are no metals involved. DISCUSS | |
| 82 91 aspartate residue_name The catalytic mechanism of Pta involves the abstraction of a thiol hydrogen by an aspartate residue, resulting in the nucleophilic attack of thiolate upon the carbonyl carbon of acetyl-phosphate, oriented by an arginine and stabilized by a serine —there are no metals involved. DISCUSS | |
| 178 194 acetyl-phosphate chemical The catalytic mechanism of Pta involves the abstraction of a thiol hydrogen by an aspartate residue, resulting in the nucleophilic attack of thiolate upon the carbonyl carbon of acetyl-phosphate, oriented by an arginine and stabilized by a serine —there are no metals involved. DISCUSS | |
| 211 219 arginine residue_name The catalytic mechanism of Pta involves the abstraction of a thiol hydrogen by an aspartate residue, resulting in the nucleophilic attack of thiolate upon the carbonyl carbon of acetyl-phosphate, oriented by an arginine and stabilized by a serine —there are no metals involved. DISCUSS | |
| 240 246 serine residue_name The catalytic mechanism of Pta involves the abstraction of a thiol hydrogen by an aspartate residue, resulting in the nucleophilic attack of thiolate upon the carbonyl carbon of acetyl-phosphate, oriented by an arginine and stabilized by a serine —there are no metals involved. DISCUSS | |
| 20 25 rPduL protein In contrast, in the rPduL structure, there are no conserved aspartate residues in or around the active site, and the only well-conserved glutamate residue in the active site is involved in coordinating one of the metal ions. DISCUSS | |
| 26 35 structure evidence In contrast, in the rPduL structure, there are no conserved aspartate residues in or around the active site, and the only well-conserved glutamate residue in the active site is involved in coordinating one of the metal ions. DISCUSS | |
| 60 69 aspartate residue_name In contrast, in the rPduL structure, there are no conserved aspartate residues in or around the active site, and the only well-conserved glutamate residue in the active site is involved in coordinating one of the metal ions. DISCUSS | |
| 96 107 active site site In contrast, in the rPduL structure, there are no conserved aspartate residues in or around the active site, and the only well-conserved glutamate residue in the active site is involved in coordinating one of the metal ions. DISCUSS | |
| 122 136 well-conserved protein_state In contrast, in the rPduL structure, there are no conserved aspartate residues in or around the active site, and the only well-conserved glutamate residue in the active site is involved in coordinating one of the metal ions. DISCUSS | |
| 137 146 glutamate residue_name In contrast, in the rPduL structure, there are no conserved aspartate residues in or around the active site, and the only well-conserved glutamate residue in the active site is involved in coordinating one of the metal ions. DISCUSS | |
| 162 173 active site site In contrast, in the rPduL structure, there are no conserved aspartate residues in or around the active site, and the only well-conserved glutamate residue in the active site is involved in coordinating one of the metal ions. DISCUSS | |
| 189 201 coordinating bond_interaction In contrast, in the rPduL structure, there are no conserved aspartate residues in or around the active site, and the only well-conserved glutamate residue in the active site is involved in coordinating one of the metal ions. DISCUSS | |
| 44 50 acidic protein_state These observations strongly suggest that an acidic residue is not directly involved in catalysis by PduL. Instead, the dimetal active site of PduL may create a nucleophile from one of the hydroxyl groups on free phosphate to attack the carbonyl carbon of the thioester bond of an acyl-CoA. In the reverse direction, the metal ion(s) could stabilize the thiolate anion that would attack the carbonyl carbon of an acyl-phosphate; a similar mechanism has been described for phosphatases where hydroxyl groups or hydroxide ions can act as a base when coordinated by a dimetal active site. DISCUSS | |
| 51 58 residue structure_element These observations strongly suggest that an acidic residue is not directly involved in catalysis by PduL. Instead, the dimetal active site of PduL may create a nucleophile from one of the hydroxyl groups on free phosphate to attack the carbonyl carbon of the thioester bond of an acyl-CoA. In the reverse direction, the metal ion(s) could stabilize the thiolate anion that would attack the carbonyl carbon of an acyl-phosphate; a similar mechanism has been described for phosphatases where hydroxyl groups or hydroxide ions can act as a base when coordinated by a dimetal active site. DISCUSS | |
| 100 104 PduL protein_type These observations strongly suggest that an acidic residue is not directly involved in catalysis by PduL. Instead, the dimetal active site of PduL may create a nucleophile from one of the hydroxyl groups on free phosphate to attack the carbonyl carbon of the thioester bond of an acyl-CoA. In the reverse direction, the metal ion(s) could stabilize the thiolate anion that would attack the carbonyl carbon of an acyl-phosphate; a similar mechanism has been described for phosphatases where hydroxyl groups or hydroxide ions can act as a base when coordinated by a dimetal active site. DISCUSS | |
| 119 138 dimetal active site site These observations strongly suggest that an acidic residue is not directly involved in catalysis by PduL. Instead, the dimetal active site of PduL may create a nucleophile from one of the hydroxyl groups on free phosphate to attack the carbonyl carbon of the thioester bond of an acyl-CoA. In the reverse direction, the metal ion(s) could stabilize the thiolate anion that would attack the carbonyl carbon of an acyl-phosphate; a similar mechanism has been described for phosphatases where hydroxyl groups or hydroxide ions can act as a base when coordinated by a dimetal active site. DISCUSS | |
| 142 146 PduL protein_type These observations strongly suggest that an acidic residue is not directly involved in catalysis by PduL. Instead, the dimetal active site of PduL may create a nucleophile from one of the hydroxyl groups on free phosphate to attack the carbonyl carbon of the thioester bond of an acyl-CoA. In the reverse direction, the metal ion(s) could stabilize the thiolate anion that would attack the carbonyl carbon of an acyl-phosphate; a similar mechanism has been described for phosphatases where hydroxyl groups or hydroxide ions can act as a base when coordinated by a dimetal active site. DISCUSS | |
| 212 221 phosphate chemical These observations strongly suggest that an acidic residue is not directly involved in catalysis by PduL. Instead, the dimetal active site of PduL may create a nucleophile from one of the hydroxyl groups on free phosphate to attack the carbonyl carbon of the thioester bond of an acyl-CoA. In the reverse direction, the metal ion(s) could stabilize the thiolate anion that would attack the carbonyl carbon of an acyl-phosphate; a similar mechanism has been described for phosphatases where hydroxyl groups or hydroxide ions can act as a base when coordinated by a dimetal active site. DISCUSS | |
| 280 288 acyl-CoA chemical These observations strongly suggest that an acidic residue is not directly involved in catalysis by PduL. Instead, the dimetal active site of PduL may create a nucleophile from one of the hydroxyl groups on free phosphate to attack the carbonyl carbon of the thioester bond of an acyl-CoA. In the reverse direction, the metal ion(s) could stabilize the thiolate anion that would attack the carbonyl carbon of an acyl-phosphate; a similar mechanism has been described for phosphatases where hydroxyl groups or hydroxide ions can act as a base when coordinated by a dimetal active site. DISCUSS | |
| 412 426 acyl-phosphate chemical These observations strongly suggest that an acidic residue is not directly involved in catalysis by PduL. Instead, the dimetal active site of PduL may create a nucleophile from one of the hydroxyl groups on free phosphate to attack the carbonyl carbon of the thioester bond of an acyl-CoA. In the reverse direction, the metal ion(s) could stabilize the thiolate anion that would attack the carbonyl carbon of an acyl-phosphate; a similar mechanism has been described for phosphatases where hydroxyl groups or hydroxide ions can act as a base when coordinated by a dimetal active site. DISCUSS | |
| 471 483 phosphatases protein_type These observations strongly suggest that an acidic residue is not directly involved in catalysis by PduL. Instead, the dimetal active site of PduL may create a nucleophile from one of the hydroxyl groups on free phosphate to attack the carbonyl carbon of the thioester bond of an acyl-CoA. In the reverse direction, the metal ion(s) could stabilize the thiolate anion that would attack the carbonyl carbon of an acyl-phosphate; a similar mechanism has been described for phosphatases where hydroxyl groups or hydroxide ions can act as a base when coordinated by a dimetal active site. DISCUSS | |
| 564 583 dimetal active site site These observations strongly suggest that an acidic residue is not directly involved in catalysis by PduL. Instead, the dimetal active site of PduL may create a nucleophile from one of the hydroxyl groups on free phosphate to attack the carbonyl carbon of the thioester bond of an acyl-CoA. In the reverse direction, the metal ion(s) could stabilize the thiolate anion that would attack the carbonyl carbon of an acyl-phosphate; a similar mechanism has been described for phosphatases where hydroxyl groups or hydroxide ions can act as a base when coordinated by a dimetal active site. DISCUSS | |
| 4 14 structures evidence Our structures provide the foundation for studies to elucidate the details of the catalytic mechanism of PduL. Conserved residues in the active site that may contribute to substrate binding and/or transition state stabilization include Ser127, Arg103, Arg194, Gln107, Gln74, and Gln/Glu77. DISCUSS | |
| 105 109 PduL protein_type Our structures provide the foundation for studies to elucidate the details of the catalytic mechanism of PduL. Conserved residues in the active site that may contribute to substrate binding and/or transition state stabilization include Ser127, Arg103, Arg194, Gln107, Gln74, and Gln/Glu77. DISCUSS | |
| 111 120 Conserved protein_state Our structures provide the foundation for studies to elucidate the details of the catalytic mechanism of PduL. Conserved residues in the active site that may contribute to substrate binding and/or transition state stabilization include Ser127, Arg103, Arg194, Gln107, Gln74, and Gln/Glu77. DISCUSS | |
| 137 148 active site site Our structures provide the foundation for studies to elucidate the details of the catalytic mechanism of PduL. Conserved residues in the active site that may contribute to substrate binding and/or transition state stabilization include Ser127, Arg103, Arg194, Gln107, Gln74, and Gln/Glu77. DISCUSS | |
| 236 242 Ser127 residue_name_number Our structures provide the foundation for studies to elucidate the details of the catalytic mechanism of PduL. Conserved residues in the active site that may contribute to substrate binding and/or transition state stabilization include Ser127, Arg103, Arg194, Gln107, Gln74, and Gln/Glu77. DISCUSS | |
| 244 250 Arg103 residue_name_number Our structures provide the foundation for studies to elucidate the details of the catalytic mechanism of PduL. Conserved residues in the active site that may contribute to substrate binding and/or transition state stabilization include Ser127, Arg103, Arg194, Gln107, Gln74, and Gln/Glu77. DISCUSS | |
| 252 258 Arg194 residue_name_number Our structures provide the foundation for studies to elucidate the details of the catalytic mechanism of PduL. Conserved residues in the active site that may contribute to substrate binding and/or transition state stabilization include Ser127, Arg103, Arg194, Gln107, Gln74, and Gln/Glu77. DISCUSS | |
| 260 266 Gln107 residue_name_number Our structures provide the foundation for studies to elucidate the details of the catalytic mechanism of PduL. Conserved residues in the active site that may contribute to substrate binding and/or transition state stabilization include Ser127, Arg103, Arg194, Gln107, Gln74, and Gln/Glu77. DISCUSS | |
| 268 273 Gln74 residue_name_number Our structures provide the foundation for studies to elucidate the details of the catalytic mechanism of PduL. Conserved residues in the active site that may contribute to substrate binding and/or transition state stabilization include Ser127, Arg103, Arg194, Gln107, Gln74, and Gln/Glu77. DISCUSS | |
| 279 282 Gln residue_name_number Our structures provide the foundation for studies to elucidate the details of the catalytic mechanism of PduL. Conserved residues in the active site that may contribute to substrate binding and/or transition state stabilization include Ser127, Arg103, Arg194, Gln107, Gln74, and Gln/Glu77. DISCUSS | |
| 283 288 Glu77 residue_name_number Our structures provide the foundation for studies to elucidate the details of the catalytic mechanism of PduL. Conserved residues in the active site that may contribute to substrate binding and/or transition state stabilization include Ser127, Arg103, Arg194, Gln107, Gln74, and Gln/Glu77. DISCUSS | |
| 7 22 phosphate-bound protein_state In the phosphate-bound crystal structure, Ser127 and Arg103 appear to position the phosphate (Fig 4b). DISCUSS | |
| 23 40 crystal structure evidence In the phosphate-bound crystal structure, Ser127 and Arg103 appear to position the phosphate (Fig 4b). DISCUSS | |
| 42 48 Ser127 residue_name_number In the phosphate-bound crystal structure, Ser127 and Arg103 appear to position the phosphate (Fig 4b). DISCUSS | |
| 53 59 Arg103 residue_name_number In the phosphate-bound crystal structure, Ser127 and Arg103 appear to position the phosphate (Fig 4b). DISCUSS | |
| 83 92 phosphate chemical In the phosphate-bound crystal structure, Ser127 and Arg103 appear to position the phosphate (Fig 4b). DISCUSS | |
| 15 21 Arg103 residue_name_number Alternatively, Arg103 might act as a base to render the phosphate more nucleophilic. DISCUSS | |
| 56 65 phosphate chemical Alternatively, Arg103 might act as a base to render the phosphate more nucleophilic. DISCUSS | |
| 25 30 Gln74 residue_name_number The functional groups of Gln74, Gln/Glu77, and Arg194 are directed away from the active site in both CoA and phosphate-bound crystal structures and do not appear to be involved in hydrogen bonding with these substrates, although they could be important for positioning an acyl-phosphate. DISCUSS | |
| 32 35 Gln residue_name_number The functional groups of Gln74, Gln/Glu77, and Arg194 are directed away from the active site in both CoA and phosphate-bound crystal structures and do not appear to be involved in hydrogen bonding with these substrates, although they could be important for positioning an acyl-phosphate. DISCUSS | |
| 36 41 Glu77 residue_name_number The functional groups of Gln74, Gln/Glu77, and Arg194 are directed away from the active site in both CoA and phosphate-bound crystal structures and do not appear to be involved in hydrogen bonding with these substrates, although they could be important for positioning an acyl-phosphate. DISCUSS | |
| 47 53 Arg194 residue_name_number The functional groups of Gln74, Gln/Glu77, and Arg194 are directed away from the active site in both CoA and phosphate-bound crystal structures and do not appear to be involved in hydrogen bonding with these substrates, although they could be important for positioning an acyl-phosphate. DISCUSS | |
| 81 92 active site site The functional groups of Gln74, Gln/Glu77, and Arg194 are directed away from the active site in both CoA and phosphate-bound crystal structures and do not appear to be involved in hydrogen bonding with these substrates, although they could be important for positioning an acyl-phosphate. DISCUSS | |
| 101 104 CoA protein_state The functional groups of Gln74, Gln/Glu77, and Arg194 are directed away from the active site in both CoA and phosphate-bound crystal structures and do not appear to be involved in hydrogen bonding with these substrates, although they could be important for positioning an acyl-phosphate. DISCUSS | |
| 109 124 phosphate-bound protein_state The functional groups of Gln74, Gln/Glu77, and Arg194 are directed away from the active site in both CoA and phosphate-bound crystal structures and do not appear to be involved in hydrogen bonding with these substrates, although they could be important for positioning an acyl-phosphate. DISCUSS | |
| 125 143 crystal structures evidence The functional groups of Gln74, Gln/Glu77, and Arg194 are directed away from the active site in both CoA and phosphate-bound crystal structures and do not appear to be involved in hydrogen bonding with these substrates, although they could be important for positioning an acyl-phosphate. DISCUSS | |
| 180 196 hydrogen bonding bond_interaction The functional groups of Gln74, Gln/Glu77, and Arg194 are directed away from the active site in both CoA and phosphate-bound crystal structures and do not appear to be involved in hydrogen bonding with these substrates, although they could be important for positioning an acyl-phosphate. DISCUSS | |
| 272 286 acyl-phosphate chemical The functional groups of Gln74, Gln/Glu77, and Arg194 are directed away from the active site in both CoA and phosphate-bound crystal structures and do not appear to be involved in hydrogen bonding with these substrates, although they could be important for positioning an acyl-phosphate. DISCUSS | |
| 9 18 CoA-bound protein_state The free CoA-bound form is presumably poised for attack upon an acyl-phosphate, indicating that the enzyme initially binds CoA as opposed to acyl-phosphate. DISCUSS | |
| 64 78 acyl-phosphate chemical The free CoA-bound form is presumably poised for attack upon an acyl-phosphate, indicating that the enzyme initially binds CoA as opposed to acyl-phosphate. DISCUSS | |
| 123 126 CoA chemical The free CoA-bound form is presumably poised for attack upon an acyl-phosphate, indicating that the enzyme initially binds CoA as opposed to acyl-phosphate. DISCUSS | |
| 141 155 acyl-phosphate chemical The free CoA-bound form is presumably poised for attack upon an acyl-phosphate, indicating that the enzyme initially binds CoA as opposed to acyl-phosphate. DISCUSS | |
| 53 62 CoA-bound protein_state This hypothesis is strengthened by the fact that the CoA-bound crystals were obtained without added CoA, indicating that the protein bound CoA from the E. coli expression strain and retained it throughout purification and crystallization. DISCUSS | |
| 63 71 crystals evidence This hypothesis is strengthened by the fact that the CoA-bound crystals were obtained without added CoA, indicating that the protein bound CoA from the E. coli expression strain and retained it throughout purification and crystallization. DISCUSS | |
| 100 103 CoA chemical This hypothesis is strengthened by the fact that the CoA-bound crystals were obtained without added CoA, indicating that the protein bound CoA from the E. coli expression strain and retained it throughout purification and crystallization. DISCUSS | |
| 133 138 bound protein_state This hypothesis is strengthened by the fact that the CoA-bound crystals were obtained without added CoA, indicating that the protein bound CoA from the E. coli expression strain and retained it throughout purification and crystallization. DISCUSS | |
| 139 142 CoA chemical This hypothesis is strengthened by the fact that the CoA-bound crystals were obtained without added CoA, indicating that the protein bound CoA from the E. coli expression strain and retained it throughout purification and crystallization. DISCUSS | |
| 152 159 E. coli species This hypothesis is strengthened by the fact that the CoA-bound crystals were obtained without added CoA, indicating that the protein bound CoA from the E. coli expression strain and retained it throughout purification and crystallization. DISCUSS | |
| 4 19 phosphate-bound protein_state The phosphate-bound structure indicates that in the opposite reaction direction phosphate is bound first, and then an acyl-CoA enters. DISCUSS | |
| 20 29 structure evidence The phosphate-bound structure indicates that in the opposite reaction direction phosphate is bound first, and then an acyl-CoA enters. DISCUSS | |
| 80 89 phosphate chemical The phosphate-bound structure indicates that in the opposite reaction direction phosphate is bound first, and then an acyl-CoA enters. DISCUSS | |
| 118 126 acyl-CoA chemical The phosphate-bound structure indicates that in the opposite reaction direction phosphate is bound first, and then an acyl-CoA enters. DISCUSS | |
| 24 42 crystal structures evidence The two high-resolution crystal structures presented here will serve as the foundation for mechanistic studies on this noncanonical PTAC enzyme to determine how the dimetal active site functions to catalyze both forward and reverse reactions. DISCUSS | |
| 132 136 PTAC protein_type The two high-resolution crystal structures presented here will serve as the foundation for mechanistic studies on this noncanonical PTAC enzyme to determine how the dimetal active site functions to catalyze both forward and reverse reactions. DISCUSS | |
| 165 184 dimetal active site site The two high-resolution crystal structures presented here will serve as the foundation for mechanistic studies on this noncanonical PTAC enzyme to determine how the dimetal active site functions to catalyze both forward and reverse reactions. DISCUSS | |
| 47 51 PduL protein_type Functional, but Not Structural, Convergence of PduL and Pta DISCUSS | |
| 56 59 Pta protein_type Functional, but Not Structural, Convergence of PduL and Pta DISCUSS | |
| 0 4 PduL protein_type PduL and Pta are mechanistically and structurally distinct enzymes that catalyze the same reaction, a prime example of evolutionary convergence upon a function. DISCUSS | |
| 9 12 Pta protein_type PduL and Pta are mechanistically and structurally distinct enzymes that catalyze the same reaction, a prime example of evolutionary convergence upon a function. DISCUSS | |
| 155 167 active sites site There are several examples of such functional convergence of enzymes, although typically the enzymes have independently evolved similar, or even identical active sites; for example, the carbonic anhydrase family. DISCUSS | |
| 186 204 carbonic anhydrase protein_type There are several examples of such functional convergence of enzymes, although typically the enzymes have independently evolved similar, or even identical active sites; for example, the carbonic anhydrase family. DISCUSS | |
| 102 114 active sites site However, apparently less frequent is functional convergence that is supported by distinctly different active sites and accordingly catalytic mechanism, as revealed by comparison of the structures of Pta and PduL. One well-studied example of this is the β-lactamase family of enzymes, in which the active site of Class A and Class C enzymes involve serine-based catalysis, but Class B enzymes are metalloproteins. DISCUSS | |
| 199 202 Pta protein_type However, apparently less frequent is functional convergence that is supported by distinctly different active sites and accordingly catalytic mechanism, as revealed by comparison of the structures of Pta and PduL. One well-studied example of this is the β-lactamase family of enzymes, in which the active site of Class A and Class C enzymes involve serine-based catalysis, but Class B enzymes are metalloproteins. DISCUSS | |
| 207 211 PduL protein_type However, apparently less frequent is functional convergence that is supported by distinctly different active sites and accordingly catalytic mechanism, as revealed by comparison of the structures of Pta and PduL. One well-studied example of this is the β-lactamase family of enzymes, in which the active site of Class A and Class C enzymes involve serine-based catalysis, but Class B enzymes are metalloproteins. DISCUSS | |
| 253 264 β-lactamase protein_type However, apparently less frequent is functional convergence that is supported by distinctly different active sites and accordingly catalytic mechanism, as revealed by comparison of the structures of Pta and PduL. One well-studied example of this is the β-lactamase family of enzymes, in which the active site of Class A and Class C enzymes involve serine-based catalysis, but Class B enzymes are metalloproteins. DISCUSS | |
| 297 308 active site site However, apparently less frequent is functional convergence that is supported by distinctly different active sites and accordingly catalytic mechanism, as revealed by comparison of the structures of Pta and PduL. One well-studied example of this is the β-lactamase family of enzymes, in which the active site of Class A and Class C enzymes involve serine-based catalysis, but Class B enzymes are metalloproteins. DISCUSS | |
| 396 411 metalloproteins protein_type However, apparently less frequent is functional convergence that is supported by distinctly different active sites and accordingly catalytic mechanism, as revealed by comparison of the structures of Pta and PduL. One well-studied example of this is the β-lactamase family of enzymes, in which the active site of Class A and Class C enzymes involve serine-based catalysis, but Class B enzymes are metalloproteins. DISCUSS | |
| 27 39 β-lactamases protein_type This is not surprising, as β-lactamases are not so widespread among bacteria and therefore would be expected to have evolved independently several times as a defense mechanism against β-lactam antibiotics. DISCUSS | |
| 68 76 bacteria taxonomy_domain This is not surprising, as β-lactamases are not so widespread among bacteria and therefore would be expected to have evolved independently several times as a defense mechanism against β-lactam antibiotics. DISCUSS | |
| 20 28 bacteria taxonomy_domain However, nearly all bacteria encode Pta, and it is not immediately clear why the Pta/PduL functional convergence should have evolved: it would seem to be evolutionarily more resourceful for the Pta-encoding gene to be duplicated and repurposed for BMCs, as is apparently the case in one type of BMC—EUT1 (Table 1). DISCUSS | |
| 36 39 Pta protein_type However, nearly all bacteria encode Pta, and it is not immediately clear why the Pta/PduL functional convergence should have evolved: it would seem to be evolutionarily more resourceful for the Pta-encoding gene to be duplicated and repurposed for BMCs, as is apparently the case in one type of BMC—EUT1 (Table 1). DISCUSS | |
| 81 84 Pta protein_type However, nearly all bacteria encode Pta, and it is not immediately clear why the Pta/PduL functional convergence should have evolved: it would seem to be evolutionarily more resourceful for the Pta-encoding gene to be duplicated and repurposed for BMCs, as is apparently the case in one type of BMC—EUT1 (Table 1). DISCUSS | |
| 85 89 PduL protein_type However, nearly all bacteria encode Pta, and it is not immediately clear why the Pta/PduL functional convergence should have evolved: it would seem to be evolutionarily more resourceful for the Pta-encoding gene to be duplicated and repurposed for BMCs, as is apparently the case in one type of BMC—EUT1 (Table 1). DISCUSS | |
| 194 211 Pta-encoding gene gene However, nearly all bacteria encode Pta, and it is not immediately clear why the Pta/PduL functional convergence should have evolved: it would seem to be evolutionarily more resourceful for the Pta-encoding gene to be duplicated and repurposed for BMCs, as is apparently the case in one type of BMC—EUT1 (Table 1). DISCUSS | |
| 248 252 BMCs complex_assembly However, nearly all bacteria encode Pta, and it is not immediately clear why the Pta/PduL functional convergence should have evolved: it would seem to be evolutionarily more resourceful for the Pta-encoding gene to be duplicated and repurposed for BMCs, as is apparently the case in one type of BMC—EUT1 (Table 1). DISCUSS | |
| 295 303 BMC—EUT1 complex_assembly However, nearly all bacteria encode Pta, and it is not immediately clear why the Pta/PduL functional convergence should have evolved: it would seem to be evolutionarily more resourceful for the Pta-encoding gene to be duplicated and repurposed for BMCs, as is apparently the case in one type of BMC—EUT1 (Table 1). DISCUSS | |
| 90 94 PduL protein_type There could be some intrinsic biochemical difference between the two enzymes that renders PduL a more attractive candidate for encapsulation in a BMC—for example, PduL might be more amenable to tight packaging, or is better suited for the chemical microenvironment formed within the lumen of the BMC, which can be quite different from the cytosol. DISCUSS | |
| 146 149 BMC complex_assembly There could be some intrinsic biochemical difference between the two enzymes that renders PduL a more attractive candidate for encapsulation in a BMC—for example, PduL might be more amenable to tight packaging, or is better suited for the chemical microenvironment formed within the lumen of the BMC, which can be quite different from the cytosol. DISCUSS | |
| 163 167 PduL protein_type There could be some intrinsic biochemical difference between the two enzymes that renders PduL a more attractive candidate for encapsulation in a BMC—for example, PduL might be more amenable to tight packaging, or is better suited for the chemical microenvironment formed within the lumen of the BMC, which can be quite different from the cytosol. DISCUSS | |
| 296 299 BMC complex_assembly There could be some intrinsic biochemical difference between the two enzymes that renders PduL a more attractive candidate for encapsulation in a BMC—for example, PduL might be more amenable to tight packaging, or is better suited for the chemical microenvironment formed within the lumen of the BMC, which can be quite different from the cytosol. DISCUSS | |
| 47 52 PTACs protein_type Further biochemical comparison between the two PTACs will likely yield exciting results that could answer this evolutionary question. DISCUSS | |
| 0 4 BMCs complex_assembly BMCs are now known to be widespread among the bacteria and are involved in critical segments of both autotrophic and heterotrophic biochemical pathways that confer to the host organism a competitive (metabolic) advantage in select niches. DISCUSS | |
| 46 54 bacteria taxonomy_domain BMCs are now known to be widespread among the bacteria and are involved in critical segments of both autotrophic and heterotrophic biochemical pathways that confer to the host organism a competitive (metabolic) advantage in select niches. DISCUSS | |
| 27 39 metabolosome complex_assembly As one of the three common metabolosome core enzymes, the structure of PduL provides a key missing piece to our structural picture of the shared core biochemistry (Fig 1) of functionally diverse catabolic BMCs. DISCUSS | |
| 58 67 structure evidence As one of the three common metabolosome core enzymes, the structure of PduL provides a key missing piece to our structural picture of the shared core biochemistry (Fig 1) of functionally diverse catabolic BMCs. DISCUSS | |
| 71 75 PduL protein_type As one of the three common metabolosome core enzymes, the structure of PduL provides a key missing piece to our structural picture of the shared core biochemistry (Fig 1) of functionally diverse catabolic BMCs. DISCUSS | |
| 195 204 catabolic protein_state As one of the three common metabolosome core enzymes, the structure of PduL provides a key missing piece to our structural picture of the shared core biochemistry (Fig 1) of functionally diverse catabolic BMCs. DISCUSS | |
| 205 209 BMCs complex_assembly As one of the three common metabolosome core enzymes, the structure of PduL provides a key missing piece to our structural picture of the shared core biochemistry (Fig 1) of functionally diverse catabolic BMCs. DISCUSS | |
| 53 57 PduL protein_type We have observed the oligomeric state differences of PduL to correlate with the presence of an EP, providing new insight into the function of this sequence extension in BMC assembly. DISCUSS | |
| 95 97 EP structure_element We have observed the oligomeric state differences of PduL to correlate with the presence of an EP, providing new insight into the function of this sequence extension in BMC assembly. DISCUSS | |
| 169 172 BMC complex_assembly We have observed the oligomeric state differences of PduL to correlate with the presence of an EP, providing new insight into the function of this sequence extension in BMC assembly. DISCUSS | |
| 42 52 Coenzyme A chemical Moreover, our results suggest a means for Coenzyme A incorporation during metabolosome biogenesis. DISCUSS | |
| 74 86 metabolosome complex_assembly Moreover, our results suggest a means for Coenzyme A incorporation during metabolosome biogenesis. DISCUSS | |
| 117 121 BMCs complex_assembly A detailed understanding of the underlying principles governing the assembly and internal structural organization of BMCs is a requisite for synthetic biologists to design custom nanoreactors that use BMC architectures as a template. DISCUSS | |
| 201 204 BMC complex_assembly A detailed understanding of the underlying principles governing the assembly and internal structural organization of BMCs is a requisite for synthetic biologists to design custom nanoreactors that use BMC architectures as a template. DISCUSS | |
| 41 54 metabolosomes complex_assembly Furthermore, given the growing number of metabolosomes implicated in pathogenesis, the PduL structure will be useful in the development of therapeutics. DISCUSS | |
| 87 91 PduL protein_type Furthermore, given the growing number of metabolosomes implicated in pathogenesis, the PduL structure will be useful in the development of therapeutics. DISCUSS | |
| 92 101 structure evidence Furthermore, given the growing number of metabolosomes implicated in pathogenesis, the PduL structure will be useful in the development of therapeutics. DISCUSS | |
| 14 18 PduL protein_type The fact that PduL is confined almost exclusively to metabolosomes can be used to develop an inhibitor that blocks only PduL and not Pta as a way to selectively disrupt BMC-based metabolism, while not affecting most commensal organisms that require PTAC activity. DISCUSS | |
| 53 66 metabolosomes complex_assembly The fact that PduL is confined almost exclusively to metabolosomes can be used to develop an inhibitor that blocks only PduL and not Pta as a way to selectively disrupt BMC-based metabolism, while not affecting most commensal organisms that require PTAC activity. DISCUSS | |
| 120 124 PduL protein_type The fact that PduL is confined almost exclusively to metabolosomes can be used to develop an inhibitor that blocks only PduL and not Pta as a way to selectively disrupt BMC-based metabolism, while not affecting most commensal organisms that require PTAC activity. DISCUSS | |
| 133 136 Pta protein_type The fact that PduL is confined almost exclusively to metabolosomes can be used to develop an inhibitor that blocks only PduL and not Pta as a way to selectively disrupt BMC-based metabolism, while not affecting most commensal organisms that require PTAC activity. DISCUSS | |
| 169 172 BMC complex_assembly The fact that PduL is confined almost exclusively to metabolosomes can be used to develop an inhibitor that blocks only PduL and not Pta as a way to selectively disrupt BMC-based metabolism, while not affecting most commensal organisms that require PTAC activity. DISCUSS | |
| 249 253 PTAC protein_type The fact that PduL is confined almost exclusively to metabolosomes can be used to develop an inhibitor that blocks only PduL and not Pta as a way to selectively disrupt BMC-based metabolism, while not affecting most commensal organisms that require PTAC activity. DISCUSS | |