|
anno_start anno_end anno_text entity_type sentence section |
|
4 27 immunity-related GTPase protein_type The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion TITLE |
|
28 33 Irga6 protein The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion TITLE |
|
34 43 dimerizes oligomeric_state The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion TITLE |
|
49 70 parallel head-to-head protein_state The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion TITLE |
|
4 28 immunity-related GTPases protein_type The immunity-related GTPases (IRGs) constitute a powerful cell-autonomous resistance system against several intracellular pathogens. ABSTRACT |
|
30 34 IRGs protein_type The immunity-related GTPases (IRGs) constitute a powerful cell-autonomous resistance system against several intracellular pathogens. ABSTRACT |
|
0 5 Irga6 protein Irga6 is a dynamin-like protein that oligomerizes at the parasitophorous vacuolar membrane (PVM) of Toxoplasma gondii leading to its vesiculation. ABSTRACT |
|
11 31 dynamin-like protein protein_type Irga6 is a dynamin-like protein that oligomerizes at the parasitophorous vacuolar membrane (PVM) of Toxoplasma gondii leading to its vesiculation. ABSTRACT |
|
100 117 Toxoplasma gondii species Irga6 is a dynamin-like protein that oligomerizes at the parasitophorous vacuolar membrane (PVM) of Toxoplasma gondii leading to its vesiculation. ABSTRACT |
|
20 40 biochemical analysis experimental_method Based on a previous biochemical analysis, it has been proposed that the GTPase domains of Irga6 dimerize in an antiparallel fashion during oligomerization. ABSTRACT |
|
72 86 GTPase domains structure_element Based on a previous biochemical analysis, it has been proposed that the GTPase domains of Irga6 dimerize in an antiparallel fashion during oligomerization. ABSTRACT |
|
90 95 Irga6 protein Based on a previous biochemical analysis, it has been proposed that the GTPase domains of Irga6 dimerize in an antiparallel fashion during oligomerization. ABSTRACT |
|
96 104 dimerize oligomeric_state Based on a previous biochemical analysis, it has been proposed that the GTPase domains of Irga6 dimerize in an antiparallel fashion during oligomerization. ABSTRACT |
|
111 123 antiparallel protein_state Based on a previous biochemical analysis, it has been proposed that the GTPase domains of Irga6 dimerize in an antiparallel fashion during oligomerization. ABSTRACT |
|
3 13 determined experimental_method We determined the crystal structure of an oligomerization-impaired Irga6 mutant bound to a non-hydrolyzable GTP analog. ABSTRACT |
|
18 35 crystal structure evidence We determined the crystal structure of an oligomerization-impaired Irga6 mutant bound to a non-hydrolyzable GTP analog. ABSTRACT |
|
42 66 oligomerization-impaired protein_state We determined the crystal structure of an oligomerization-impaired Irga6 mutant bound to a non-hydrolyzable GTP analog. ABSTRACT |
|
67 72 Irga6 protein We determined the crystal structure of an oligomerization-impaired Irga6 mutant bound to a non-hydrolyzable GTP analog. ABSTRACT |
|
73 79 mutant protein_state We determined the crystal structure of an oligomerization-impaired Irga6 mutant bound to a non-hydrolyzable GTP analog. ABSTRACT |
|
80 88 bound to protein_state We determined the crystal structure of an oligomerization-impaired Irga6 mutant bound to a non-hydrolyzable GTP analog. ABSTRACT |
|
108 111 GTP chemical We determined the crystal structure of an oligomerization-impaired Irga6 mutant bound to a non-hydrolyzable GTP analog. ABSTRACT |
|
36 45 structure evidence Contrary to the previous model, the structure shows that the GTPase domains dimerize in a parallel fashion. ABSTRACT |
|
61 75 GTPase domains structure_element Contrary to the previous model, the structure shows that the GTPase domains dimerize in a parallel fashion. ABSTRACT |
|
76 84 dimerize oligomeric_state Contrary to the previous model, the structure shows that the GTPase domains dimerize in a parallel fashion. ABSTRACT |
|
90 98 parallel protein_state Contrary to the previous model, the structure shows that the GTPase domains dimerize in a parallel fashion. ABSTRACT |
|
4 15 nucleotides chemical The nucleotides in the center of the interface participate in dimerization by forming symmetric contacts with each other and with the switch I region of the opposing Irga6 molecule. ABSTRACT |
|
37 46 interface site The nucleotides in the center of the interface participate in dimerization by forming symmetric contacts with each other and with the switch I region of the opposing Irga6 molecule. ABSTRACT |
|
134 142 switch I site The nucleotides in the center of the interface participate in dimerization by forming symmetric contacts with each other and with the switch I region of the opposing Irga6 molecule. ABSTRACT |
|
166 171 Irga6 protein The nucleotides in the center of the interface participate in dimerization by forming symmetric contacts with each other and with the switch I region of the opposing Irga6 molecule. ABSTRACT |
|
39 42 GTP chemical The latter contact appears to activate GTP hydrolysis by stabilizing the position of the catalytic glutamate 106 in switch I close to the active site. ABSTRACT |
|
89 98 catalytic protein_state The latter contact appears to activate GTP hydrolysis by stabilizing the position of the catalytic glutamate 106 in switch I close to the active site. ABSTRACT |
|
99 112 glutamate 106 residue_name_number The latter contact appears to activate GTP hydrolysis by stabilizing the position of the catalytic glutamate 106 in switch I close to the active site. ABSTRACT |
|
116 124 switch I site The latter contact appears to activate GTP hydrolysis by stabilizing the position of the catalytic glutamate 106 in switch I close to the active site. ABSTRACT |
|
138 149 active site site The latter contact appears to activate GTP hydrolysis by stabilizing the position of the catalytic glutamate 106 in switch I close to the active site. ABSTRACT |
|
38 47 switch II site Further dimerization contacts involve switch II, the G4 helix and the trans stabilizing loop. ABSTRACT |
|
53 61 G4 helix structure_element Further dimerization contacts involve switch II, the G4 helix and the trans stabilizing loop. ABSTRACT |
|
70 92 trans stabilizing loop structure_element Further dimerization contacts involve switch II, the G4 helix and the trans stabilizing loop. ABSTRACT |
|
4 9 Irga6 protein The Irga6 structure features a parallel GTPase domain dimer, which appears to be a unifying feature of all dynamin and septin superfamily members. ABSTRACT |
|
10 19 structure evidence The Irga6 structure features a parallel GTPase domain dimer, which appears to be a unifying feature of all dynamin and septin superfamily members. ABSTRACT |
|
31 39 parallel protein_state The Irga6 structure features a parallel GTPase domain dimer, which appears to be a unifying feature of all dynamin and septin superfamily members. ABSTRACT |
|
40 53 GTPase domain structure_element The Irga6 structure features a parallel GTPase domain dimer, which appears to be a unifying feature of all dynamin and septin superfamily members. ABSTRACT |
|
54 59 dimer oligomeric_state The Irga6 structure features a parallel GTPase domain dimer, which appears to be a unifying feature of all dynamin and septin superfamily members. ABSTRACT |
|
107 114 dynamin protein_type The Irga6 structure features a parallel GTPase domain dimer, which appears to be a unifying feature of all dynamin and septin superfamily members. ABSTRACT |
|
119 125 septin protein_type The Irga6 structure features a parallel GTPase domain dimer, which appears to be a unifying feature of all dynamin and septin superfamily members. ABSTRACT |
|
88 91 IRG protein_type This study contributes important insights into the assembly and catalytic mechanisms of IRG proteins as prerequisite to understand their anti-microbial action. ABSTRACT |
|
0 24 Immunity-related GTPases protein_type Immunity-related GTPases (IRGs) comprise a family of dynamin-related cell-autonomous resistance proteins targeting intracellular pathogens, such as Mycobacterium tuberculosis, Mycobacterium avium, Listeria monocytogenes, Trypanosoma cruzi, and Toxoplasma gondii. INTRO |
|
26 30 IRGs protein_type Immunity-related GTPases (IRGs) comprise a family of dynamin-related cell-autonomous resistance proteins targeting intracellular pathogens, such as Mycobacterium tuberculosis, Mycobacterium avium, Listeria monocytogenes, Trypanosoma cruzi, and Toxoplasma gondii. INTRO |
|
53 104 dynamin-related cell-autonomous resistance proteins protein_type Immunity-related GTPases (IRGs) comprise a family of dynamin-related cell-autonomous resistance proteins targeting intracellular pathogens, such as Mycobacterium tuberculosis, Mycobacterium avium, Listeria monocytogenes, Trypanosoma cruzi, and Toxoplasma gondii. INTRO |
|
148 174 Mycobacterium tuberculosis species Immunity-related GTPases (IRGs) comprise a family of dynamin-related cell-autonomous resistance proteins targeting intracellular pathogens, such as Mycobacterium tuberculosis, Mycobacterium avium, Listeria monocytogenes, Trypanosoma cruzi, and Toxoplasma gondii. INTRO |
|
176 195 Mycobacterium avium species Immunity-related GTPases (IRGs) comprise a family of dynamin-related cell-autonomous resistance proteins targeting intracellular pathogens, such as Mycobacterium tuberculosis, Mycobacterium avium, Listeria monocytogenes, Trypanosoma cruzi, and Toxoplasma gondii. INTRO |
|
197 219 Listeria monocytogenes species Immunity-related GTPases (IRGs) comprise a family of dynamin-related cell-autonomous resistance proteins targeting intracellular pathogens, such as Mycobacterium tuberculosis, Mycobacterium avium, Listeria monocytogenes, Trypanosoma cruzi, and Toxoplasma gondii. INTRO |
|
221 238 Trypanosoma cruzi species Immunity-related GTPases (IRGs) comprise a family of dynamin-related cell-autonomous resistance proteins targeting intracellular pathogens, such as Mycobacterium tuberculosis, Mycobacterium avium, Listeria monocytogenes, Trypanosoma cruzi, and Toxoplasma gondii. INTRO |
|
244 261 Toxoplasma gondii species Immunity-related GTPases (IRGs) comprise a family of dynamin-related cell-autonomous resistance proteins targeting intracellular pathogens, such as Mycobacterium tuberculosis, Mycobacterium avium, Listeria monocytogenes, Trypanosoma cruzi, and Toxoplasma gondii. INTRO |
|
3 7 mice taxonomy_domain In mice, the 23 IRG members are induced by interferons, whereas the single human homologue is constitutively expressed in some tissues, especially in testis. INTRO |
|
16 19 IRG protein_type In mice, the 23 IRG members are induced by interferons, whereas the single human homologue is constitutively expressed in some tissues, especially in testis. INTRO |
|
43 54 interferons protein_type In mice, the 23 IRG members are induced by interferons, whereas the single human homologue is constitutively expressed in some tissues, especially in testis. INTRO |
|
75 80 human species In mice, the 23 IRG members are induced by interferons, whereas the single human homologue is constitutively expressed in some tissues, especially in testis. INTRO |
|
28 32 IRGs protein_type In non-infected cells, most IRGs are largely cytosolic. INTRO |
|
13 17 IRGs protein_type In this way, IRGs contribute to the release of the pathogen into the cytoplasm and its subsequent destruction. INTRO |
|
0 5 Irga6 protein Irga6, one of the effector IRG proteins, localizes to the intact parasitophorous vacuole membrane (PVM) and, after disruption of the PVM, is found associated with vesicular accumulations, presumably derived from the PVM. INTRO |
|
27 30 IRG protein_type Irga6, one of the effector IRG proteins, localizes to the intact parasitophorous vacuole membrane (PVM) and, after disruption of the PVM, is found associated with vesicular accumulations, presumably derived from the PVM. INTRO |
|
2 21 myristoylation site site A myristoylation site at Gly2 is necessary for the recruitment to the PVM but not for the weak constitutive binding to the ER membrane. INTRO |
|
25 29 Gly2 residue_name_number A myristoylation site at Gly2 is necessary for the recruitment to the PVM but not for the weak constitutive binding to the ER membrane. INTRO |
|
43 50 helix A structure_element An internally oriented antibody epitope on helix A between positions 20 and 24 was demonstrated to be accessible in the GTP-, but not in the GDP-bound state. INTRO |
|
69 78 20 and 24 residue_range An internally oriented antibody epitope on helix A between positions 20 and 24 was demonstrated to be accessible in the GTP-, but not in the GDP-bound state. INTRO |
|
120 125 GTP-, protein_state An internally oriented antibody epitope on helix A between positions 20 and 24 was demonstrated to be accessible in the GTP-, but not in the GDP-bound state. INTRO |
|
141 150 GDP-bound protein_state An internally oriented antibody epitope on helix A between positions 20 and 24 was demonstrated to be accessible in the GTP-, but not in the GDP-bound state. INTRO |
|
51 54 GTP chemical This indicates large-scale structural changes upon GTP binding that probably include exposure of the myristoyl group, enhancing binding to the PVM. INTRO |
|
0 19 Biochemical studies experimental_method Biochemical studies indicated that Irga6 hydrolyses GTP in a cooperative manner and forms GTP-dependent oligomers in vitro and in vivo. INTRO |
|
35 40 Irga6 protein Biochemical studies indicated that Irga6 hydrolyses GTP in a cooperative manner and forms GTP-dependent oligomers in vitro and in vivo. INTRO |
|
52 55 GTP chemical Biochemical studies indicated that Irga6 hydrolyses GTP in a cooperative manner and forms GTP-dependent oligomers in vitro and in vivo. INTRO |
|
90 103 GTP-dependent protein_state Biochemical studies indicated that Irga6 hydrolyses GTP in a cooperative manner and forms GTP-dependent oligomers in vitro and in vivo. INTRO |
|
104 113 oligomers oligomeric_state Biochemical studies indicated that Irga6 hydrolyses GTP in a cooperative manner and forms GTP-dependent oligomers in vitro and in vivo. INTRO |
|
0 18 Crystal structures evidence Crystal structures of Irga6 in various nucleotide-loaded states revealed the basic architecture of IRG proteins, including a GTPase domain and a composite helical domain. INTRO |
|
22 27 Irga6 protein Crystal structures of Irga6 in various nucleotide-loaded states revealed the basic architecture of IRG proteins, including a GTPase domain and a composite helical domain. INTRO |
|
39 56 nucleotide-loaded protein_state Crystal structures of Irga6 in various nucleotide-loaded states revealed the basic architecture of IRG proteins, including a GTPase domain and a composite helical domain. INTRO |
|
99 102 IRG protein_type Crystal structures of Irga6 in various nucleotide-loaded states revealed the basic architecture of IRG proteins, including a GTPase domain and a composite helical domain. INTRO |
|
125 138 GTPase domain structure_element Crystal structures of Irga6 in various nucleotide-loaded states revealed the basic architecture of IRG proteins, including a GTPase domain and a composite helical domain. INTRO |
|
145 169 composite helical domain structure_element Crystal structures of Irga6 in various nucleotide-loaded states revealed the basic architecture of IRG proteins, including a GTPase domain and a composite helical domain. INTRO |
|
36 58 dimerization interface site These studies additionally showed a dimerization interface in the nucleotide-free protein as well as in all nucleotide-bound states. INTRO |
|
66 81 nucleotide-free protein_state These studies additionally showed a dimerization interface in the nucleotide-free protein as well as in all nucleotide-bound states. INTRO |
|
108 124 nucleotide-bound protein_state These studies additionally showed a dimerization interface in the nucleotide-free protein as well as in all nucleotide-bound states. INTRO |
|
14 35 GTPase domain surface site It involves a GTPase domain surface, which is located at the opposite side of the nucleotide, and an interface in the helical domain, with a water-filled gap between the two contact surfaces. INTRO |
|
101 110 interface site It involves a GTPase domain surface, which is located at the opposite side of the nucleotide, and an interface in the helical domain, with a water-filled gap between the two contact surfaces. INTRO |
|
118 132 helical domain structure_element It involves a GTPase domain surface, which is located at the opposite side of the nucleotide, and an interface in the helical domain, with a water-filled gap between the two contact surfaces. INTRO |
|
141 146 water chemical It involves a GTPase domain surface, which is located at the opposite side of the nucleotide, and an interface in the helical domain, with a water-filled gap between the two contact surfaces. INTRO |
|
174 190 contact surfaces site It involves a GTPase domain surface, which is located at the opposite side of the nucleotide, and an interface in the helical domain, with a water-filled gap between the two contact surfaces. INTRO |
|
0 11 Mutagenesis experimental_method "Mutagenesis of the contact surfaces suggests that this ""backside"" interface is not required for GTP-dependent oligomerization or cooperative hydrolysis, despite an earlier suggestion to the contrary." INTRO |
|
19 35 contact surfaces site "Mutagenesis of the contact surfaces suggests that this ""backside"" interface is not required for GTP-dependent oligomerization or cooperative hydrolysis, despite an earlier suggestion to the contrary." INTRO |
|
56 64 backside site "Mutagenesis of the contact surfaces suggests that this ""backside"" interface is not required for GTP-dependent oligomerization or cooperative hydrolysis, despite an earlier suggestion to the contrary." INTRO |
|
66 75 interface site "Mutagenesis of the contact surfaces suggests that this ""backside"" interface is not required for GTP-dependent oligomerization or cooperative hydrolysis, despite an earlier suggestion to the contrary." INTRO |
|
96 99 GTP chemical "Mutagenesis of the contact surfaces suggests that this ""backside"" interface is not required for GTP-dependent oligomerization or cooperative hydrolysis, despite an earlier suggestion to the contrary." INTRO |
|
10 29 biochemical studies experimental_method Extensive biochemical studies suggested that GTP-induced oligomerization of Irga6 requires an interface in the GTPase domain across the nucleotide-binding site. INTRO |
|
45 48 GTP chemical Extensive biochemical studies suggested that GTP-induced oligomerization of Irga6 requires an interface in the GTPase domain across the nucleotide-binding site. INTRO |
|
76 81 Irga6 protein Extensive biochemical studies suggested that GTP-induced oligomerization of Irga6 requires an interface in the GTPase domain across the nucleotide-binding site. INTRO |
|
94 103 interface site Extensive biochemical studies suggested that GTP-induced oligomerization of Irga6 requires an interface in the GTPase domain across the nucleotide-binding site. INTRO |
|
111 124 GTPase domain structure_element Extensive biochemical studies suggested that GTP-induced oligomerization of Irga6 requires an interface in the GTPase domain across the nucleotide-binding site. INTRO |
|
136 159 nucleotide-binding site site Extensive biochemical studies suggested that GTP-induced oligomerization of Irga6 requires an interface in the GTPase domain across the nucleotide-binding site. INTRO |
|
7 25 structural studies experimental_method Recent structural studies indicated that a 'G interface' is typical of dynamin superfamily members, such as dynamin, MxA, the guanylate binding protein-1 (GBP-1), atlastin and the bacterial dynamin-like proteins (BDLP). INTRO |
|
44 55 G interface site Recent structural studies indicated that a 'G interface' is typical of dynamin superfamily members, such as dynamin, MxA, the guanylate binding protein-1 (GBP-1), atlastin and the bacterial dynamin-like proteins (BDLP). INTRO |
|
71 78 dynamin protein_type Recent structural studies indicated that a 'G interface' is typical of dynamin superfamily members, such as dynamin, MxA, the guanylate binding protein-1 (GBP-1), atlastin and the bacterial dynamin-like proteins (BDLP). INTRO |
|
108 115 dynamin protein_type Recent structural studies indicated that a 'G interface' is typical of dynamin superfamily members, such as dynamin, MxA, the guanylate binding protein-1 (GBP-1), atlastin and the bacterial dynamin-like proteins (BDLP). INTRO |
|
117 120 MxA protein Recent structural studies indicated that a 'G interface' is typical of dynamin superfamily members, such as dynamin, MxA, the guanylate binding protein-1 (GBP-1), atlastin and the bacterial dynamin-like proteins (BDLP). INTRO |
|
126 153 guanylate binding protein-1 protein Recent structural studies indicated that a 'G interface' is typical of dynamin superfamily members, such as dynamin, MxA, the guanylate binding protein-1 (GBP-1), atlastin and the bacterial dynamin-like proteins (BDLP). INTRO |
|
155 160 GBP-1 protein Recent structural studies indicated that a 'G interface' is typical of dynamin superfamily members, such as dynamin, MxA, the guanylate binding protein-1 (GBP-1), atlastin and the bacterial dynamin-like proteins (BDLP). INTRO |
|
163 171 atlastin protein_type Recent structural studies indicated that a 'G interface' is typical of dynamin superfamily members, such as dynamin, MxA, the guanylate binding protein-1 (GBP-1), atlastin and the bacterial dynamin-like proteins (BDLP). INTRO |
|
180 189 bacterial taxonomy_domain Recent structural studies indicated that a 'G interface' is typical of dynamin superfamily members, such as dynamin, MxA, the guanylate binding protein-1 (GBP-1), atlastin and the bacterial dynamin-like proteins (BDLP). INTRO |
|
190 211 dynamin-like proteins protein_type Recent structural studies indicated that a 'G interface' is typical of dynamin superfamily members, such as dynamin, MxA, the guanylate binding protein-1 (GBP-1), atlastin and the bacterial dynamin-like proteins (BDLP). INTRO |
|
213 217 BDLP protein_type Recent structural studies indicated that a 'G interface' is typical of dynamin superfamily members, such as dynamin, MxA, the guanylate binding protein-1 (GBP-1), atlastin and the bacterial dynamin-like proteins (BDLP). INTRO |
|
48 59 G interface site For several of these proteins, formation of the G interface was shown to trigger GTP hydrolysis by inducing rearrangements of catalytic residues in cis. INTRO |
|
81 84 GTP chemical For several of these proteins, formation of the G interface was shown to trigger GTP hydrolysis by inducing rearrangements of catalytic residues in cis. INTRO |
|
3 10 dynamin protein_type In dynamin, the G interface includes residues in the phosphate binding loop, the two switch regions, the 'trans stabilizing loop' and the 'G4 loop'. INTRO |
|
16 27 G interface site In dynamin, the G interface includes residues in the phosphate binding loop, the two switch regions, the 'trans stabilizing loop' and the 'G4 loop'. INTRO |
|
53 75 phosphate binding loop structure_element In dynamin, the G interface includes residues in the phosphate binding loop, the two switch regions, the 'trans stabilizing loop' and the 'G4 loop'. INTRO |
|
85 99 switch regions site In dynamin, the G interface includes residues in the phosphate binding loop, the two switch regions, the 'trans stabilizing loop' and the 'G4 loop'. INTRO |
|
106 128 trans stabilizing loop structure_element In dynamin, the G interface includes residues in the phosphate binding loop, the two switch regions, the 'trans stabilizing loop' and the 'G4 loop'. INTRO |
|
139 146 G4 loop structure_element In dynamin, the G interface includes residues in the phosphate binding loop, the two switch regions, the 'trans stabilizing loop' and the 'G4 loop'. INTRO |
|
4 9 Irga6 protein For Irga6, it was demonstrated that besides residues in the switch I and switch II regions, the 3'-OH group of the ribose participates in this interface. INTRO |
|
60 68 switch I site For Irga6, it was demonstrated that besides residues in the switch I and switch II regions, the 3'-OH group of the ribose participates in this interface. INTRO |
|
73 82 switch II site For Irga6, it was demonstrated that besides residues in the switch I and switch II regions, the 3'-OH group of the ribose participates in this interface. INTRO |
|
143 152 interface site For Irga6, it was demonstrated that besides residues in the switch I and switch II regions, the 3'-OH group of the ribose participates in this interface. INTRO |
|
10 44 signal recognition particle GTPase protein_type Since the signal recognition particle GTPase and its homologous receptor (called FfH and FtsY in bacteria) also employ the 3'-OH ribose group to dimerize in an anti-parallel orientation therefore activating its GTPase, an analogous dimerization model was proposed for Irga6. INTRO |
|
64 72 receptor protein_type Since the signal recognition particle GTPase and its homologous receptor (called FfH and FtsY in bacteria) also employ the 3'-OH ribose group to dimerize in an anti-parallel orientation therefore activating its GTPase, an analogous dimerization model was proposed for Irga6. INTRO |
|
81 84 FfH protein Since the signal recognition particle GTPase and its homologous receptor (called FfH and FtsY in bacteria) also employ the 3'-OH ribose group to dimerize in an anti-parallel orientation therefore activating its GTPase, an analogous dimerization model was proposed for Irga6. INTRO |
|
89 93 FtsY protein Since the signal recognition particle GTPase and its homologous receptor (called FfH and FtsY in bacteria) also employ the 3'-OH ribose group to dimerize in an anti-parallel orientation therefore activating its GTPase, an analogous dimerization model was proposed for Irga6. INTRO |
|
97 105 bacteria taxonomy_domain Since the signal recognition particle GTPase and its homologous receptor (called FfH and FtsY in bacteria) also employ the 3'-OH ribose group to dimerize in an anti-parallel orientation therefore activating its GTPase, an analogous dimerization model was proposed for Irga6. INTRO |
|
145 153 dimerize oligomeric_state Since the signal recognition particle GTPase and its homologous receptor (called FfH and FtsY in bacteria) also employ the 3'-OH ribose group to dimerize in an anti-parallel orientation therefore activating its GTPase, an analogous dimerization model was proposed for Irga6. INTRO |
|
160 173 anti-parallel protein_state Since the signal recognition particle GTPase and its homologous receptor (called FfH and FtsY in bacteria) also employ the 3'-OH ribose group to dimerize in an anti-parallel orientation therefore activating its GTPase, an analogous dimerization model was proposed for Irga6. INTRO |
|
211 217 GTPase protein_type Since the signal recognition particle GTPase and its homologous receptor (called FfH and FtsY in bacteria) also employ the 3'-OH ribose group to dimerize in an anti-parallel orientation therefore activating its GTPase, an analogous dimerization model was proposed for Irga6. INTRO |
|
268 273 Irga6 protein Since the signal recognition particle GTPase and its homologous receptor (called FfH and FtsY in bacteria) also employ the 3'-OH ribose group to dimerize in an anti-parallel orientation therefore activating its GTPase, an analogous dimerization model was proposed for Irga6. INTRO |
|
13 30 crystal structure evidence However, the crystal structure of Irga6 in the presence of the non-hydrolyzable GTP analogue 5'-guanylyl imidodiphosphate (GMPPNP) showed only subtle differences relative to the apo or GDP-bound protein and did not reveal a new dimer interface associated with the GTPase domain. INTRO |
|
34 39 Irga6 protein However, the crystal structure of Irga6 in the presence of the non-hydrolyzable GTP analogue 5'-guanylyl imidodiphosphate (GMPPNP) showed only subtle differences relative to the apo or GDP-bound protein and did not reveal a new dimer interface associated with the GTPase domain. INTRO |
|
47 58 presence of protein_state However, the crystal structure of Irga6 in the presence of the non-hydrolyzable GTP analogue 5'-guanylyl imidodiphosphate (GMPPNP) showed only subtle differences relative to the apo or GDP-bound protein and did not reveal a new dimer interface associated with the GTPase domain. INTRO |
|
80 83 GTP chemical However, the crystal structure of Irga6 in the presence of the non-hydrolyzable GTP analogue 5'-guanylyl imidodiphosphate (GMPPNP) showed only subtle differences relative to the apo or GDP-bound protein and did not reveal a new dimer interface associated with the GTPase domain. INTRO |
|
93 121 5'-guanylyl imidodiphosphate chemical However, the crystal structure of Irga6 in the presence of the non-hydrolyzable GTP analogue 5'-guanylyl imidodiphosphate (GMPPNP) showed only subtle differences relative to the apo or GDP-bound protein and did not reveal a new dimer interface associated with the GTPase domain. INTRO |
|
123 129 GMPPNP chemical However, the crystal structure of Irga6 in the presence of the non-hydrolyzable GTP analogue 5'-guanylyl imidodiphosphate (GMPPNP) showed only subtle differences relative to the apo or GDP-bound protein and did not reveal a new dimer interface associated with the GTPase domain. INTRO |
|
178 181 apo protein_state However, the crystal structure of Irga6 in the presence of the non-hydrolyzable GTP analogue 5'-guanylyl imidodiphosphate (GMPPNP) showed only subtle differences relative to the apo or GDP-bound protein and did not reveal a new dimer interface associated with the GTPase domain. INTRO |
|
185 194 GDP-bound protein_state However, the crystal structure of Irga6 in the presence of the non-hydrolyzable GTP analogue 5'-guanylyl imidodiphosphate (GMPPNP) showed only subtle differences relative to the apo or GDP-bound protein and did not reveal a new dimer interface associated with the GTPase domain. INTRO |
|
228 243 dimer interface site However, the crystal structure of Irga6 in the presence of the non-hydrolyzable GTP analogue 5'-guanylyl imidodiphosphate (GMPPNP) showed only subtle differences relative to the apo or GDP-bound protein and did not reveal a new dimer interface associated with the GTPase domain. INTRO |
|
264 277 GTPase domain structure_element However, the crystal structure of Irga6 in the presence of the non-hydrolyzable GTP analogue 5'-guanylyl imidodiphosphate (GMPPNP) showed only subtle differences relative to the apo or GDP-bound protein and did not reveal a new dimer interface associated with the GTPase domain. INTRO |
|
5 14 structure evidence This structure was obtained by soaking GMPPNP in nucleotide-free crystals of Irga6, an approach which may have interfered with nucleotide-induced domain rearrangements. INTRO |
|
31 38 soaking experimental_method This structure was obtained by soaking GMPPNP in nucleotide-free crystals of Irga6, an approach which may have interfered with nucleotide-induced domain rearrangements. INTRO |
|
39 45 GMPPNP chemical This structure was obtained by soaking GMPPNP in nucleotide-free crystals of Irga6, an approach which may have interfered with nucleotide-induced domain rearrangements. INTRO |
|
49 64 nucleotide-free protein_state This structure was obtained by soaking GMPPNP in nucleotide-free crystals of Irga6, an approach which may have interfered with nucleotide-induced domain rearrangements. INTRO |
|
65 73 crystals evidence This structure was obtained by soaking GMPPNP in nucleotide-free crystals of Irga6, an approach which may have interfered with nucleotide-induced domain rearrangements. INTRO |
|
77 82 Irga6 protein This structure was obtained by soaking GMPPNP in nucleotide-free crystals of Irga6, an approach which may have interfered with nucleotide-induced domain rearrangements. INTRO |
|
41 52 G interface site To clarify the dimerization mode via the G interface, we determined the GMPPNP-bound crystal structure of a non-oligomerizing Irga6 variant. INTRO |
|
57 67 determined experimental_method To clarify the dimerization mode via the G interface, we determined the GMPPNP-bound crystal structure of a non-oligomerizing Irga6 variant. INTRO |
|
72 84 GMPPNP-bound protein_state To clarify the dimerization mode via the G interface, we determined the GMPPNP-bound crystal structure of a non-oligomerizing Irga6 variant. INTRO |
|
85 102 crystal structure evidence To clarify the dimerization mode via the G interface, we determined the GMPPNP-bound crystal structure of a non-oligomerizing Irga6 variant. INTRO |
|
108 125 non-oligomerizing protein_state To clarify the dimerization mode via the G interface, we determined the GMPPNP-bound crystal structure of a non-oligomerizing Irga6 variant. INTRO |
|
126 131 Irga6 protein To clarify the dimerization mode via the G interface, we determined the GMPPNP-bound crystal structure of a non-oligomerizing Irga6 variant. INTRO |
|
132 139 variant protein_state To clarify the dimerization mode via the G interface, we determined the GMPPNP-bound crystal structure of a non-oligomerizing Irga6 variant. INTRO |
|
4 13 structure evidence The structure revealed that Irga6 can dimerize via the G interface in a parallel head-to-head fashion. INTRO |
|
28 33 Irga6 protein The structure revealed that Irga6 can dimerize via the G interface in a parallel head-to-head fashion. INTRO |
|
38 46 dimerize oligomeric_state The structure revealed that Irga6 can dimerize via the G interface in a parallel head-to-head fashion. INTRO |
|
55 66 G interface site The structure revealed that Irga6 can dimerize via the G interface in a parallel head-to-head fashion. INTRO |
|
72 93 parallel head-to-head protein_state The structure revealed that Irga6 can dimerize via the G interface in a parallel head-to-head fashion. INTRO |
|
24 32 parallel protein_state Our data suggest that a parallel dimerization mode may be a unifying feature in all dynamin and septin superfamily proteins. INTRO |
|
84 91 dynamin protein_type Our data suggest that a parallel dimerization mode may be a unifying feature in all dynamin and septin superfamily proteins. INTRO |
|
96 102 septin protein_type Our data suggest that a parallel dimerization mode may be a unifying feature in all dynamin and septin superfamily proteins. INTRO |
|
32 37 Irga6 protein "Previous results indicated that Irga6 mutations in a loosely defined surface region (the ""secondary patch""), which is distant from the G-interface and only slightly overlapping with the backside interface (see below), individually reduced GTP-dependent oligomerization." RESULTS |
|
38 47 mutations experimental_method "Previous results indicated that Irga6 mutations in a loosely defined surface region (the ""secondary patch""), which is distant from the G-interface and only slightly overlapping with the backside interface (see below), individually reduced GTP-dependent oligomerization." RESULTS |
|
69 83 surface region site "Previous results indicated that Irga6 mutations in a loosely defined surface region (the ""secondary patch""), which is distant from the G-interface and only slightly overlapping with the backside interface (see below), individually reduced GTP-dependent oligomerization." RESULTS |
|
90 105 secondary patch site "Previous results indicated that Irga6 mutations in a loosely defined surface region (the ""secondary patch""), which is distant from the G-interface and only slightly overlapping with the backside interface (see below), individually reduced GTP-dependent oligomerization." RESULTS |
|
135 146 G-interface site "Previous results indicated that Irga6 mutations in a loosely defined surface region (the ""secondary patch""), which is distant from the G-interface and only slightly overlapping with the backside interface (see below), individually reduced GTP-dependent oligomerization." RESULTS |
|
186 204 backside interface site "Previous results indicated that Irga6 mutations in a loosely defined surface region (the ""secondary patch""), which is distant from the G-interface and only slightly overlapping with the backside interface (see below), individually reduced GTP-dependent oligomerization." RESULTS |
|
239 242 GTP chemical "Previous results indicated that Irga6 mutations in a loosely defined surface region (the ""secondary patch""), which is distant from the G-interface and only slightly overlapping with the backside interface (see below), individually reduced GTP-dependent oligomerization." RESULTS |
|
2 40 combination of four of these mutations experimental_method A combination of four of these mutations (R31E, K32E, K176E, and K246E) essentially eliminated GTP-dependent assembly (Additional file 1: Figure S1) and allowed crystallization of Irga6 in the presence of GMPPNP. RESULTS |
|
42 46 R31E mutant A combination of four of these mutations (R31E, K32E, K176E, and K246E) essentially eliminated GTP-dependent assembly (Additional file 1: Figure S1) and allowed crystallization of Irga6 in the presence of GMPPNP. RESULTS |
|
48 52 K32E mutant A combination of four of these mutations (R31E, K32E, K176E, and K246E) essentially eliminated GTP-dependent assembly (Additional file 1: Figure S1) and allowed crystallization of Irga6 in the presence of GMPPNP. RESULTS |
|
54 59 K176E mutant A combination of four of these mutations (R31E, K32E, K176E, and K246E) essentially eliminated GTP-dependent assembly (Additional file 1: Figure S1) and allowed crystallization of Irga6 in the presence of GMPPNP. RESULTS |
|
65 70 K246E mutant A combination of four of these mutations (R31E, K32E, K176E, and K246E) essentially eliminated GTP-dependent assembly (Additional file 1: Figure S1) and allowed crystallization of Irga6 in the presence of GMPPNP. RESULTS |
|
84 94 eliminated protein_state A combination of four of these mutations (R31E, K32E, K176E, and K246E) essentially eliminated GTP-dependent assembly (Additional file 1: Figure S1) and allowed crystallization of Irga6 in the presence of GMPPNP. RESULTS |
|
95 98 GTP chemical A combination of four of these mutations (R31E, K32E, K176E, and K246E) essentially eliminated GTP-dependent assembly (Additional file 1: Figure S1) and allowed crystallization of Irga6 in the presence of GMPPNP. RESULTS |
|
161 176 crystallization experimental_method A combination of four of these mutations (R31E, K32E, K176E, and K246E) essentially eliminated GTP-dependent assembly (Additional file 1: Figure S1) and allowed crystallization of Irga6 in the presence of GMPPNP. RESULTS |
|
180 185 Irga6 protein A combination of four of these mutations (R31E, K32E, K176E, and K246E) essentially eliminated GTP-dependent assembly (Additional file 1: Figure S1) and allowed crystallization of Irga6 in the presence of GMPPNP. RESULTS |
|
193 204 presence of protein_state A combination of four of these mutations (R31E, K32E, K176E, and K246E) essentially eliminated GTP-dependent assembly (Additional file 1: Figure S1) and allowed crystallization of Irga6 in the presence of GMPPNP. RESULTS |
|
205 211 GMPPNP chemical A combination of four of these mutations (R31E, K32E, K176E, and K246E) essentially eliminated GTP-dependent assembly (Additional file 1: Figure S1) and allowed crystallization of Irga6 in the presence of GMPPNP. RESULTS |
|
0 8 Crystals evidence Crystals diffracted to 3.2 Γ
resolution and displayed one exceptionally long unit cell axis of 1289 Γ
(Additional file 1: Table S1). RESULTS |
|
4 13 structure evidence The structure was solved by molecular replacement and refined to Rwork/Rfree of 29.7 %/31.7 % (Additional file 1: Table S2). RESULTS |
|
28 49 molecular replacement experimental_method The structure was solved by molecular replacement and refined to Rwork/Rfree of 29.7 %/31.7 % (Additional file 1: Table S2). RESULTS |
|
65 70 Rwork evidence The structure was solved by molecular replacement and refined to Rwork/Rfree of 29.7 %/31.7 % (Additional file 1: Table S2). RESULTS |
|
71 76 Rfree evidence The structure was solved by molecular replacement and refined to Rwork/Rfree of 29.7 %/31.7 % (Additional file 1: Table S2). RESULTS |
|
36 41 Irga6 protein The asymmetric unit contained seven Irga6 molecules that were arranged in a helical pattern along the long cell axis (Additional file 1: Figure S2). RESULTS |
|
0 9 Structure evidence Structure of the Irga6 dimer. FIG |
|
17 22 Irga6 protein Structure of the Irga6 dimer. FIG |
|
23 28 dimer oligomeric_state Structure of the Irga6 dimer. FIG |
|
47 52 mouse taxonomy_domain a Schematic view of the domain architecture of mouse Irga6. FIG |
|
53 58 Irga6 protein a Schematic view of the domain architecture of mouse Irga6. FIG |
|
36 41 Irga6 protein b Ribbon-type representation of the Irga6 dimer. FIG |
|
42 47 dimer oligomeric_state b Ribbon-type representation of the Irga6 dimer. FIG |
|
19 23 Mg2+ chemical The nucleotide and Mg2+ ion (green) are shown in sphere representation. FIG |
|
4 17 GTPase domain structure_element The GTPase domain dimer is boxed. FIG |
|
18 23 dimer oligomeric_state The GTPase domain dimer is boxed. FIG |
|
70 83 GTPase domain structure_element Secondary structure was numbered according to ref.. c Top view on the GTPase domain dimer. FIG |
|
84 89 dimer oligomeric_state Secondary structure was numbered according to ref.. c Top view on the GTPase domain dimer. FIG |
|
23 36 contact sites site d Magnification of the contact sites. FIG |
|
2 15 Superposition experimental_method e Superposition of different switch I conformations in the asymmetric unit; the same colors as in Additional file 1: Figure S2 are used for the switch I regions of the individual subunits. FIG |
|
29 37 switch I site e Superposition of different switch I conformations in the asymmetric unit; the same colors as in Additional file 1: Figure S2 are used for the switch I regions of the individual subunits. FIG |
|
144 152 switch I site e Superposition of different switch I conformations in the asymmetric unit; the same colors as in Additional file 1: Figure S2 are used for the switch I regions of the individual subunits. FIG |
|
0 8 Switch I site Switch I residues of subunit A (yellow) involved in ribose binding are labelled and shown in stick representation. FIG |
|
29 30 A structure_element Switch I residues of subunit A (yellow) involved in ribose binding are labelled and shown in stick representation. FIG |
|
0 5 Irga6 protein Irga6 immunity-related GTPase 6 FIG |
|
6 31 immunity-related GTPase 6 protein Irga6 immunity-related GTPase 6 FIG |
|
11 18 dynamin protein_type Like other dynamin superfamily members, the GTPase domain of Irga6 comprises a canonical GTPase domain fold, with a central Ξ²-sheet surrounded by helices on both sides (Fig.Β 1a-c). RESULTS |
|
44 57 GTPase domain structure_element Like other dynamin superfamily members, the GTPase domain of Irga6 comprises a canonical GTPase domain fold, with a central Ξ²-sheet surrounded by helices on both sides (Fig.Β 1a-c). RESULTS |
|
61 66 Irga6 protein Like other dynamin superfamily members, the GTPase domain of Irga6 comprises a canonical GTPase domain fold, with a central Ξ²-sheet surrounded by helices on both sides (Fig.Β 1a-c). RESULTS |
|
89 102 GTPase domain structure_element Like other dynamin superfamily members, the GTPase domain of Irga6 comprises a canonical GTPase domain fold, with a central Ξ²-sheet surrounded by helices on both sides (Fig.Β 1a-c). RESULTS |
|
124 131 Ξ²-sheet structure_element Like other dynamin superfamily members, the GTPase domain of Irga6 comprises a canonical GTPase domain fold, with a central Ξ²-sheet surrounded by helices on both sides (Fig.Β 1a-c). RESULTS |
|
146 153 helices structure_element Like other dynamin superfamily members, the GTPase domain of Irga6 comprises a canonical GTPase domain fold, with a central Ξ²-sheet surrounded by helices on both sides (Fig.Β 1a-c). RESULTS |
|
4 18 helical domain structure_element The helical domain is a bipartite structure composed of helices Ξ±A-C at the N-terminus and helix Ξ±F-L at the C-terminus of the GTPase domain. RESULTS |
|
56 63 helices structure_element The helical domain is a bipartite structure composed of helices Ξ±A-C at the N-terminus and helix Ξ±F-L at the C-terminus of the GTPase domain. RESULTS |
|
64 68 Ξ±A-C structure_element The helical domain is a bipartite structure composed of helices Ξ±A-C at the N-terminus and helix Ξ±F-L at the C-terminus of the GTPase domain. RESULTS |
|
91 96 helix structure_element The helical domain is a bipartite structure composed of helices Ξ±A-C at the N-terminus and helix Ξ±F-L at the C-terminus of the GTPase domain. RESULTS |
|
97 101 Ξ±F-L structure_element The helical domain is a bipartite structure composed of helices Ξ±A-C at the N-terminus and helix Ξ±F-L at the C-terminus of the GTPase domain. RESULTS |
|
127 140 GTPase domain structure_element The helical domain is a bipartite structure composed of helices Ξ±A-C at the N-terminus and helix Ξ±F-L at the C-terminus of the GTPase domain. RESULTS |
|
89 116 root mean square deviations evidence Overall, the seven molecules in the asymmetric unit are very similar to each other, with root mean square deviations (rmsd) ranging from 0.32 β 0.45 Γ
over all CΞ± atoms. RESULTS |
|
118 122 rmsd evidence Overall, the seven molecules in the asymmetric unit are very similar to each other, with root mean square deviations (rmsd) ranging from 0.32 β 0.45 Γ
over all CΞ± atoms. RESULTS |
|
4 14 structures evidence The structures of the seven molecules also agree well with the previously determined structure of native GMPPNP-bound Irga6 (PDB: 1TQ6; rmsd of 1.00-1.13 Γ
over all CΞ± atoms). RESULTS |
|
85 94 structure evidence The structures of the seven molecules also agree well with the previously determined structure of native GMPPNP-bound Irga6 (PDB: 1TQ6; rmsd of 1.00-1.13 Γ
over all CΞ± atoms). RESULTS |
|
98 104 native protein_state The structures of the seven molecules also agree well with the previously determined structure of native GMPPNP-bound Irga6 (PDB: 1TQ6; rmsd of 1.00-1.13 Γ
over all CΞ± atoms). RESULTS |
|
105 117 GMPPNP-bound protein_state The structures of the seven molecules also agree well with the previously determined structure of native GMPPNP-bound Irga6 (PDB: 1TQ6; rmsd of 1.00-1.13 Γ
over all CΞ± atoms). RESULTS |
|
118 123 Irga6 protein The structures of the seven molecules also agree well with the previously determined structure of native GMPPNP-bound Irga6 (PDB: 1TQ6; rmsd of 1.00-1.13 Γ
over all CΞ± atoms). RESULTS |
|
136 140 rmsd evidence The structures of the seven molecules also agree well with the previously determined structure of native GMPPNP-bound Irga6 (PDB: 1TQ6; rmsd of 1.00-1.13 Γ
over all CΞ± atoms). RESULTS |
|
10 15 Irga6 protein The seven Irga6 molecules in the asymmetric unit form various higher order contacts in the crystals. RESULTS |
|
91 99 crystals evidence The seven Irga6 molecules in the asymmetric unit form various higher order contacts in the crystals. RESULTS |
|
42 50 dimerize oligomeric_state Within the asymmetric unit, six molecules dimerize via the symmetric backside dimer interface (buried surface area 930 Γ
2), and the remaining seventh molecule forms the same type of interaction with its symmetry mate of the adjacent asymmetric unit (Additional file 1: Figure S2a, b, Figure S3). RESULTS |
|
69 93 backside dimer interface site Within the asymmetric unit, six molecules dimerize via the symmetric backside dimer interface (buried surface area 930 Γ
2), and the remaining seventh molecule forms the same type of interaction with its symmetry mate of the adjacent asymmetric unit (Additional file 1: Figure S2a, b, Figure S3). RESULTS |
|
35 44 mutations experimental_method This indicates that the introduced mutations in the secondary patch, from which only Lys176 is part of the backside interface, do, in fact, not prevent this interaction. RESULTS |
|
52 67 secondary patch site This indicates that the introduced mutations in the secondary patch, from which only Lys176 is part of the backside interface, do, in fact, not prevent this interaction. RESULTS |
|
85 91 Lys176 residue_name_number This indicates that the introduced mutations in the secondary patch, from which only Lys176 is part of the backside interface, do, in fact, not prevent this interaction. RESULTS |
|
107 125 backside interface site This indicates that the introduced mutations in the secondary patch, from which only Lys176 is part of the backside interface, do, in fact, not prevent this interaction. RESULTS |
|
8 26 assembly interface site Another assembly interface with a buried surface area of 450 Γ
2, which we call the βtertiary patchβ, was formed via two interaction sites in the helical domains (Additional file 1: Figure S2c, d, S3). RESULTS |
|
84 98 tertiary patch site Another assembly interface with a buried surface area of 450 Γ
2, which we call the βtertiary patchβ, was formed via two interaction sites in the helical domains (Additional file 1: Figure S2c, d, S3). RESULTS |
|
120 137 interaction sites site Another assembly interface with a buried surface area of 450 Γ
2, which we call the βtertiary patchβ, was formed via two interaction sites in the helical domains (Additional file 1: Figure S2c, d, S3). RESULTS |
|
145 160 helical domains structure_element Another assembly interface with a buried surface area of 450 Γ
2, which we call the βtertiary patchβ, was formed via two interaction sites in the helical domains (Additional file 1: Figure S2c, d, S3). RESULTS |
|
8 17 interface site In this interface, helices Ξ±K from two adjacent molecules form a hydrogen bonding network involving residues 373-376. RESULTS |
|
19 26 helices structure_element In this interface, helices Ξ±K from two adjacent molecules form a hydrogen bonding network involving residues 373-376. RESULTS |
|
27 29 Ξ±K structure_element In this interface, helices Ξ±K from two adjacent molecules form a hydrogen bonding network involving residues 373-376. RESULTS |
|
65 89 hydrogen bonding network bond_interaction In this interface, helices Ξ±K from two adjacent molecules form a hydrogen bonding network involving residues 373-376. RESULTS |
|
109 116 373-376 residue_range In this interface, helices Ξ±K from two adjacent molecules form a hydrogen bonding network involving residues 373-376. RESULTS |
|
26 33 helices structure_element Furthermore, two adjacent helices Ξ±A form hydrophobic contacts. RESULTS |
|
34 36 Ξ±A structure_element Furthermore, two adjacent helices Ξ±A form hydrophobic contacts. RESULTS |
|
42 62 hydrophobic contacts bond_interaction Furthermore, two adjacent helices Ξ±A form hydrophobic contacts. RESULTS |
|
33 48 double mutation protein_state It was previously shown that the double mutation L372R/A373R did not prevent GTP-induced assembly, so there is currently no evidence supporting an involvement of this interface in higher-order oligomerization. RESULTS |
|
49 54 L372R mutant It was previously shown that the double mutation L372R/A373R did not prevent GTP-induced assembly, so there is currently no evidence supporting an involvement of this interface in higher-order oligomerization. RESULTS |
|
55 60 A373R mutant It was previously shown that the double mutation L372R/A373R did not prevent GTP-induced assembly, so there is currently no evidence supporting an involvement of this interface in higher-order oligomerization. RESULTS |
|
77 80 GTP chemical It was previously shown that the double mutation L372R/A373R did not prevent GTP-induced assembly, so there is currently no evidence supporting an involvement of this interface in higher-order oligomerization. RESULTS |
|
167 176 interface site It was previously shown that the double mutation L372R/A373R did not prevent GTP-induced assembly, so there is currently no evidence supporting an involvement of this interface in higher-order oligomerization. RESULTS |
|
21 22 A structure_element Strikingly, molecule A of one asymmetric unit assembled with an equivalent molecule of the adjacent asymmetric unit via the G-interface in a symmetric parallel fashion via a 470 Γ
2 interface. RESULTS |
|
124 135 G-interface site Strikingly, molecule A of one asymmetric unit assembled with an equivalent molecule of the adjacent asymmetric unit via the G-interface in a symmetric parallel fashion via a 470 Γ
2 interface. RESULTS |
|
151 159 parallel protein_state Strikingly, molecule A of one asymmetric unit assembled with an equivalent molecule of the adjacent asymmetric unit via the G-interface in a symmetric parallel fashion via a 470 Γ
2 interface. RESULTS |
|
27 43 butterfly-shaped protein_state This assembly results in a butterfly-shaped Irga6 dimer in which the helical domains protrude in parallel orientations (Fig.Β 1b, Additional file 1: Figure S3). RESULTS |
|
44 49 Irga6 protein This assembly results in a butterfly-shaped Irga6 dimer in which the helical domains protrude in parallel orientations (Fig.Β 1b, Additional file 1: Figure S3). RESULTS |
|
50 55 dimer oligomeric_state This assembly results in a butterfly-shaped Irga6 dimer in which the helical domains protrude in parallel orientations (Fig.Β 1b, Additional file 1: Figure S3). RESULTS |
|
69 84 helical domains structure_element This assembly results in a butterfly-shaped Irga6 dimer in which the helical domains protrude in parallel orientations (Fig.Β 1b, Additional file 1: Figure S3). RESULTS |
|
97 105 parallel protein_state This assembly results in a butterfly-shaped Irga6 dimer in which the helical domains protrude in parallel orientations (Fig.Β 1b, Additional file 1: Figure S3). RESULTS |
|
84 95 G interface site In contrast, the other six molecules in the asymmetric unit do not assemble via the G interface. RESULTS |
|
4 15 G interface site The G interface in molecule A can be subdivided into three distinct contact sites (Fig.Β 1c, d). RESULTS |
|
68 81 contact sites site The G interface in molecule A can be subdivided into three distinct contact sites (Fig.Β 1c, d). RESULTS |
|
0 14 Contact site I site Contact site I is formed between R159 and K161 in the trans stabilizing loops, and S132 in the switch II regions of the opposing molecules. RESULTS |
|
33 37 R159 residue_name_number Contact site I is formed between R159 and K161 in the trans stabilizing loops, and S132 in the switch II regions of the opposing molecules. RESULTS |
|
42 46 K161 residue_name_number Contact site I is formed between R159 and K161 in the trans stabilizing loops, and S132 in the switch II regions of the opposing molecules. RESULTS |
|
54 77 trans stabilizing loops structure_element Contact site I is formed between R159 and K161 in the trans stabilizing loops, and S132 in the switch II regions of the opposing molecules. RESULTS |
|
83 87 S132 residue_name_number Contact site I is formed between R159 and K161 in the trans stabilizing loops, and S132 in the switch II regions of the opposing molecules. RESULTS |
|
95 104 switch II site Contact site I is formed between R159 and K161 in the trans stabilizing loops, and S132 in the switch II regions of the opposing molecules. RESULTS |
|
0 15 Contact site II site Contact site II features polar and hydrophobic interactions formed by switch I (V104, V107) with a helix following the guanine specificity motif (G4 helix, K184 and S187) and the trans stabilizing loop (T158) of the opposing GTPase domain. RESULTS |
|
25 59 polar and hydrophobic interactions bond_interaction Contact site II features polar and hydrophobic interactions formed by switch I (V104, V107) with a helix following the guanine specificity motif (G4 helix, K184 and S187) and the trans stabilizing loop (T158) of the opposing GTPase domain. RESULTS |
|
70 78 switch I site Contact site II features polar and hydrophobic interactions formed by switch I (V104, V107) with a helix following the guanine specificity motif (G4 helix, K184 and S187) and the trans stabilizing loop (T158) of the opposing GTPase domain. RESULTS |
|
80 84 V104 residue_name_number Contact site II features polar and hydrophobic interactions formed by switch I (V104, V107) with a helix following the guanine specificity motif (G4 helix, K184 and S187) and the trans stabilizing loop (T158) of the opposing GTPase domain. RESULTS |
|
86 90 V107 residue_name_number Contact site II features polar and hydrophobic interactions formed by switch I (V104, V107) with a helix following the guanine specificity motif (G4 helix, K184 and S187) and the trans stabilizing loop (T158) of the opposing GTPase domain. RESULTS |
|
99 104 helix structure_element Contact site II features polar and hydrophobic interactions formed by switch I (V104, V107) with a helix following the guanine specificity motif (G4 helix, K184 and S187) and the trans stabilizing loop (T158) of the opposing GTPase domain. RESULTS |
|
119 144 guanine specificity motif structure_element Contact site II features polar and hydrophobic interactions formed by switch I (V104, V107) with a helix following the guanine specificity motif (G4 helix, K184 and S187) and the trans stabilizing loop (T158) of the opposing GTPase domain. RESULTS |
|
146 154 G4 helix structure_element Contact site II features polar and hydrophobic interactions formed by switch I (V104, V107) with a helix following the guanine specificity motif (G4 helix, K184 and S187) and the trans stabilizing loop (T158) of the opposing GTPase domain. RESULTS |
|
156 160 K184 residue_name_number Contact site II features polar and hydrophobic interactions formed by switch I (V104, V107) with a helix following the guanine specificity motif (G4 helix, K184 and S187) and the trans stabilizing loop (T158) of the opposing GTPase domain. RESULTS |
|
165 169 S187 residue_name_number Contact site II features polar and hydrophobic interactions formed by switch I (V104, V107) with a helix following the guanine specificity motif (G4 helix, K184 and S187) and the trans stabilizing loop (T158) of the opposing GTPase domain. RESULTS |
|
179 201 trans stabilizing loop structure_element Contact site II features polar and hydrophobic interactions formed by switch I (V104, V107) with a helix following the guanine specificity motif (G4 helix, K184 and S187) and the trans stabilizing loop (T158) of the opposing GTPase domain. RESULTS |
|
203 207 T158 residue_name_number Contact site II features polar and hydrophobic interactions formed by switch I (V104, V107) with a helix following the guanine specificity motif (G4 helix, K184 and S187) and the trans stabilizing loop (T158) of the opposing GTPase domain. RESULTS |
|
225 238 GTPase domain structure_element Contact site II features polar and hydrophobic interactions formed by switch I (V104, V107) with a helix following the guanine specificity motif (G4 helix, K184 and S187) and the trans stabilizing loop (T158) of the opposing GTPase domain. RESULTS |
|
3 19 contact site III site In contact site III, G103 of switch I interacts via its main chain nitrogen with the exocyclic 2β-OH and 3β-OH groups of the opposing ribose in trans, whereas the two opposing exocyclic 3β-OH group of the ribose form hydrogen bonds with each other. RESULTS |
|
21 25 G103 residue_name_number In contact site III, G103 of switch I interacts via its main chain nitrogen with the exocyclic 2β-OH and 3β-OH groups of the opposing ribose in trans, whereas the two opposing exocyclic 3β-OH group of the ribose form hydrogen bonds with each other. RESULTS |
|
29 37 switch I site In contact site III, G103 of switch I interacts via its main chain nitrogen with the exocyclic 2β-OH and 3β-OH groups of the opposing ribose in trans, whereas the two opposing exocyclic 3β-OH group of the ribose form hydrogen bonds with each other. RESULTS |
|
134 140 ribose chemical In contact site III, G103 of switch I interacts via its main chain nitrogen with the exocyclic 2β-OH and 3β-OH groups of the opposing ribose in trans, whereas the two opposing exocyclic 3β-OH group of the ribose form hydrogen bonds with each other. RESULTS |
|
205 211 ribose chemical In contact site III, G103 of switch I interacts via its main chain nitrogen with the exocyclic 2β-OH and 3β-OH groups of the opposing ribose in trans, whereas the two opposing exocyclic 3β-OH group of the ribose form hydrogen bonds with each other. RESULTS |
|
217 231 hydrogen bonds bond_interaction In contact site III, G103 of switch I interacts via its main chain nitrogen with the exocyclic 2β-OH and 3β-OH groups of the opposing ribose in trans, whereas the two opposing exocyclic 3β-OH group of the ribose form hydrogen bonds with each other. RESULTS |
|
8 14 ribose chemical Via the ribose contact, switch I is pulled towards the opposing nucleotide (Fig.Β 1e). RESULTS |
|
24 32 switch I site Via the ribose contact, switch I is pulled towards the opposing nucleotide (Fig.Β 1e). RESULTS |
|
64 74 nucleotide chemical Via the ribose contact, switch I is pulled towards the opposing nucleotide (Fig.Β 1e). RESULTS |
|
9 13 E106 residue_name_number In turn, E106 of switch I reorients towards the nucleotide and now participates in the coordination of the Mg2+ ion (Fig.Β 1e, Additional file 1: Figure S4). RESULTS |
|
17 25 switch I site In turn, E106 of switch I reorients towards the nucleotide and now participates in the coordination of the Mg2+ ion (Fig.Β 1e, Additional file 1: Figure S4). RESULTS |
|
48 58 nucleotide chemical In turn, E106 of switch I reorients towards the nucleotide and now participates in the coordination of the Mg2+ ion (Fig.Β 1e, Additional file 1: Figure S4). RESULTS |
|
87 102 coordination of bond_interaction In turn, E106 of switch I reorients towards the nucleotide and now participates in the coordination of the Mg2+ ion (Fig.Β 1e, Additional file 1: Figure S4). RESULTS |
|
107 111 Mg2+ chemical In turn, E106 of switch I reorients towards the nucleotide and now participates in the coordination of the Mg2+ ion (Fig.Β 1e, Additional file 1: Figure S4). RESULTS |
|
0 4 E106 residue_name_number E106 was previously shown to be essential for catalysis, and the observed interactions in contact site III explain how dimerization via the ribose is directly coupled to the activation of GTP hydrolysis. RESULTS |
|
90 106 contact site III site E106 was previously shown to be essential for catalysis, and the observed interactions in contact site III explain how dimerization via the ribose is directly coupled to the activation of GTP hydrolysis. RESULTS |
|
140 146 ribose chemical E106 was previously shown to be essential for catalysis, and the observed interactions in contact site III explain how dimerization via the ribose is directly coupled to the activation of GTP hydrolysis. RESULTS |
|
188 191 GTP chemical E106 was previously shown to be essential for catalysis, and the observed interactions in contact site III explain how dimerization via the ribose is directly coupled to the activation of GTP hydrolysis. RESULTS |
|
4 15 G interface site The G interface is in full agreement with previously published biochemical data that indicate crucial roles of E77, G103, E106, S132, R159, K161, K162, D164, N191, and K196 for oligomerization and oligomerization-induced GTP hydrolysis. RESULTS |
|
111 114 E77 residue_name_number The G interface is in full agreement with previously published biochemical data that indicate crucial roles of E77, G103, E106, S132, R159, K161, K162, D164, N191, and K196 for oligomerization and oligomerization-induced GTP hydrolysis. RESULTS |
|
116 120 G103 residue_name_number The G interface is in full agreement with previously published biochemical data that indicate crucial roles of E77, G103, E106, S132, R159, K161, K162, D164, N191, and K196 for oligomerization and oligomerization-induced GTP hydrolysis. RESULTS |
|
122 126 E106 residue_name_number The G interface is in full agreement with previously published biochemical data that indicate crucial roles of E77, G103, E106, S132, R159, K161, K162, D164, N191, and K196 for oligomerization and oligomerization-induced GTP hydrolysis. RESULTS |
|
128 132 S132 residue_name_number The G interface is in full agreement with previously published biochemical data that indicate crucial roles of E77, G103, E106, S132, R159, K161, K162, D164, N191, and K196 for oligomerization and oligomerization-induced GTP hydrolysis. RESULTS |
|
134 138 R159 residue_name_number The G interface is in full agreement with previously published biochemical data that indicate crucial roles of E77, G103, E106, S132, R159, K161, K162, D164, N191, and K196 for oligomerization and oligomerization-induced GTP hydrolysis. RESULTS |
|
140 144 K161 residue_name_number The G interface is in full agreement with previously published biochemical data that indicate crucial roles of E77, G103, E106, S132, R159, K161, K162, D164, N191, and K196 for oligomerization and oligomerization-induced GTP hydrolysis. RESULTS |
|
146 150 K162 residue_name_number The G interface is in full agreement with previously published biochemical data that indicate crucial roles of E77, G103, E106, S132, R159, K161, K162, D164, N191, and K196 for oligomerization and oligomerization-induced GTP hydrolysis. RESULTS |
|
152 156 D164 residue_name_number The G interface is in full agreement with previously published biochemical data that indicate crucial roles of E77, G103, E106, S132, R159, K161, K162, D164, N191, and K196 for oligomerization and oligomerization-induced GTP hydrolysis. RESULTS |
|
158 162 N191 residue_name_number The G interface is in full agreement with previously published biochemical data that indicate crucial roles of E77, G103, E106, S132, R159, K161, K162, D164, N191, and K196 for oligomerization and oligomerization-induced GTP hydrolysis. RESULTS |
|
168 172 K196 residue_name_number The G interface is in full agreement with previously published biochemical data that indicate crucial roles of E77, G103, E106, S132, R159, K161, K162, D164, N191, and K196 for oligomerization and oligomerization-induced GTP hydrolysis. RESULTS |
|
221 224 GTP chemical The G interface is in full agreement with previously published biochemical data that indicate crucial roles of E77, G103, E106, S132, R159, K161, K162, D164, N191, and K196 for oligomerization and oligomerization-induced GTP hydrolysis. RESULTS |
|
56 60 G103 residue_name_number All of these residues directly participate in contacts (G103, S132, R159, and K161) or are in direct vicinity to the interface (E77, E106, K162, D164, and N191). RESULTS |
|
62 66 S132 residue_name_number All of these residues directly participate in contacts (G103, S132, R159, and K161) or are in direct vicinity to the interface (E77, E106, K162, D164, and N191). RESULTS |
|
68 72 R159 residue_name_number All of these residues directly participate in contacts (G103, S132, R159, and K161) or are in direct vicinity to the interface (E77, E106, K162, D164, and N191). RESULTS |
|
78 82 K161 residue_name_number All of these residues directly participate in contacts (G103, S132, R159, and K161) or are in direct vicinity to the interface (E77, E106, K162, D164, and N191). RESULTS |
|
117 126 interface site All of these residues directly participate in contacts (G103, S132, R159, and K161) or are in direct vicinity to the interface (E77, E106, K162, D164, and N191). RESULTS |
|
128 131 E77 residue_name_number All of these residues directly participate in contacts (G103, S132, R159, and K161) or are in direct vicinity to the interface (E77, E106, K162, D164, and N191). RESULTS |
|
133 137 E106 residue_name_number All of these residues directly participate in contacts (G103, S132, R159, and K161) or are in direct vicinity to the interface (E77, E106, K162, D164, and N191). RESULTS |
|
139 143 K162 residue_name_number All of these residues directly participate in contacts (G103, S132, R159, and K161) or are in direct vicinity to the interface (E77, E106, K162, D164, and N191). RESULTS |
|
145 149 D164 residue_name_number All of these residues directly participate in contacts (G103, S132, R159, and K161) or are in direct vicinity to the interface (E77, E106, K162, D164, and N191). RESULTS |
|
155 159 N191 residue_name_number All of these residues directly participate in contacts (G103, S132, R159, and K161) or are in direct vicinity to the interface (E77, E106, K162, D164, and N191). RESULTS |
|
9 12 E77 residue_name_number Residues E77, K162, and D164 appear to orient the trans stabilizing loop which is involved in interface formation in contact site II. RESULTS |
|
14 18 K162 residue_name_number Residues E77, K162, and D164 appear to orient the trans stabilizing loop which is involved in interface formation in contact site II. RESULTS |
|
24 28 D164 residue_name_number Residues E77, K162, and D164 appear to orient the trans stabilizing loop which is involved in interface formation in contact site II. RESULTS |
|
50 72 trans stabilizing loop structure_element Residues E77, K162, and D164 appear to orient the trans stabilizing loop which is involved in interface formation in contact site II. RESULTS |
|
94 103 interface site Residues E77, K162, and D164 appear to orient the trans stabilizing loop which is involved in interface formation in contact site II. RESULTS |
|
117 132 contact site II site Residues E77, K162, and D164 appear to orient the trans stabilizing loop which is involved in interface formation in contact site II. RESULTS |
|
27 40 anti-parallel protein_state In the earlier model of an anti-parallel G interface, it was not possible to position the side chain of R159 to avoid steric conflict. RESULTS |
|
41 52 G interface site In the earlier model of an anti-parallel G interface, it was not possible to position the side chain of R159 to avoid steric conflict. RESULTS |
|
104 108 R159 residue_name_number In the earlier model of an anti-parallel G interface, it was not possible to position the side chain of R159 to avoid steric conflict. RESULTS |
|
15 24 structure evidence In the present structure, the side-chain of R159 projects laterally along the G interface and, therefore, does not cause a steric conflict. RESULTS |
|
44 48 R159 residue_name_number In the present structure, the side-chain of R159 projects laterally along the G interface and, therefore, does not cause a steric conflict. RESULTS |
|
78 89 G interface site In the present structure, the side-chain of R159 projects laterally along the G interface and, therefore, does not cause a steric conflict. RESULTS |
|
38 49 G interface site A conserved dimerization mode via the G interface in dynamin and septin GTPases. FIG |
|
53 60 dynamin protein_type A conserved dimerization mode via the G interface in dynamin and septin GTPases. FIG |
|
65 79 septin GTPases protein_type A conserved dimerization mode via the G interface in dynamin and septin GTPases. FIG |
|
32 40 parallel protein_state The overall architecture of the parallel GTPase domain dimer of Irga6 is related to that of other dynamin and septin superfamily proteins. FIG |
|
41 54 GTPase domain structure_element The overall architecture of the parallel GTPase domain dimer of Irga6 is related to that of other dynamin and septin superfamily proteins. FIG |
|
55 60 dimer oligomeric_state The overall architecture of the parallel GTPase domain dimer of Irga6 is related to that of other dynamin and septin superfamily proteins. FIG |
|
64 69 Irga6 protein The overall architecture of the parallel GTPase domain dimer of Irga6 is related to that of other dynamin and septin superfamily proteins. FIG |
|
98 105 dynamin protein_type The overall architecture of the parallel GTPase domain dimer of Irga6 is related to that of other dynamin and septin superfamily proteins. FIG |
|
110 116 septin protein_type The overall architecture of the parallel GTPase domain dimer of Irga6 is related to that of other dynamin and septin superfamily proteins. FIG |
|
14 24 structures evidence The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
97 111 GTPase domains structure_element The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
119 131 GMPPNP-bound protein_state The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
132 137 Irga6 protein The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
138 143 dimer oligomeric_state The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
168 177 dynamin 1 protein The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
178 192 GTPase-minimal structure_element The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
225 234 GDP-bound protein_state The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
235 245 atlastin 1 protein The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
246 251 dimer oligomeric_state The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
270 285 GDP-AlF3- bound protein_state The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
286 290 GBP1 protein The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
291 304 GTPase domain structure_element The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
305 310 dimer oligomeric_state The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
329 333 BDLP protein_type The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
334 339 dimer oligomeric_state The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
340 348 bound to protein_state The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
349 352 GDP chemical The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
374 383 GTP-bound protein_state The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
384 390 GIMAP2 protein The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
391 396 dimer oligomeric_state The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 |
|
4 18 GTPase domains structure_element The GTPase domains of the left molecules are shown in orange, helical domains or extensions in blue. FIG |
|
62 77 helical domains structure_element The GTPase domains of the left molecules are shown in orange, helical domains or extensions in blue. FIG |
|
12 16 Mg2+ chemical Nucleotide, Mg2+ (green) and AlF4 - are shown in sphere representation, the buried interface sizes per molecule are indicated on the right. FIG |
|
83 92 interface site Nucleotide, Mg2+ (green) and AlF4 - are shown in sphere representation, the buried interface sizes per molecule are indicated on the right. FIG |
|
0 5 Irga6 protein Irga6 immunity-related GTPase 6, GMPPNP 5'-guanylyl imidodiphosphate, GTP guanosine-triphosphate, BDLP bacterial dynamin like protein, GIMAP2, GTPase of immunity associated protein 2 FIG |
|
6 31 immunity-related GTPase 6 protein Irga6 immunity-related GTPase 6, GMPPNP 5'-guanylyl imidodiphosphate, GTP guanosine-triphosphate, BDLP bacterial dynamin like protein, GIMAP2, GTPase of immunity associated protein 2 FIG |
|
33 39 GMPPNP chemical Irga6 immunity-related GTPase 6, GMPPNP 5'-guanylyl imidodiphosphate, GTP guanosine-triphosphate, BDLP bacterial dynamin like protein, GIMAP2, GTPase of immunity associated protein 2 FIG |
|
40 68 5'-guanylyl imidodiphosphate chemical Irga6 immunity-related GTPase 6, GMPPNP 5'-guanylyl imidodiphosphate, GTP guanosine-triphosphate, BDLP bacterial dynamin like protein, GIMAP2, GTPase of immunity associated protein 2 FIG |
|
70 73 GTP chemical Irga6 immunity-related GTPase 6, GMPPNP 5'-guanylyl imidodiphosphate, GTP guanosine-triphosphate, BDLP bacterial dynamin like protein, GIMAP2, GTPase of immunity associated protein 2 FIG |
|
74 96 guanosine-triphosphate chemical Irga6 immunity-related GTPase 6, GMPPNP 5'-guanylyl imidodiphosphate, GTP guanosine-triphosphate, BDLP bacterial dynamin like protein, GIMAP2, GTPase of immunity associated protein 2 FIG |
|
98 102 BDLP protein_type Irga6 immunity-related GTPase 6, GMPPNP 5'-guanylyl imidodiphosphate, GTP guanosine-triphosphate, BDLP bacterial dynamin like protein, GIMAP2, GTPase of immunity associated protein 2 FIG |
|
103 112 bacterial taxonomy_domain Irga6 immunity-related GTPase 6, GMPPNP 5'-guanylyl imidodiphosphate, GTP guanosine-triphosphate, BDLP bacterial dynamin like protein, GIMAP2, GTPase of immunity associated protein 2 FIG |
|
113 133 dynamin like protein protein_type Irga6 immunity-related GTPase 6, GMPPNP 5'-guanylyl imidodiphosphate, GTP guanosine-triphosphate, BDLP bacterial dynamin like protein, GIMAP2, GTPase of immunity associated protein 2 FIG |
|
135 141 GIMAP2 protein Irga6 immunity-related GTPase 6, GMPPNP 5'-guanylyl imidodiphosphate, GTP guanosine-triphosphate, BDLP bacterial dynamin like protein, GIMAP2, GTPase of immunity associated protein 2 FIG |
|
143 182 GTPase of immunity associated protein 2 protein Irga6 immunity-related GTPase 6, GMPPNP 5'-guanylyl imidodiphosphate, GTP guanosine-triphosphate, BDLP bacterial dynamin like protein, GIMAP2, GTPase of immunity associated protein 2 FIG |
|
50 61 G interface site The buried surface area per molecule (BSA) of the G interface in Irga6 is relatively small (470 Γ
2) compared to that of other dynamin superfamily members, such as dynamin (BSA: 1400 Γ
2), atlastin (BSA: 820 Γ
2), GBP-1 (BSA: 2060 Γ
2), BDLP (BSA: 2300 Γ
2) or the septin-related GTPase of immunity associated protein 2 (GIMAP2) (BSA: 590 Γ
2) (Fig.Β 2). RESULTS |
|
65 70 Irga6 protein The buried surface area per molecule (BSA) of the G interface in Irga6 is relatively small (470 Γ
2) compared to that of other dynamin superfamily members, such as dynamin (BSA: 1400 Γ
2), atlastin (BSA: 820 Γ
2), GBP-1 (BSA: 2060 Γ
2), BDLP (BSA: 2300 Γ
2) or the septin-related GTPase of immunity associated protein 2 (GIMAP2) (BSA: 590 Γ
2) (Fig.Β 2). RESULTS |
|
126 133 dynamin protein_type The buried surface area per molecule (BSA) of the G interface in Irga6 is relatively small (470 Γ
2) compared to that of other dynamin superfamily members, such as dynamin (BSA: 1400 Γ
2), atlastin (BSA: 820 Γ
2), GBP-1 (BSA: 2060 Γ
2), BDLP (BSA: 2300 Γ
2) or the septin-related GTPase of immunity associated protein 2 (GIMAP2) (BSA: 590 Γ
2) (Fig.Β 2). RESULTS |
|
163 170 dynamin protein_type The buried surface area per molecule (BSA) of the G interface in Irga6 is relatively small (470 Γ
2) compared to that of other dynamin superfamily members, such as dynamin (BSA: 1400 Γ
2), atlastin (BSA: 820 Γ
2), GBP-1 (BSA: 2060 Γ
2), BDLP (BSA: 2300 Γ
2) or the septin-related GTPase of immunity associated protein 2 (GIMAP2) (BSA: 590 Γ
2) (Fig.Β 2). RESULTS |
|
187 195 atlastin protein_type The buried surface area per molecule (BSA) of the G interface in Irga6 is relatively small (470 Γ
2) compared to that of other dynamin superfamily members, such as dynamin (BSA: 1400 Γ
2), atlastin (BSA: 820 Γ
2), GBP-1 (BSA: 2060 Γ
2), BDLP (BSA: 2300 Γ
2) or the septin-related GTPase of immunity associated protein 2 (GIMAP2) (BSA: 590 Γ
2) (Fig.Β 2). RESULTS |
|
211 216 GBP-1 protein The buried surface area per molecule (BSA) of the G interface in Irga6 is relatively small (470 Γ
2) compared to that of other dynamin superfamily members, such as dynamin (BSA: 1400 Γ
2), atlastin (BSA: 820 Γ
2), GBP-1 (BSA: 2060 Γ
2), BDLP (BSA: 2300 Γ
2) or the septin-related GTPase of immunity associated protein 2 (GIMAP2) (BSA: 590 Γ
2) (Fig.Β 2). RESULTS |
|
233 237 BDLP protein_type The buried surface area per molecule (BSA) of the G interface in Irga6 is relatively small (470 Γ
2) compared to that of other dynamin superfamily members, such as dynamin (BSA: 1400 Γ
2), atlastin (BSA: 820 Γ
2), GBP-1 (BSA: 2060 Γ
2), BDLP (BSA: 2300 Γ
2) or the septin-related GTPase of immunity associated protein 2 (GIMAP2) (BSA: 590 Γ
2) (Fig.Β 2). RESULTS |
|
260 314 septin-related GTPase of immunity associated protein 2 protein The buried surface area per molecule (BSA) of the G interface in Irga6 is relatively small (470 Γ
2) compared to that of other dynamin superfamily members, such as dynamin (BSA: 1400 Γ
2), atlastin (BSA: 820 Γ
2), GBP-1 (BSA: 2060 Γ
2), BDLP (BSA: 2300 Γ
2) or the septin-related GTPase of immunity associated protein 2 (GIMAP2) (BSA: 590 Γ
2) (Fig.Β 2). RESULTS |
|
316 322 GIMAP2 protein The buried surface area per molecule (BSA) of the G interface in Irga6 is relatively small (470 Γ
2) compared to that of other dynamin superfamily members, such as dynamin (BSA: 1400 Γ
2), atlastin (BSA: 820 Γ
2), GBP-1 (BSA: 2060 Γ
2), BDLP (BSA: 2300 Γ
2) or the septin-related GTPase of immunity associated protein 2 (GIMAP2) (BSA: 590 Γ
2) (Fig.Β 2). RESULTS |
|
42 56 GTPase domains structure_element However, the relative orientations of the GTPase domains in these dimers are strikingly similar, and the same elements, such as switch I, switch II, the trans activating and G4 loops are involved in the parallel dimerization mode in all of these GTPase families. RESULTS |
|
66 72 dimers oligomeric_state However, the relative orientations of the GTPase domains in these dimers are strikingly similar, and the same elements, such as switch I, switch II, the trans activating and G4 loops are involved in the parallel dimerization mode in all of these GTPase families. RESULTS |
|
128 136 switch I site However, the relative orientations of the GTPase domains in these dimers are strikingly similar, and the same elements, such as switch I, switch II, the trans activating and G4 loops are involved in the parallel dimerization mode in all of these GTPase families. RESULTS |
|
138 147 switch II site However, the relative orientations of the GTPase domains in these dimers are strikingly similar, and the same elements, such as switch I, switch II, the trans activating and G4 loops are involved in the parallel dimerization mode in all of these GTPase families. RESULTS |
|
153 182 trans activating and G4 loops structure_element However, the relative orientations of the GTPase domains in these dimers are strikingly similar, and the same elements, such as switch I, switch II, the trans activating and G4 loops are involved in the parallel dimerization mode in all of these GTPase families. RESULTS |
|
203 211 parallel protein_state However, the relative orientations of the GTPase domains in these dimers are strikingly similar, and the same elements, such as switch I, switch II, the trans activating and G4 loops are involved in the parallel dimerization mode in all of these GTPase families. RESULTS |
|
246 252 GTPase protein_type However, the relative orientations of the GTPase domains in these dimers are strikingly similar, and the same elements, such as switch I, switch II, the trans activating and G4 loops are involved in the parallel dimerization mode in all of these GTPase families. RESULTS |
|
0 3 IRG protein_type IRG proteins are crucial mediators of the innate immune response in mice against a specific subset of intracellular pathogens, all of which enter the cell to form a membrane-bounded vacuole without engagement of the phagocytic machinery. DISCUSS |
|
68 72 mice taxonomy_domain IRG proteins are crucial mediators of the innate immune response in mice against a specific subset of intracellular pathogens, all of which enter the cell to form a membrane-bounded vacuole without engagement of the phagocytic machinery. DISCUSS |
|
18 25 dynamin protein_type As members of the dynamin superfamily, IRGs oligomerize at cellular membranes in response to GTP binding. DISCUSS |
|
39 43 IRGs protein_type As members of the dynamin superfamily, IRGs oligomerize at cellular membranes in response to GTP binding. DISCUSS |
|
93 96 GTP chemical As members of the dynamin superfamily, IRGs oligomerize at cellular membranes in response to GTP binding. DISCUSS |
|
44 47 GTP chemical Oligomerization and oligomerization-induced GTP hydrolysis are thought to induce membrane remodeling events ultimately leading to disruption of the PVM. DISCUSS |
|
7 42 structural and mechanistic analyses experimental_method Recent structural and mechanistic analyses have begun to unravel the molecular basis for the membrane-remodeling activity and mechano-chemical function of some members (reviewed in). DISCUSS |
|
17 24 dynamin protein_type For example, for dynamin and atlastin, it was shown that GTP binding and/or hydrolysis leads to dimerization of the GTPase domains and to the reorientation of the adjacent helical domains. DISCUSS |
|
29 37 atlastin protein_type For example, for dynamin and atlastin, it was shown that GTP binding and/or hydrolysis leads to dimerization of the GTPase domains and to the reorientation of the adjacent helical domains. DISCUSS |
|
57 60 GTP chemical For example, for dynamin and atlastin, it was shown that GTP binding and/or hydrolysis leads to dimerization of the GTPase domains and to the reorientation of the adjacent helical domains. DISCUSS |
|
116 130 GTPase domains structure_element For example, for dynamin and atlastin, it was shown that GTP binding and/or hydrolysis leads to dimerization of the GTPase domains and to the reorientation of the adjacent helical domains. DISCUSS |
|
172 187 helical domains structure_element For example, for dynamin and atlastin, it was shown that GTP binding and/or hydrolysis leads to dimerization of the GTPase domains and to the reorientation of the adjacent helical domains. DISCUSS |
|
19 26 dynamin protein_type However, for other dynamin superfamily members such as IRGs, the molecular basis for GTP hydrolysis and the exact role of the mechano-chemical function are still unclear. DISCUSS |
|
55 59 IRGs protein_type However, for other dynamin superfamily members such as IRGs, the molecular basis for GTP hydrolysis and the exact role of the mechano-chemical function are still unclear. DISCUSS |
|
85 88 GTP chemical However, for other dynamin superfamily members such as IRGs, the molecular basis for GTP hydrolysis and the exact role of the mechano-chemical function are still unclear. DISCUSS |
|
4 23 structural analysis experimental_method Our structural analysis of an oligomerization- and GTPase-defective Irga6 mutant indicates that Irga6 dimerizes via the G interface in a parallel orientation. DISCUSS |
|
30 67 oligomerization- and GTPase-defective protein_state Our structural analysis of an oligomerization- and GTPase-defective Irga6 mutant indicates that Irga6 dimerizes via the G interface in a parallel orientation. DISCUSS |
|
68 73 Irga6 protein Our structural analysis of an oligomerization- and GTPase-defective Irga6 mutant indicates that Irga6 dimerizes via the G interface in a parallel orientation. DISCUSS |
|
74 80 mutant protein_state Our structural analysis of an oligomerization- and GTPase-defective Irga6 mutant indicates that Irga6 dimerizes via the G interface in a parallel orientation. DISCUSS |
|
96 101 Irga6 protein Our structural analysis of an oligomerization- and GTPase-defective Irga6 mutant indicates that Irga6 dimerizes via the G interface in a parallel orientation. DISCUSS |
|
102 111 dimerizes oligomeric_state Our structural analysis of an oligomerization- and GTPase-defective Irga6 mutant indicates that Irga6 dimerizes via the G interface in a parallel orientation. DISCUSS |
|
120 131 G interface site Our structural analysis of an oligomerization- and GTPase-defective Irga6 mutant indicates that Irga6 dimerizes via the G interface in a parallel orientation. DISCUSS |
|
137 145 parallel protein_state Our structural analysis of an oligomerization- and GTPase-defective Irga6 mutant indicates that Irga6 dimerizes via the G interface in a parallel orientation. DISCUSS |
|
22 27 Irga6 protein Only one of the seven Irga6 molecules in the asymmetric unit formed this contact pointing to a low affinity interaction via the G interface, which is in agreement with its small size. DISCUSS |
|
128 139 G interface site Only one of the seven Irga6 molecules in the asymmetric unit formed this contact pointing to a low affinity interaction via the G interface, which is in agreement with its small size. DISCUSS |
|
7 15 crystals evidence In the crystals, dimerization via the G interface is promoted by the high protein concentrations which may mimic a situation when Irga6 oligomerizes on a membrane surface. DISCUSS |
|
38 49 G interface site In the crystals, dimerization via the G interface is promoted by the high protein concentrations which may mimic a situation when Irga6 oligomerizes on a membrane surface. DISCUSS |
|
130 135 Irga6 protein In the crystals, dimerization via the G interface is promoted by the high protein concentrations which may mimic a situation when Irga6 oligomerizes on a membrane surface. DISCUSS |
|
90 93 GTP chemical Such a low affinity interaction mode may allow reversibility of oligomerization following GTP hydrolysis. DISCUSS |
|
21 32 G interface site Similar low affinity G interface interactions were reported for dynamin and MxA. DISCUSS |
|
64 71 dynamin protein_type Similar low affinity G interface interactions were reported for dynamin and MxA. DISCUSS |
|
76 79 MxA protein Similar low affinity G interface interactions were reported for dynamin and MxA. DISCUSS |
|
75 88 anti-parallel protein_state The dimerization mode is strikingly different from the previously proposed anti-parallel model that was based on the crystal structure of the signal recognition particle GTPase, SRP54 and its homologous receptor. DISCUSS |
|
117 134 crystal structure evidence The dimerization mode is strikingly different from the previously proposed anti-parallel model that was based on the crystal structure of the signal recognition particle GTPase, SRP54 and its homologous receptor. DISCUSS |
|
142 176 signal recognition particle GTPase protein_type The dimerization mode is strikingly different from the previously proposed anti-parallel model that was based on the crystal structure of the signal recognition particle GTPase, SRP54 and its homologous receptor. DISCUSS |
|
178 183 SRP54 protein The dimerization mode is strikingly different from the previously proposed anti-parallel model that was based on the crystal structure of the signal recognition particle GTPase, SRP54 and its homologous receptor. DISCUSS |
|
13 30 G dimer interface site However, the G dimer interface is reminiscent of the GTPase domain dimers observed for several other dynamin superfamily members, such as dynamin, GBP1, atlastin, and BDLP. DISCUSS |
|
53 66 GTPase domain structure_element However, the G dimer interface is reminiscent of the GTPase domain dimers observed for several other dynamin superfamily members, such as dynamin, GBP1, atlastin, and BDLP. DISCUSS |
|
67 73 dimers oligomeric_state However, the G dimer interface is reminiscent of the GTPase domain dimers observed for several other dynamin superfamily members, such as dynamin, GBP1, atlastin, and BDLP. DISCUSS |
|
101 108 dynamin protein_type However, the G dimer interface is reminiscent of the GTPase domain dimers observed for several other dynamin superfamily members, such as dynamin, GBP1, atlastin, and BDLP. DISCUSS |
|
138 145 dynamin protein_type However, the G dimer interface is reminiscent of the GTPase domain dimers observed for several other dynamin superfamily members, such as dynamin, GBP1, atlastin, and BDLP. DISCUSS |
|
147 151 GBP1 protein However, the G dimer interface is reminiscent of the GTPase domain dimers observed for several other dynamin superfamily members, such as dynamin, GBP1, atlastin, and BDLP. DISCUSS |
|
153 161 atlastin protein_type However, the G dimer interface is reminiscent of the GTPase domain dimers observed for several other dynamin superfamily members, such as dynamin, GBP1, atlastin, and BDLP. DISCUSS |
|
167 171 BDLP protein_type However, the G dimer interface is reminiscent of the GTPase domain dimers observed for several other dynamin superfamily members, such as dynamin, GBP1, atlastin, and BDLP. DISCUSS |
|
27 33 septin protein_type It was recently shown that septin and septin-related GTPases, such as the Tocs GTPases or GTPases of immunity related proteins (GIMAPs), also employ a GTP-dependent parallel dimerization mode. DISCUSS |
|
38 60 septin-related GTPases protein_type It was recently shown that septin and septin-related GTPases, such as the Tocs GTPases or GTPases of immunity related proteins (GIMAPs), also employ a GTP-dependent parallel dimerization mode. DISCUSS |
|
74 86 Tocs GTPases protein_type It was recently shown that septin and septin-related GTPases, such as the Tocs GTPases or GTPases of immunity related proteins (GIMAPs), also employ a GTP-dependent parallel dimerization mode. DISCUSS |
|
90 126 GTPases of immunity related proteins protein_type It was recently shown that septin and septin-related GTPases, such as the Tocs GTPases or GTPases of immunity related proteins (GIMAPs), also employ a GTP-dependent parallel dimerization mode. DISCUSS |
|
128 134 GIMAPs protein_type It was recently shown that septin and septin-related GTPases, such as the Tocs GTPases or GTPases of immunity related proteins (GIMAPs), also employ a GTP-dependent parallel dimerization mode. DISCUSS |
|
151 154 GTP chemical It was recently shown that septin and septin-related GTPases, such as the Tocs GTPases or GTPases of immunity related proteins (GIMAPs), also employ a GTP-dependent parallel dimerization mode. DISCUSS |
|
165 173 parallel protein_state It was recently shown that septin and septin-related GTPases, such as the Tocs GTPases or GTPases of immunity related proteins (GIMAPs), also employ a GTP-dependent parallel dimerization mode. DISCUSS |
|
9 45 phylogenetic and structural analysis experimental_method Based on phylogenetic and structural analysis, these observations suggest that dynamin and septin superfamilies are derived from a common ancestral membrane-associated GTPase that featured a GTP-dependent parallel dimerization mode. DISCUSS |
|
79 86 dynamin protein_type Based on phylogenetic and structural analysis, these observations suggest that dynamin and septin superfamilies are derived from a common ancestral membrane-associated GTPase that featured a GTP-dependent parallel dimerization mode. DISCUSS |
|
91 97 septin protein_type Based on phylogenetic and structural analysis, these observations suggest that dynamin and septin superfamilies are derived from a common ancestral membrane-associated GTPase that featured a GTP-dependent parallel dimerization mode. DISCUSS |
|
148 174 membrane-associated GTPase protein_type Based on phylogenetic and structural analysis, these observations suggest that dynamin and septin superfamilies are derived from a common ancestral membrane-associated GTPase that featured a GTP-dependent parallel dimerization mode. DISCUSS |
|
191 194 GTP chemical Based on phylogenetic and structural analysis, these observations suggest that dynamin and septin superfamilies are derived from a common ancestral membrane-associated GTPase that featured a GTP-dependent parallel dimerization mode. DISCUSS |
|
205 213 parallel protein_state Based on phylogenetic and structural analysis, these observations suggest that dynamin and septin superfamilies are derived from a common ancestral membrane-associated GTPase that featured a GTP-dependent parallel dimerization mode. DISCUSS |
|
41 45 IRGs protein_type Importantly, our analysis indicates that IRGs are not outliers, but bona-fide representatives of the dynamin superfamily. DISCUSS |
|
101 108 dynamin protein_type Importantly, our analysis indicates that IRGs are not outliers, but bona-fide representatives of the dynamin superfamily. DISCUSS |
|
52 58 septin protein_type Whereas the overall dimerization mode is similar in septin and dynamin GTPases, family-specific differences in the G interface and the oligomerization interfaces exist. DISCUSS |
|
63 78 dynamin GTPases protein_type Whereas the overall dimerization mode is similar in septin and dynamin GTPases, family-specific differences in the G interface and the oligomerization interfaces exist. DISCUSS |
|
115 126 G interface site Whereas the overall dimerization mode is similar in septin and dynamin GTPases, family-specific differences in the G interface and the oligomerization interfaces exist. DISCUSS |
|
135 161 oligomerization interfaces site Whereas the overall dimerization mode is similar in septin and dynamin GTPases, family-specific differences in the G interface and the oligomerization interfaces exist. DISCUSS |
|
63 69 ribose chemical For example, the involvement of the 2β and 3β-OH groups of the ribose in the dimerization interface of Irga6 has not been observed for other dynamin and septin superfamily members. DISCUSS |
|
77 99 dimerization interface site For example, the involvement of the 2β and 3β-OH groups of the ribose in the dimerization interface of Irga6 has not been observed for other dynamin and septin superfamily members. DISCUSS |
|
103 108 Irga6 protein For example, the involvement of the 2β and 3β-OH groups of the ribose in the dimerization interface of Irga6 has not been observed for other dynamin and septin superfamily members. DISCUSS |
|
141 148 dynamin protein_type For example, the involvement of the 2β and 3β-OH groups of the ribose in the dimerization interface of Irga6 has not been observed for other dynamin and septin superfamily members. DISCUSS |
|
153 159 septin protein_type For example, the involvement of the 2β and 3β-OH groups of the ribose in the dimerization interface of Irga6 has not been observed for other dynamin and septin superfamily members. DISCUSS |
|
50 55 Irga6 protein The surface-exposed location of the ribose in the Irga6 structure, with a wide-open nucleotide-binding pocket, facilitates its engagement in the dimerization interface. DISCUSS |
|
56 65 structure evidence The surface-exposed location of the ribose in the Irga6 structure, with a wide-open nucleotide-binding pocket, facilitates its engagement in the dimerization interface. DISCUSS |
|
74 83 wide-open protein_state The surface-exposed location of the ribose in the Irga6 structure, with a wide-open nucleotide-binding pocket, facilitates its engagement in the dimerization interface. DISCUSS |
|
84 109 nucleotide-binding pocket site The surface-exposed location of the ribose in the Irga6 structure, with a wide-open nucleotide-binding pocket, facilitates its engagement in the dimerization interface. DISCUSS |
|
145 167 dimerization interface site The surface-exposed location of the ribose in the Irga6 structure, with a wide-open nucleotide-binding pocket, facilitates its engagement in the dimerization interface. DISCUSS |
|
43 46 GTP chemical This contact, in turn, appears to activate GTP hydrolysis by inducing rearrangements in switch I and the positioning of the catalytic E106. DISCUSS |
|
88 96 switch I site This contact, in turn, appears to activate GTP hydrolysis by inducing rearrangements in switch I and the positioning of the catalytic E106. DISCUSS |
|
124 133 catalytic protein_state This contact, in turn, appears to activate GTP hydrolysis by inducing rearrangements in switch I and the positioning of the catalytic E106. DISCUSS |
|
134 138 E106 residue_name_number This contact, in turn, appears to activate GTP hydrolysis by inducing rearrangements in switch I and the positioning of the catalytic E106. DISCUSS |
|
23 27 GBP1 protein During dimerization of GBP1, an arginine finger from the P loop reorients towards the nucleotide in cis to trigger GTP hydrolysis. DISCUSS |
|
32 47 arginine finger structure_element During dimerization of GBP1, an arginine finger from the P loop reorients towards the nucleotide in cis to trigger GTP hydrolysis. DISCUSS |
|
57 63 P loop structure_element During dimerization of GBP1, an arginine finger from the P loop reorients towards the nucleotide in cis to trigger GTP hydrolysis. DISCUSS |
|
86 96 nucleotide chemical During dimerization of GBP1, an arginine finger from the P loop reorients towards the nucleotide in cis to trigger GTP hydrolysis. DISCUSS |
|
115 118 GTP chemical During dimerization of GBP1, an arginine finger from the P loop reorients towards the nucleotide in cis to trigger GTP hydrolysis. DISCUSS |
|
3 10 dynamin protein_type In dynamin, the corresponding serine residue coordinates a sodium ion that is crucial for GTP hydrolysis. DISCUSS |
|
30 36 serine residue_name In dynamin, the corresponding serine residue coordinates a sodium ion that is crucial for GTP hydrolysis. DISCUSS |
|
59 65 sodium chemical In dynamin, the corresponding serine residue coordinates a sodium ion that is crucial for GTP hydrolysis. DISCUSS |
|
90 93 GTP chemical In dynamin, the corresponding serine residue coordinates a sodium ion that is crucial for GTP hydrolysis. DISCUSS |
|
0 5 Irga6 protein Irga6 bears Gly79 at this position, which in the dimerizing molecule A appears to approach the bridging imido group of GMPPNP via a main chain hydrogen bond. DISCUSS |
|
12 17 Gly79 residue_name_number Irga6 bears Gly79 at this position, which in the dimerizing molecule A appears to approach the bridging imido group of GMPPNP via a main chain hydrogen bond. DISCUSS |
|
49 59 dimerizing oligomeric_state Irga6 bears Gly79 at this position, which in the dimerizing molecule A appears to approach the bridging imido group of GMPPNP via a main chain hydrogen bond. DISCUSS |
|
69 70 A structure_element Irga6 bears Gly79 at this position, which in the dimerizing molecule A appears to approach the bridging imido group of GMPPNP via a main chain hydrogen bond. DISCUSS |
|
119 125 GMPPNP chemical Irga6 bears Gly79 at this position, which in the dimerizing molecule A appears to approach the bridging imido group of GMPPNP via a main chain hydrogen bond. DISCUSS |
|
143 156 hydrogen bond bond_interaction Irga6 bears Gly79 at this position, which in the dimerizing molecule A appears to approach the bridging imido group of GMPPNP via a main chain hydrogen bond. DISCUSS |
|
18 28 structures evidence Higher resolution structures of the Irga6 dimer in the presence of a transition state analogue are required to show whether Gly79 directly participates in GTP hydrolysis or whether it may also position a catalytic cation. DISCUSS |
|
36 41 Irga6 protein Higher resolution structures of the Irga6 dimer in the presence of a transition state analogue are required to show whether Gly79 directly participates in GTP hydrolysis or whether it may also position a catalytic cation. DISCUSS |
|
42 47 dimer oligomeric_state Higher resolution structures of the Irga6 dimer in the presence of a transition state analogue are required to show whether Gly79 directly participates in GTP hydrolysis or whether it may also position a catalytic cation. DISCUSS |
|
55 66 presence of protein_state Higher resolution structures of the Irga6 dimer in the presence of a transition state analogue are required to show whether Gly79 directly participates in GTP hydrolysis or whether it may also position a catalytic cation. DISCUSS |
|
124 129 Gly79 residue_name_number Higher resolution structures of the Irga6 dimer in the presence of a transition state analogue are required to show whether Gly79 directly participates in GTP hydrolysis or whether it may also position a catalytic cation. DISCUSS |
|
155 158 GTP chemical Higher resolution structures of the Irga6 dimer in the presence of a transition state analogue are required to show whether Gly79 directly participates in GTP hydrolysis or whether it may also position a catalytic cation. DISCUSS |
|
3 10 dynamin protein_type In dynamin, further assembly sites are provided by the helical domains which assemble in a criss-cross fashion to form a helical filament. DISCUSS |
|
20 34 assembly sites site In dynamin, further assembly sites are provided by the helical domains which assemble in a criss-cross fashion to form a helical filament. DISCUSS |
|
55 70 helical domains structure_element In dynamin, further assembly sites are provided by the helical domains which assemble in a criss-cross fashion to form a helical filament. DISCUSS |
|
121 137 helical filament structure_element In dynamin, further assembly sites are provided by the helical domains which assemble in a criss-cross fashion to form a helical filament. DISCUSS |
|
3 60 dynamin-related Eps15 homology domain containing proteins protein_type In dynamin-related Eps15 homology domain containing proteins (EHDs), a second assembly interface is present in the GTPase domain. DISCUSS |
|
62 66 EHDs protein_type In dynamin-related Eps15 homology domain containing proteins (EHDs), a second assembly interface is present in the GTPase domain. DISCUSS |
|
71 96 second assembly interface site In dynamin-related Eps15 homology domain containing proteins (EHDs), a second assembly interface is present in the GTPase domain. DISCUSS |
|
115 128 GTPase domain structure_element In dynamin-related Eps15 homology domain containing proteins (EHDs), a second assembly interface is present in the GTPase domain. DISCUSS |
|
4 9 Irga6 protein For Irga6, additional interfaces in the helical domain are presumably involved in oligomerization, such as the secondary patch residues whose mutation prevented oligomerization in the crystallized mutant. DISCUSS |
|
22 32 interfaces site For Irga6, additional interfaces in the helical domain are presumably involved in oligomerization, such as the secondary patch residues whose mutation prevented oligomerization in the crystallized mutant. DISCUSS |
|
40 54 helical domain structure_element For Irga6, additional interfaces in the helical domain are presumably involved in oligomerization, such as the secondary patch residues whose mutation prevented oligomerization in the crystallized mutant. DISCUSS |
|
111 126 secondary patch site For Irga6, additional interfaces in the helical domain are presumably involved in oligomerization, such as the secondary patch residues whose mutation prevented oligomerization in the crystallized mutant. DISCUSS |
|
142 150 mutation experimental_method For Irga6, additional interfaces in the helical domain are presumably involved in oligomerization, such as the secondary patch residues whose mutation prevented oligomerization in the crystallized mutant. DISCUSS |
|
184 196 crystallized evidence For Irga6, additional interfaces in the helical domain are presumably involved in oligomerization, such as the secondary patch residues whose mutation prevented oligomerization in the crystallized mutant. DISCUSS |
|
197 203 mutant protein_state For Irga6, additional interfaces in the helical domain are presumably involved in oligomerization, such as the secondary patch residues whose mutation prevented oligomerization in the crystallized mutant. DISCUSS |
|
8 26 structural studies experimental_method Further structural studies, especially electron microscopy analysis of the Irga6 oligomers, are required to clarify the assembly mode via the helical domains and to show how these interfaces cooperate with the G interface to mediate the regulated assembly on a membrane surface. DISCUSS |
|
39 67 electron microscopy analysis experimental_method Further structural studies, especially electron microscopy analysis of the Irga6 oligomers, are required to clarify the assembly mode via the helical domains and to show how these interfaces cooperate with the G interface to mediate the regulated assembly on a membrane surface. DISCUSS |
|
75 80 Irga6 protein Further structural studies, especially electron microscopy analysis of the Irga6 oligomers, are required to clarify the assembly mode via the helical domains and to show how these interfaces cooperate with the G interface to mediate the regulated assembly on a membrane surface. DISCUSS |
|
81 90 oligomers oligomeric_state Further structural studies, especially electron microscopy analysis of the Irga6 oligomers, are required to clarify the assembly mode via the helical domains and to show how these interfaces cooperate with the G interface to mediate the regulated assembly on a membrane surface. DISCUSS |
|
142 157 helical domains structure_element Further structural studies, especially electron microscopy analysis of the Irga6 oligomers, are required to clarify the assembly mode via the helical domains and to show how these interfaces cooperate with the G interface to mediate the regulated assembly on a membrane surface. DISCUSS |
|
180 190 interfaces site Further structural studies, especially electron microscopy analysis of the Irga6 oligomers, are required to clarify the assembly mode via the helical domains and to show how these interfaces cooperate with the G interface to mediate the regulated assembly on a membrane surface. DISCUSS |
|
210 221 G interface site Further structural studies, especially electron microscopy analysis of the Irga6 oligomers, are required to clarify the assembly mode via the helical domains and to show how these interfaces cooperate with the G interface to mediate the regulated assembly on a membrane surface. DISCUSS |
|
56 70 helical domain structure_element Notably, we did not observe major rearrangements of the helical domain versus the GTPase domain in the Irga6 molecules that dimerized via the G interface. DISCUSS |
|
82 95 GTPase domain structure_element Notably, we did not observe major rearrangements of the helical domain versus the GTPase domain in the Irga6 molecules that dimerized via the G interface. DISCUSS |
|
103 108 Irga6 protein Notably, we did not observe major rearrangements of the helical domain versus the GTPase domain in the Irga6 molecules that dimerized via the G interface. DISCUSS |
|
124 133 dimerized protein_state Notably, we did not observe major rearrangements of the helical domain versus the GTPase domain in the Irga6 molecules that dimerized via the G interface. DISCUSS |
|
142 153 G interface site Notably, we did not observe major rearrangements of the helical domain versus the GTPase domain in the Irga6 molecules that dimerized via the G interface. DISCUSS |
|
23 27 BDLP protein_type In a manner similar to BDLP, such large-scale conformational changes may be induced by membrane binding. DISCUSS |
|
4 23 structural analysis experimental_method Our structural analysis and the identification of the G-interface paves the way for determining the specific assembly of Irga6 into a membrane-associated scaffold as the prerequisite to understand its action as an anti-parasitic machine. DISCUSS |
|
54 65 G-interface site Our structural analysis and the identification of the G-interface paves the way for determining the specific assembly of Irga6 into a membrane-associated scaffold as the prerequisite to understand its action as an anti-parasitic machine. DISCUSS |
|
121 126 Irga6 protein Our structural analysis and the identification of the G-interface paves the way for determining the specific assembly of Irga6 into a membrane-associated scaffold as the prerequisite to understand its action as an anti-parasitic machine. DISCUSS |
|
25 28 Irg protein_type Our study indicates that Irg proteins dimerize via the G interface in a parallel head-to-head fashion thereby facilitating GTPase activation. CONCL |
|
38 46 dimerize oligomeric_state Our study indicates that Irg proteins dimerize via the G interface in a parallel head-to-head fashion thereby facilitating GTPase activation. CONCL |
|
55 66 G interface site Our study indicates that Irg proteins dimerize via the G interface in a parallel head-to-head fashion thereby facilitating GTPase activation. CONCL |
|
72 93 parallel head-to-head protein_state Our study indicates that Irg proteins dimerize via the G interface in a parallel head-to-head fashion thereby facilitating GTPase activation. CONCL |
|
123 129 GTPase protein_type Our study indicates that Irg proteins dimerize via the G interface in a parallel head-to-head fashion thereby facilitating GTPase activation. CONCL |
|
91 94 Irg protein_type These findings contribute to a molecular understanding of the anti-parasitic action of the Irg protein family and suggest that Irgs are bona-fide members of the dynamin superfamily. CONCL |
|
127 131 Irgs protein_type These findings contribute to a molecular understanding of the anti-parasitic action of the Irg protein family and suggest that Irgs are bona-fide members of the dynamin superfamily. CONCL |
|
161 168 dynamin protein_type These findings contribute to a molecular understanding of the anti-parasitic action of the Irg protein family and suggest that Irgs are bona-fide members of the dynamin superfamily. CONCL |
|
|
