| anno_start anno_end anno_text entity_type sentence section | |
| 75 92 Thg1-like protein protein_type Template-dependent nucleotide addition in the reverse (3′-5′) direction by Thg1-like protein TITLE | |
| 0 10 Structures evidence Structures of Thg1-like proteins provide insight into the template-dependent nucleotide addition in the reverse (3′-5′) direction. ABSTRACT | |
| 14 32 Thg1-like proteins protein_type Structures of Thg1-like proteins provide insight into the template-dependent nucleotide addition in the reverse (3′-5′) direction. ABSTRACT | |
| 0 17 Thg1-like protein protein_type Thg1-like protein (TLP) catalyzes the addition of a nucleotide to the 5′-end of truncated transfer RNA (tRNA) species in a Watson-Crick template–dependent manner. ABSTRACT | |
| 19 22 TLP protein_type Thg1-like protein (TLP) catalyzes the addition of a nucleotide to the 5′-end of truncated transfer RNA (tRNA) species in a Watson-Crick template–dependent manner. ABSTRACT | |
| 90 102 transfer RNA chemical Thg1-like protein (TLP) catalyzes the addition of a nucleotide to the 5′-end of truncated transfer RNA (tRNA) species in a Watson-Crick template–dependent manner. ABSTRACT | |
| 104 108 tRNA chemical Thg1-like protein (TLP) catalyzes the addition of a nucleotide to the 5′-end of truncated transfer RNA (tRNA) species in a Watson-Crick template–dependent manner. ABSTRACT | |
| 68 93 adenosine 5′-triphosphate chemical The reaction proceeds in two steps: the activation of the 5′-end by adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleotide addition. ABSTRACT | |
| 95 98 ATP chemical The reaction proceeds in two steps: the activation of the 5′-end by adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleotide addition. ABSTRACT | |
| 100 125 guanosine 5′-triphosphate chemical The reaction proceeds in two steps: the activation of the 5′-end by adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleotide addition. ABSTRACT | |
| 127 130 GTP chemical The reaction proceeds in two steps: the activation of the 5′-end by adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleotide addition. ABSTRACT | |
| 0 19 Structural analyses experimental_method Structural analyses of the TLP and its reaction intermediates have revealed the atomic detail of the template-dependent elongation reaction in the 3′-5′ direction. ABSTRACT | |
| 27 30 TLP protein_type Structural analyses of the TLP and its reaction intermediates have revealed the atomic detail of the template-dependent elongation reaction in the 3′-5′ direction. ABSTRACT | |
| 23 46 substrate binding sites site The enzyme creates two substrate binding sites for the first- and second-step reactions in the vicinity of one reaction center consisting of two Mg2+ ions, and the two reactions are executed at the same reaction center in a stepwise fashion. ABSTRACT | |
| 111 126 reaction center site The enzyme creates two substrate binding sites for the first- and second-step reactions in the vicinity of one reaction center consisting of two Mg2+ ions, and the two reactions are executed at the same reaction center in a stepwise fashion. ABSTRACT | |
| 145 149 Mg2+ chemical The enzyme creates two substrate binding sites for the first- and second-step reactions in the vicinity of one reaction center consisting of two Mg2+ ions, and the two reactions are executed at the same reaction center in a stepwise fashion. ABSTRACT | |
| 203 218 reaction center site The enzyme creates two substrate binding sites for the first- and second-step reactions in the vicinity of one reaction center consisting of two Mg2+ ions, and the two reactions are executed at the same reaction center in a stepwise fashion. ABSTRACT | |
| 18 28 nucleotide chemical When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3′-OH of the incoming nucleotide and the 5′-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred. ABSTRACT | |
| 32 40 bound to protein_state When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3′-OH of the incoming nucleotide and the 5′-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred. ABSTRACT | |
| 45 64 second binding site site When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3′-OH of the incoming nucleotide and the 5′-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred. ABSTRACT | |
| 70 97 Watson-Crick hydrogen bonds bond_interaction When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3′-OH of the incoming nucleotide and the 5′-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred. ABSTRACT | |
| 144 159 5′-triphosphate chemical When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3′-OH of the incoming nucleotide and the 5′-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred. ABSTRACT | |
| 167 171 tRNA chemical When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3′-OH of the incoming nucleotide and the 5′-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred. ABSTRACT | |
| 189 204 reaction center site When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3′-OH of the incoming nucleotide and the 5′-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred. ABSTRACT | |
| 9 32 3′-5′ elongation enzyme protein_type That the 3′-5′ elongation enzyme performs this elaborate two-step reaction in one catalytic center suggests that these two reactions have been inseparable throughout the process of protein evolution. ABSTRACT | |
| 82 98 catalytic center site That the 3′-5′ elongation enzyme performs this elaborate two-step reaction in one catalytic center suggests that these two reactions have been inseparable throughout the process of protein evolution. ABSTRACT | |
| 9 12 TLP protein_type Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNAHis-specific G−1 addition enzyme. ABSTRACT | |
| 17 21 Thg1 protein Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNAHis-specific G−1 addition enzyme. ABSTRACT | |
| 35 45 tetrameric oligomeric_state Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNAHis-specific G−1 addition enzyme. ABSTRACT | |
| 64 68 tRNA chemical Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNAHis-specific G−1 addition enzyme. ABSTRACT | |
| 85 88 TLP protein_type Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNAHis-specific G−1 addition enzyme. ABSTRACT | |
| 115 119 Thg1 protein Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNAHis-specific G−1 addition enzyme. ABSTRACT | |
| 123 159 tRNAHis-specific G−1 addition enzyme protein_type Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNAHis-specific G−1 addition enzyme. ABSTRACT | |
| 5 12 tRNAHis chemical Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin. ABSTRACT | |
| 40 44 Thg1 protein Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin. ABSTRACT | |
| 45 53 tetramer oligomeric_state Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin. ABSTRACT | |
| 54 62 subunits structure_element Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin. ABSTRACT | |
| 75 78 TLP protein_type Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin. ABSTRACT | |
| 80 84 tRNA chemical Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin. ABSTRACT | |
| 101 116 dimer interface site Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin. ABSTRACT | |
| 176 189 accepter stem structure_element Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin. ABSTRACT | |
| 209 217 flexible protein_state Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin. ABSTRACT | |
| 218 227 β-hairpin structure_element Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin. ABSTRACT | |
| 13 32 mutational analyses experimental_method Furthermore, mutational analyses show that tRNAHis is bound to TLP in a similar manner as Thg1, thus indicating that TLP has a dual binding mode. ABSTRACT | |
| 43 50 tRNAHis chemical Furthermore, mutational analyses show that tRNAHis is bound to TLP in a similar manner as Thg1, thus indicating that TLP has a dual binding mode. ABSTRACT | |
| 54 62 bound to protein_state Furthermore, mutational analyses show that tRNAHis is bound to TLP in a similar manner as Thg1, thus indicating that TLP has a dual binding mode. ABSTRACT | |
| 63 66 TLP protein_type Furthermore, mutational analyses show that tRNAHis is bound to TLP in a similar manner as Thg1, thus indicating that TLP has a dual binding mode. ABSTRACT | |
| 90 94 Thg1 protein Furthermore, mutational analyses show that tRNAHis is bound to TLP in a similar manner as Thg1, thus indicating that TLP has a dual binding mode. ABSTRACT | |
| 117 120 TLP protein_type Furthermore, mutational analyses show that tRNAHis is bound to TLP in a similar manner as Thg1, thus indicating that TLP has a dual binding mode. ABSTRACT | |
| 60 63 DNA chemical All polynucleotide chain elongation reactions, whether with DNA or RNA, proceed in the 5′-3′ direction. INTRO | |
| 67 70 RNA chemical All polynucleotide chain elongation reactions, whether with DNA or RNA, proceed in the 5′-3′ direction. INTRO | |
| 118 127 phosphate chemical This reaction involves the nucleophilic attack of a 3′-OH of the terminal nucleotide in the elongating chain on the α-phosphate of an incoming nucleotide. INTRO | |
| 28 31 DNA chemical This elongation reaction of DNA/RNA chains is in clear contrast to the elongation of protein chains in which the high energy of the incoming aminoacyl-tRNA is not used for its own addition but for the addition of the next monomer (termed head polymerization). INTRO | |
| 32 35 RNA chemical This elongation reaction of DNA/RNA chains is in clear contrast to the elongation of protein chains in which the high energy of the incoming aminoacyl-tRNA is not used for its own addition but for the addition of the next monomer (termed head polymerization). INTRO | |
| 141 155 aminoacyl-tRNA chemical This elongation reaction of DNA/RNA chains is in clear contrast to the elongation of protein chains in which the high energy of the incoming aminoacyl-tRNA is not used for its own addition but for the addition of the next monomer (termed head polymerization). INTRO | |
| 222 229 monomer oligomeric_state This elongation reaction of DNA/RNA chains is in clear contrast to the elongation of protein chains in which the high energy of the incoming aminoacyl-tRNA is not used for its own addition but for the addition of the next monomer (termed head polymerization). INTRO | |
| 44 48 Thg1 protein However, recent studies have shown that the Thg1/Thg1-like protein (TLP) family of proteins extends tRNA nucleotide chains in the reverse (3′-5′) direction. INTRO | |
| 49 66 Thg1-like protein protein_type However, recent studies have shown that the Thg1/Thg1-like protein (TLP) family of proteins extends tRNA nucleotide chains in the reverse (3′-5′) direction. INTRO | |
| 68 71 TLP protein_type However, recent studies have shown that the Thg1/Thg1-like protein (TLP) family of proteins extends tRNA nucleotide chains in the reverse (3′-5′) direction. INTRO | |
| 100 104 tRNA chemical However, recent studies have shown that the Thg1/Thg1-like protein (TLP) family of proteins extends tRNA nucleotide chains in the reverse (3′-5′) direction. INTRO | |
| 28 32 tRNA chemical In this case, the 5′-end of tRNA is first activated using adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleophilic attack of a 3′-OH on the incoming nucleotide [nucleoside 5′-triphosphate (NTP)] to yield pppN-tRNA. INTRO | |
| 58 83 adenosine 5′-triphosphate chemical In this case, the 5′-end of tRNA is first activated using adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleophilic attack of a 3′-OH on the incoming nucleotide [nucleoside 5′-triphosphate (NTP)] to yield pppN-tRNA. INTRO | |
| 85 88 ATP chemical In this case, the 5′-end of tRNA is first activated using adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleophilic attack of a 3′-OH on the incoming nucleotide [nucleoside 5′-triphosphate (NTP)] to yield pppN-tRNA. INTRO | |
| 90 115 guanosine 5′-triphosphate chemical In this case, the 5′-end of tRNA is first activated using adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleophilic attack of a 3′-OH on the incoming nucleotide [nucleoside 5′-triphosphate (NTP)] to yield pppN-tRNA. INTRO | |
| 117 120 GTP chemical In this case, the 5′-end of tRNA is first activated using adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleophilic attack of a 3′-OH on the incoming nucleotide [nucleoside 5′-triphosphate (NTP)] to yield pppN-tRNA. INTRO | |
| 194 220 nucleoside 5′-triphosphate chemical In this case, the 5′-end of tRNA is first activated using adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleophilic attack of a 3′-OH on the incoming nucleotide [nucleoside 5′-triphosphate (NTP)] to yield pppN-tRNA. INTRO | |
| 222 225 NTP chemical In this case, the 5′-end of tRNA is first activated using adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleophilic attack of a 3′-OH on the incoming nucleotide [nucleoside 5′-triphosphate (NTP)] to yield pppN-tRNA. INTRO | |
| 237 246 pppN-tRNA chemical In this case, the 5′-end of tRNA is first activated using adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleophilic attack of a 3′-OH on the incoming nucleotide [nucleoside 5′-triphosphate (NTP)] to yield pppN-tRNA. INTRO | |
| 24 36 triphosphate chemical Thus, the energy in the triphosphate bond of the incoming nucleotide is not used for its own addition but is reserved for subsequent polymerization (that is, head polymerization) (Fig. 1). INTRO | |
| 44 48 Thg1 protein Top: Reaction scheme of 3′-5′ elongation by Thg1/TLP family proteins. FIG | |
| 49 52 TLP protein_type Top: Reaction scheme of 3′-5′ elongation by Thg1/TLP family proteins. FIG | |
| 47 66 DNA/RNA polymerases protein_type Bottom: Reaction scheme of 5′-3′ elongation by DNA/RNA polymerases. FIG | |
| 23 27 Thg1 protein In 3′-5′ elongation by Thg1/TLP family proteins, the 5′-monophosphate of the tRNA is first activated by ATP/GTP, followed by the actual elongation reaction. FIG | |
| 28 31 TLP protein_type In 3′-5′ elongation by Thg1/TLP family proteins, the 5′-monophosphate of the tRNA is first activated by ATP/GTP, followed by the actual elongation reaction. FIG | |
| 53 69 5′-monophosphate chemical In 3′-5′ elongation by Thg1/TLP family proteins, the 5′-monophosphate of the tRNA is first activated by ATP/GTP, followed by the actual elongation reaction. FIG | |
| 77 81 tRNA chemical In 3′-5′ elongation by Thg1/TLP family proteins, the 5′-monophosphate of the tRNA is first activated by ATP/GTP, followed by the actual elongation reaction. FIG | |
| 104 107 ATP chemical In 3′-5′ elongation by Thg1/TLP family proteins, the 5′-monophosphate of the tRNA is first activated by ATP/GTP, followed by the actual elongation reaction. FIG | |
| 108 111 GTP chemical In 3′-5′ elongation by Thg1/TLP family proteins, the 5′-monophosphate of the tRNA is first activated by ATP/GTP, followed by the actual elongation reaction. FIG | |
| 23 42 DNA/RNA polymerases protein_type In 5′-3′ elongation by DNA/RNA polymerases, the energy of the incoming nucleotide is used for its own addition (tail polymerization). FIG | |
| 60 70 eukaryotic taxonomy_domain The best-characterized member of this family of proteins is eukaryotic Thg1 (tRNAHis guanylyltransferase), which catalyzes the nontemplated addition of a guanylate to the 5′-end of immature tRNAHis. INTRO | |
| 71 75 Thg1 protein The best-characterized member of this family of proteins is eukaryotic Thg1 (tRNAHis guanylyltransferase), which catalyzes the nontemplated addition of a guanylate to the 5′-end of immature tRNAHis. INTRO | |
| 77 104 tRNAHis guanylyltransferase protein_type The best-characterized member of this family of proteins is eukaryotic Thg1 (tRNAHis guanylyltransferase), which catalyzes the nontemplated addition of a guanylate to the 5′-end of immature tRNAHis. INTRO | |
| 190 197 tRNAHis chemical The best-characterized member of this family of proteins is eukaryotic Thg1 (tRNAHis guanylyltransferase), which catalyzes the nontemplated addition of a guanylate to the 5′-end of immature tRNAHis. INTRO | |
| 5 14 guanosine chemical This guanosine at position −1 (G−1) of tRNAHis is a critical identity element for recognition by the histidyl-tRNA synthase. INTRO | |
| 27 29 −1 residue_number This guanosine at position −1 (G−1) of tRNAHis is a critical identity element for recognition by the histidyl-tRNA synthase. INTRO | |
| 31 34 G−1 residue_name_number This guanosine at position −1 (G−1) of tRNAHis is a critical identity element for recognition by the histidyl-tRNA synthase. INTRO | |
| 39 46 tRNAHis chemical This guanosine at position −1 (G−1) of tRNAHis is a critical identity element for recognition by the histidyl-tRNA synthase. INTRO | |
| 101 123 histidyl-tRNA synthase protein_type This guanosine at position −1 (G−1) of tRNAHis is a critical identity element for recognition by the histidyl-tRNA synthase. INTRO | |
| 11 15 Thg1 protein Therefore, Thg1 is essential to the fidelity of protein synthesis in eukaryotes. INTRO | |
| 69 79 eukaryotes taxonomy_domain Therefore, Thg1 is essential to the fidelity of protein synthesis in eukaryotes. INTRO | |
| 9 13 Thg1 protein However, Thg1 homologs or TLPs are found in organisms in which G−1 is genetically encoded, and thus, posttranscriptional modification is not required. INTRO | |
| 26 30 TLPs protein_type However, Thg1 homologs or TLPs are found in organisms in which G−1 is genetically encoded, and thus, posttranscriptional modification is not required. INTRO | |
| 63 66 G−1 residue_name_number However, Thg1 homologs or TLPs are found in organisms in which G−1 is genetically encoded, and thus, posttranscriptional modification is not required. INTRO | |
| 27 31 TLPs protein_type This finding suggests that TLPs may have potential functions other than tRNAHis maturation. INTRO | |
| 72 79 tRNAHis chemical This finding suggests that TLPs may have potential functions other than tRNAHis maturation. INTRO | |
| 0 4 TLPs protein_type TLPs have been shown to catalyze 5′-end nucleotide addition to truncated tRNA species in vitro in a Watson-Crick template–dependent manner. INTRO | |
| 73 77 tRNA chemical TLPs have been shown to catalyze 5′-end nucleotide addition to truncated tRNA species in vitro in a Watson-Crick template–dependent manner. INTRO | |
| 17 21 TLPs protein_type This function of TLPs is not limited to tRNAHis but occurs efficiently with other tRNAs. INTRO | |
| 40 47 tRNAHis chemical This function of TLPs is not limited to tRNAHis but occurs efficiently with other tRNAs. INTRO | |
| 82 87 tRNAs chemical This function of TLPs is not limited to tRNAHis but occurs efficiently with other tRNAs. INTRO | |
| 17 22 yeast taxonomy_domain Furthermore, the yeast homolog (Thg1p) has been shown to interact with the replication origin recognition complex for DNA replication, and the plant homolog (ICA1) was identified as a protein affecting the capacity to repair DNA damage. INTRO | |
| 32 37 Thg1p protein Furthermore, the yeast homolog (Thg1p) has been shown to interact with the replication origin recognition complex for DNA replication, and the plant homolog (ICA1) was identified as a protein affecting the capacity to repair DNA damage. INTRO | |
| 118 121 DNA chemical Furthermore, the yeast homolog (Thg1p) has been shown to interact with the replication origin recognition complex for DNA replication, and the plant homolog (ICA1) was identified as a protein affecting the capacity to repair DNA damage. INTRO | |
| 143 148 plant taxonomy_domain Furthermore, the yeast homolog (Thg1p) has been shown to interact with the replication origin recognition complex for DNA replication, and the plant homolog (ICA1) was identified as a protein affecting the capacity to repair DNA damage. INTRO | |
| 158 162 ICA1 protein Furthermore, the yeast homolog (Thg1p) has been shown to interact with the replication origin recognition complex for DNA replication, and the plant homolog (ICA1) was identified as a protein affecting the capacity to repair DNA damage. INTRO | |
| 225 228 DNA chemical Furthermore, the yeast homolog (Thg1p) has been shown to interact with the replication origin recognition complex for DNA replication, and the plant homolog (ICA1) was identified as a protein affecting the capacity to repair DNA damage. INTRO | |
| 32 36 TLPs protein_type These observations suggest that TLPs may have more general functions in DNA/RNA repair. INTRO | |
| 72 75 DNA chemical These observations suggest that TLPs may have more general functions in DNA/RNA repair. INTRO | |
| 76 79 RNA chemical These observations suggest that TLPs may have more general functions in DNA/RNA repair. INTRO | |
| 41 45 Thg1 protein The 3′-5′ addition reaction catalyzed by Thg1 occurs through three reaction steps. INTRO | |
| 45 52 tRNAHis chemical In the first step, the 5′-monophosphorylated tRNAHis, which is cleaved by ribonuclease P from pre-tRNAHis, is activated by ATP, creating a 5′-adenylylated tRNAHis intermediate. INTRO | |
| 74 88 ribonuclease P protein_type In the first step, the 5′-monophosphorylated tRNAHis, which is cleaved by ribonuclease P from pre-tRNAHis, is activated by ATP, creating a 5′-adenylylated tRNAHis intermediate. INTRO | |
| 94 105 pre-tRNAHis chemical In the first step, the 5′-monophosphorylated tRNAHis, which is cleaved by ribonuclease P from pre-tRNAHis, is activated by ATP, creating a 5′-adenylylated tRNAHis intermediate. INTRO | |
| 123 126 ATP chemical In the first step, the 5′-monophosphorylated tRNAHis, which is cleaved by ribonuclease P from pre-tRNAHis, is activated by ATP, creating a 5′-adenylylated tRNAHis intermediate. INTRO | |
| 155 162 tRNAHis chemical In the first step, the 5′-monophosphorylated tRNAHis, which is cleaved by ribonuclease P from pre-tRNAHis, is activated by ATP, creating a 5′-adenylylated tRNAHis intermediate. INTRO | |
| 46 49 GTP chemical In the second step, the 3′-OH of the incoming GTP attacks the activated intermediate, yielding pppG−1-tRNAHis. INTRO | |
| 95 109 pppG−1-tRNAHis chemical In the second step, the 3′-OH of the incoming GTP attacks the activated intermediate, yielding pppG−1-tRNAHis. INTRO | |
| 13 26 pyrophosphate chemical Finally, the pyrophosphate is removed, and mature pG−1-tRNAHis is created. INTRO | |
| 50 62 pG−1-tRNAHis chemical Finally, the pyrophosphate is removed, and mature pG−1-tRNAHis is created. INTRO | |
| 4 21 crystal structure evidence The crystal structure of human Thg1 (HsThg1) shows that its catalytic core shares structural homology with canonical 5′-3′ nucleotide polymerases, such as T7 DNA/RNA polymerases. INTRO | |
| 25 30 human species The crystal structure of human Thg1 (HsThg1) shows that its catalytic core shares structural homology with canonical 5′-3′ nucleotide polymerases, such as T7 DNA/RNA polymerases. INTRO | |
| 31 35 Thg1 protein The crystal structure of human Thg1 (HsThg1) shows that its catalytic core shares structural homology with canonical 5′-3′ nucleotide polymerases, such as T7 DNA/RNA polymerases. INTRO | |
| 37 43 HsThg1 protein The crystal structure of human Thg1 (HsThg1) shows that its catalytic core shares structural homology with canonical 5′-3′ nucleotide polymerases, such as T7 DNA/RNA polymerases. INTRO | |
| 60 74 catalytic core site The crystal structure of human Thg1 (HsThg1) shows that its catalytic core shares structural homology with canonical 5′-3′ nucleotide polymerases, such as T7 DNA/RNA polymerases. INTRO | |
| 117 145 5′-3′ nucleotide polymerases protein_type The crystal structure of human Thg1 (HsThg1) shows that its catalytic core shares structural homology with canonical 5′-3′ nucleotide polymerases, such as T7 DNA/RNA polymerases. INTRO | |
| 155 177 T7 DNA/RNA polymerases protein_type The crystal structure of human Thg1 (HsThg1) shows that its catalytic core shares structural homology with canonical 5′-3′ nucleotide polymerases, such as T7 DNA/RNA polymerases. INTRO | |
| 27 51 3′-5′ elongation enzymes protein_type This finding suggests that 3′-5′ elongation enzymes are related to 5′-3′ polymerases and raises important questions on why 5′-3′ polymerases predominate in nature. INTRO | |
| 67 84 5′-3′ polymerases protein_type This finding suggests that 3′-5′ elongation enzymes are related to 5′-3′ polymerases and raises important questions on why 5′-3′ polymerases predominate in nature. INTRO | |
| 123 140 5′-3′ polymerases protein_type This finding suggests that 3′-5′ elongation enzymes are related to 5′-3′ polymerases and raises important questions on why 5′-3′ polymerases predominate in nature. INTRO | |
| 4 21 crystal structure evidence The crystal structure of TLP from Bacillus thuringiensis shows that it shares a similar tetrameric assembly and active-site architecture with HsThg1. INTRO | |
| 25 28 TLP protein_type The crystal structure of TLP from Bacillus thuringiensis shows that it shares a similar tetrameric assembly and active-site architecture with HsThg1. INTRO | |
| 34 56 Bacillus thuringiensis species The crystal structure of TLP from Bacillus thuringiensis shows that it shares a similar tetrameric assembly and active-site architecture with HsThg1. INTRO | |
| 88 98 tetrameric oligomeric_state The crystal structure of TLP from Bacillus thuringiensis shows that it shares a similar tetrameric assembly and active-site architecture with HsThg1. INTRO | |
| 112 123 active-site site The crystal structure of TLP from Bacillus thuringiensis shows that it shares a similar tetrameric assembly and active-site architecture with HsThg1. INTRO | |
| 142 148 HsThg1 protein The crystal structure of TLP from Bacillus thuringiensis shows that it shares a similar tetrameric assembly and active-site architecture with HsThg1. INTRO | |
| 17 26 structure evidence Furthermore, the structure of Candida albicans Thg1 (CaThg1) complexed with tRNAHis reveals that the tRNA substrate accesses the reaction center from a direction opposite to that of canonical DNA/RNA polymerase. INTRO | |
| 30 46 Candida albicans species Furthermore, the structure of Candida albicans Thg1 (CaThg1) complexed with tRNAHis reveals that the tRNA substrate accesses the reaction center from a direction opposite to that of canonical DNA/RNA polymerase. INTRO | |
| 47 51 Thg1 protein Furthermore, the structure of Candida albicans Thg1 (CaThg1) complexed with tRNAHis reveals that the tRNA substrate accesses the reaction center from a direction opposite to that of canonical DNA/RNA polymerase. INTRO | |
| 53 59 CaThg1 protein Furthermore, the structure of Candida albicans Thg1 (CaThg1) complexed with tRNAHis reveals that the tRNA substrate accesses the reaction center from a direction opposite to that of canonical DNA/RNA polymerase. INTRO | |
| 61 75 complexed with protein_state Furthermore, the structure of Candida albicans Thg1 (CaThg1) complexed with tRNAHis reveals that the tRNA substrate accesses the reaction center from a direction opposite to that of canonical DNA/RNA polymerase. INTRO | |
| 76 83 tRNAHis chemical Furthermore, the structure of Candida albicans Thg1 (CaThg1) complexed with tRNAHis reveals that the tRNA substrate accesses the reaction center from a direction opposite to that of canonical DNA/RNA polymerase. INTRO | |
| 101 105 tRNA chemical Furthermore, the structure of Candida albicans Thg1 (CaThg1) complexed with tRNAHis reveals that the tRNA substrate accesses the reaction center from a direction opposite to that of canonical DNA/RNA polymerase. INTRO | |
| 129 144 reaction center site Furthermore, the structure of Candida albicans Thg1 (CaThg1) complexed with tRNAHis reveals that the tRNA substrate accesses the reaction center from a direction opposite to that of canonical DNA/RNA polymerase. INTRO | |
| 192 210 DNA/RNA polymerase protein_type Furthermore, the structure of Candida albicans Thg1 (CaThg1) complexed with tRNAHis reveals that the tRNA substrate accesses the reaction center from a direction opposite to that of canonical DNA/RNA polymerase. INTRO | |
| 17 36 structural analysis experimental_method However, in this structural analysis, the 5′-end of tRNAHis was not activated and the second substrate (GTP) was not bound. INTRO | |
| 52 59 tRNAHis chemical However, in this structural analysis, the 5′-end of tRNAHis was not activated and the second substrate (GTP) was not bound. INTRO | |
| 104 107 GTP chemical However, in this structural analysis, the 5′-end of tRNAHis was not activated and the second substrate (GTP) was not bound. INTRO | |
| 113 122 not bound protein_state However, in this structural analysis, the 5′-end of tRNAHis was not activated and the second substrate (GTP) was not bound. INTRO | |
| 22 28 solved experimental_method Here, we successfully solved the structure of TLP from the methanogenic archaeon Methanosarcina acetivorans (MaTLP) in complex with ppptRNAPheΔ1, which mimics the activated intermediate of the repair substrate. INTRO | |
| 33 42 structure evidence Here, we successfully solved the structure of TLP from the methanogenic archaeon Methanosarcina acetivorans (MaTLP) in complex with ppptRNAPheΔ1, which mimics the activated intermediate of the repair substrate. INTRO | |
| 46 49 TLP protein_type Here, we successfully solved the structure of TLP from the methanogenic archaeon Methanosarcina acetivorans (MaTLP) in complex with ppptRNAPheΔ1, which mimics the activated intermediate of the repair substrate. INTRO | |
| 59 80 methanogenic archaeon taxonomy_domain Here, we successfully solved the structure of TLP from the methanogenic archaeon Methanosarcina acetivorans (MaTLP) in complex with ppptRNAPheΔ1, which mimics the activated intermediate of the repair substrate. INTRO | |
| 81 107 Methanosarcina acetivorans species Here, we successfully solved the structure of TLP from the methanogenic archaeon Methanosarcina acetivorans (MaTLP) in complex with ppptRNAPheΔ1, which mimics the activated intermediate of the repair substrate. INTRO | |
| 109 114 MaTLP protein Here, we successfully solved the structure of TLP from the methanogenic archaeon Methanosarcina acetivorans (MaTLP) in complex with ppptRNAPheΔ1, which mimics the activated intermediate of the repair substrate. INTRO | |
| 116 131 in complex with protein_state Here, we successfully solved the structure of TLP from the methanogenic archaeon Methanosarcina acetivorans (MaTLP) in complex with ppptRNAPheΔ1, which mimics the activated intermediate of the repair substrate. INTRO | |
| 132 144 ppptRNAPheΔ1 chemical Here, we successfully solved the structure of TLP from the methanogenic archaeon Methanosarcina acetivorans (MaTLP) in complex with ppptRNAPheΔ1, which mimics the activated intermediate of the repair substrate. INTRO | |
| 9 12 TLP protein_type Although TLP and Thg1 have similar tetrameric organization, the mode of tRNA binding is different in TLP. INTRO | |
| 17 21 Thg1 protein Although TLP and Thg1 have similar tetrameric organization, the mode of tRNA binding is different in TLP. INTRO | |
| 35 45 tetrameric oligomeric_state Although TLP and Thg1 have similar tetrameric organization, the mode of tRNA binding is different in TLP. INTRO | |
| 72 76 tRNA chemical Although TLP and Thg1 have similar tetrameric organization, the mode of tRNA binding is different in TLP. INTRO | |
| 101 104 TLP protein_type Although TLP and Thg1 have similar tetrameric organization, the mode of tRNA binding is different in TLP. INTRO | |
| 29 38 structure evidence Furthermore, we obtained the structure in which the GTP analog (GDPNP) was inserted into this complex to form a Watson-Crick base pair with C72 at the 3′-end region of the tRNA. INTRO | |
| 52 55 GTP chemical Furthermore, we obtained the structure in which the GTP analog (GDPNP) was inserted into this complex to form a Watson-Crick base pair with C72 at the 3′-end region of the tRNA. INTRO | |
| 64 69 GDPNP chemical Furthermore, we obtained the structure in which the GTP analog (GDPNP) was inserted into this complex to form a Watson-Crick base pair with C72 at the 3′-end region of the tRNA. INTRO | |
| 112 134 Watson-Crick base pair bond_interaction Furthermore, we obtained the structure in which the GTP analog (GDPNP) was inserted into this complex to form a Watson-Crick base pair with C72 at the 3′-end region of the tRNA. INTRO | |
| 140 143 C72 residue_name_number Furthermore, we obtained the structure in which the GTP analog (GDPNP) was inserted into this complex to form a Watson-Crick base pair with C72 at the 3′-end region of the tRNA. INTRO | |
| 172 176 tRNA chemical Furthermore, we obtained the structure in which the GTP analog (GDPNP) was inserted into this complex to form a Watson-Crick base pair with C72 at the 3′-end region of the tRNA. INTRO | |
| 22 32 structures evidence On the basis of these structures, we discuss the reaction mechanism of template-dependent reverse (3′-5′) polymerization in comparison with canonical 5′-3′ polymerization. INTRO | |
| 33 45 ppptRNAPheΔ1 chemical Anticodon-independent binding of ppptRNAPheΔ1 to MaTLP RESULTS | |
| 49 54 MaTLP protein Anticodon-independent binding of ppptRNAPheΔ1 to MaTLP RESULTS | |
| 9 32 biochemical experiments experimental_method Previous biochemical experiments have suggested that ppptRNAPheΔ1, in which the 5′-end of tRNAPhe was triphosphorylated and G1 was deleted, can be an efficient substrate for the repair reaction (guanylyl transfer) of Thg1/TLP. RESULTS | |
| 53 65 ppptRNAPheΔ1 chemical Previous biochemical experiments have suggested that ppptRNAPheΔ1, in which the 5′-end of tRNAPhe was triphosphorylated and G1 was deleted, can be an efficient substrate for the repair reaction (guanylyl transfer) of Thg1/TLP. RESULTS | |
| 90 97 tRNAPhe chemical Previous biochemical experiments have suggested that ppptRNAPheΔ1, in which the 5′-end of tRNAPhe was triphosphorylated and G1 was deleted, can be an efficient substrate for the repair reaction (guanylyl transfer) of Thg1/TLP. RESULTS | |
| 124 126 G1 residue_name_number Previous biochemical experiments have suggested that ppptRNAPheΔ1, in which the 5′-end of tRNAPhe was triphosphorylated and G1 was deleted, can be an efficient substrate for the repair reaction (guanylyl transfer) of Thg1/TLP. RESULTS | |
| 131 138 deleted experimental_method Previous biochemical experiments have suggested that ppptRNAPheΔ1, in which the 5′-end of tRNAPhe was triphosphorylated and G1 was deleted, can be an efficient substrate for the repair reaction (guanylyl transfer) of Thg1/TLP. RESULTS | |
| 217 221 Thg1 protein Previous biochemical experiments have suggested that ppptRNAPheΔ1, in which the 5′-end of tRNAPhe was triphosphorylated and G1 was deleted, can be an efficient substrate for the repair reaction (guanylyl transfer) of Thg1/TLP. RESULTS | |
| 222 225 TLP protein_type Previous biochemical experiments have suggested that ppptRNAPheΔ1, in which the 5′-end of tRNAPhe was triphosphorylated and G1 was deleted, can be an efficient substrate for the repair reaction (guanylyl transfer) of Thg1/TLP. RESULTS | |
| 25 32 crystal evidence Therefore, we prepared a crystal of MaTLP complexed with ppptRNAPheΔ1 and solved its structure to study the template-directed 3′-5′ elongation reaction by TLP (fig. S1). RESULTS | |
| 36 41 MaTLP protein Therefore, we prepared a crystal of MaTLP complexed with ppptRNAPheΔ1 and solved its structure to study the template-directed 3′-5′ elongation reaction by TLP (fig. S1). RESULTS | |
| 42 56 complexed with protein_state Therefore, we prepared a crystal of MaTLP complexed with ppptRNAPheΔ1 and solved its structure to study the template-directed 3′-5′ elongation reaction by TLP (fig. S1). RESULTS | |
| 57 69 ppptRNAPheΔ1 chemical Therefore, we prepared a crystal of MaTLP complexed with ppptRNAPheΔ1 and solved its structure to study the template-directed 3′-5′ elongation reaction by TLP (fig. S1). RESULTS | |
| 74 80 solved experimental_method Therefore, we prepared a crystal of MaTLP complexed with ppptRNAPheΔ1 and solved its structure to study the template-directed 3′-5′ elongation reaction by TLP (fig. S1). RESULTS | |
| 85 94 structure evidence Therefore, we prepared a crystal of MaTLP complexed with ppptRNAPheΔ1 and solved its structure to study the template-directed 3′-5′ elongation reaction by TLP (fig. S1). RESULTS | |
| 155 158 TLP protein_type Therefore, we prepared a crystal of MaTLP complexed with ppptRNAPheΔ1 and solved its structure to study the template-directed 3′-5′ elongation reaction by TLP (fig. S1). RESULTS | |
| 4 11 crystal evidence The crystal contained a dimer of TLP (A and B molecules) and one tRNA in an asymmetric unit. RESULTS | |
| 24 29 dimer oligomeric_state The crystal contained a dimer of TLP (A and B molecules) and one tRNA in an asymmetric unit. RESULTS | |
| 33 36 TLP protein_type The crystal contained a dimer of TLP (A and B molecules) and one tRNA in an asymmetric unit. RESULTS | |
| 38 39 A structure_element The crystal contained a dimer of TLP (A and B molecules) and one tRNA in an asymmetric unit. RESULTS | |
| 44 45 B structure_element The crystal contained a dimer of TLP (A and B molecules) and one tRNA in an asymmetric unit. RESULTS | |
| 65 69 tRNA chemical The crystal contained a dimer of TLP (A and B molecules) and one tRNA in an asymmetric unit. RESULTS | |
| 4 10 dimers oligomeric_state Two dimers in the crystal further assembled as a dimer of dimers by the crystallographic twofold axis (Fig. 2). RESULTS | |
| 18 25 crystal evidence Two dimers in the crystal further assembled as a dimer of dimers by the crystallographic twofold axis (Fig. 2). RESULTS | |
| 49 54 dimer oligomeric_state Two dimers in the crystal further assembled as a dimer of dimers by the crystallographic twofold axis (Fig. 2). RESULTS | |
| 58 64 dimers oligomeric_state Two dimers in the crystal further assembled as a dimer of dimers by the crystallographic twofold axis (Fig. 2). RESULTS | |
| 5 15 tetrameric oligomeric_state This tetrameric structure and 4:2 stoichiometry of the TLP-tRNA complex are the same as those of the CaThg1-tRNA complex. RESULTS | |
| 16 25 structure evidence This tetrameric structure and 4:2 stoichiometry of the TLP-tRNA complex are the same as those of the CaThg1-tRNA complex. RESULTS | |
| 55 63 TLP-tRNA complex_assembly This tetrameric structure and 4:2 stoichiometry of the TLP-tRNA complex are the same as those of the CaThg1-tRNA complex. RESULTS | |
| 101 112 CaThg1-tRNA complex_assembly This tetrameric structure and 4:2 stoichiometry of the TLP-tRNA complex are the same as those of the CaThg1-tRNA complex. RESULTS | |
| 21 23 AB structure_element However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region. RESULTS | |
| 28 30 CD structure_element However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region. RESULTS | |
| 31 37 dimers oligomeric_state However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region. RESULTS | |
| 41 51 tetrameric oligomeric_state However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region. RESULTS | |
| 52 58 CaThg1 protein However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region. RESULTS | |
| 110 123 accepter stem structure_element However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region. RESULTS | |
| 141 148 tRNAHis chemical However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region. RESULTS | |
| 154 156 AB structure_element However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region. RESULTS | |
| 157 162 dimer oligomeric_state However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region. RESULTS | |
| 186 188 CD structure_element However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region. RESULTS | |
| 189 194 dimer oligomeric_state However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region. RESULTS | |
| 199 209 tetrameric oligomeric_state However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region. RESULTS | |
| 210 215 MaTLP protein However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region. RESULTS | |
| 251 255 tRNA chemical However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region. RESULTS | |
| 283 287 tRNA chemical However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region. RESULTS | |
| 288 301 accepter stem structure_element However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region. RESULTS | |
| 306 318 elbow region structure_element However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region. RESULTS | |
| 38 43 MaTLP protein Thus, consistent with the notion that MaTLP is an anticodon-independent repair enzyme, the anticodon was not recognized in the MaTLP-tRNA complex, whereas the binding mode of CaThg1 is for the G−1 addition reaction, therefore the His anticodon has to be recognized (see “Dual binding mode for tRNA repair”). RESULTS | |
| 50 85 anticodon-independent repair enzyme protein_type Thus, consistent with the notion that MaTLP is an anticodon-independent repair enzyme, the anticodon was not recognized in the MaTLP-tRNA complex, whereas the binding mode of CaThg1 is for the G−1 addition reaction, therefore the His anticodon has to be recognized (see “Dual binding mode for tRNA repair”). RESULTS | |
| 127 137 MaTLP-tRNA complex_assembly Thus, consistent with the notion that MaTLP is an anticodon-independent repair enzyme, the anticodon was not recognized in the MaTLP-tRNA complex, whereas the binding mode of CaThg1 is for the G−1 addition reaction, therefore the His anticodon has to be recognized (see “Dual binding mode for tRNA repair”). RESULTS | |
| 175 181 CaThg1 protein Thus, consistent with the notion that MaTLP is an anticodon-independent repair enzyme, the anticodon was not recognized in the MaTLP-tRNA complex, whereas the binding mode of CaThg1 is for the G−1 addition reaction, therefore the His anticodon has to be recognized (see “Dual binding mode for tRNA repair”). RESULTS | |
| 193 196 G−1 residue_name_number Thus, consistent with the notion that MaTLP is an anticodon-independent repair enzyme, the anticodon was not recognized in the MaTLP-tRNA complex, whereas the binding mode of CaThg1 is for the G−1 addition reaction, therefore the His anticodon has to be recognized (see “Dual binding mode for tRNA repair”). RESULTS | |
| 230 233 His residue_name Thus, consistent with the notion that MaTLP is an anticodon-independent repair enzyme, the anticodon was not recognized in the MaTLP-tRNA complex, whereas the binding mode of CaThg1 is for the G−1 addition reaction, therefore the His anticodon has to be recognized (see “Dual binding mode for tRNA repair”). RESULTS | |
| 293 297 tRNA chemical Thus, consistent with the notion that MaTLP is an anticodon-independent repair enzyme, the anticodon was not recognized in the MaTLP-tRNA complex, whereas the binding mode of CaThg1 is for the G−1 addition reaction, therefore the His anticodon has to be recognized (see “Dual binding mode for tRNA repair”). RESULTS | |
| 0 9 Structure evidence Structure of the MaTLP complex with ppptRNAPheΔ1. FIG | |
| 17 22 MaTLP protein Structure of the MaTLP complex with ppptRNAPheΔ1. FIG | |
| 23 35 complex with protein_state Structure of the MaTLP complex with ppptRNAPheΔ1. FIG | |
| 36 48 ppptRNAPheΔ1 chemical Structure of the MaTLP complex with ppptRNAPheΔ1. FIG | |
| 26 30 tRNA chemical Left: One molecule of the tRNA substrate (ppptRNAPheΔ1) is bound to the MaTLP dimer. FIG | |
| 42 54 ppptRNAPheΔ1 chemical Left: One molecule of the tRNA substrate (ppptRNAPheΔ1) is bound to the MaTLP dimer. FIG | |
| 59 67 bound to protein_state Left: One molecule of the tRNA substrate (ppptRNAPheΔ1) is bound to the MaTLP dimer. FIG | |
| 72 77 MaTLP protein Left: One molecule of the tRNA substrate (ppptRNAPheΔ1) is bound to the MaTLP dimer. FIG | |
| 78 83 dimer oligomeric_state Left: One molecule of the tRNA substrate (ppptRNAPheΔ1) is bound to the MaTLP dimer. FIG | |
| 4 6 AB structure_element The AB and CD dimers are further dimerized by the crystallographic twofold axis to form a tetrameric structure (dimer of dimers). FIG | |
| 11 13 CD structure_element The AB and CD dimers are further dimerized by the crystallographic twofold axis to form a tetrameric structure (dimer of dimers). FIG | |
| 14 20 dimers oligomeric_state The AB and CD dimers are further dimerized by the crystallographic twofold axis to form a tetrameric structure (dimer of dimers). FIG | |
| 33 42 dimerized oligomeric_state The AB and CD dimers are further dimerized by the crystallographic twofold axis to form a tetrameric structure (dimer of dimers). FIG | |
| 90 100 tetrameric oligomeric_state The AB and CD dimers are further dimerized by the crystallographic twofold axis to form a tetrameric structure (dimer of dimers). FIG | |
| 101 110 structure evidence The AB and CD dimers are further dimerized by the crystallographic twofold axis to form a tetrameric structure (dimer of dimers). FIG | |
| 112 117 dimer oligomeric_state The AB and CD dimers are further dimerized by the crystallographic twofold axis to form a tetrameric structure (dimer of dimers). FIG | |
| 121 127 dimers oligomeric_state The AB and CD dimers are further dimerized by the crystallographic twofold axis to form a tetrameric structure (dimer of dimers). FIG | |
| 4 6 CD structure_element The CD dimer is omitted for clarity. FIG | |
| 7 12 dimer oligomeric_state The CD dimer is omitted for clarity. FIG | |
| 4 17 accepter stem structure_element The accepter stem of the tRNA is recognized by molecule A (yellow), and the elbow region by molecule B (blue). FIG | |
| 25 29 tRNA chemical The accepter stem of the tRNA is recognized by molecule A (yellow), and the elbow region by molecule B (blue). FIG | |
| 76 88 elbow region structure_element The accepter stem of the tRNA is recognized by molecule A (yellow), and the elbow region by molecule B (blue). FIG | |
| 4 13 β-hairpin structure_element The β-hairpin region of molecule B is shown in red. FIG | |
| 4 16 elbow region structure_element The elbow region of the tRNA substrate was recognized by the β-hairpin of molecule B of MaTLP. RESULTS | |
| 24 28 tRNA chemical The elbow region of the tRNA substrate was recognized by the β-hairpin of molecule B of MaTLP. RESULTS | |
| 61 70 β-hairpin structure_element The elbow region of the tRNA substrate was recognized by the β-hairpin of molecule B of MaTLP. RESULTS | |
| 88 93 MaTLP protein The elbow region of the tRNA substrate was recognized by the β-hairpin of molecule B of MaTLP. RESULTS | |
| 33 37 R215 residue_name_number The N atoms in the side chain of R215 in the β-hairpin region of MaTLP were hydrogen-bonded to the phosphate groups of U55 and G57. RESULTS | |
| 45 54 β-hairpin structure_element The N atoms in the side chain of R215 in the β-hairpin region of MaTLP were hydrogen-bonded to the phosphate groups of U55 and G57. RESULTS | |
| 65 70 MaTLP protein The N atoms in the side chain of R215 in the β-hairpin region of MaTLP were hydrogen-bonded to the phosphate groups of U55 and G57. RESULTS | |
| 76 91 hydrogen-bonded bond_interaction The N atoms in the side chain of R215 in the β-hairpin region of MaTLP were hydrogen-bonded to the phosphate groups of U55 and G57. RESULTS | |
| 99 108 phosphate chemical The N atoms in the side chain of R215 in the β-hairpin region of MaTLP were hydrogen-bonded to the phosphate groups of U55 and G57. RESULTS | |
| 119 122 U55 residue_name_number The N atoms in the side chain of R215 in the β-hairpin region of MaTLP were hydrogen-bonded to the phosphate groups of U55 and G57. RESULTS | |
| 127 130 G57 residue_name_number The N atoms in the side chain of R215 in the β-hairpin region of MaTLP were hydrogen-bonded to the phosphate groups of U55 and G57. RESULTS | |
| 18 22 S213 residue_name_number The O atom on the S213 side chain was also hydrogen-bonded to the phosphate moiety of G57 of the tRNA (Fig. 2). RESULTS | |
| 43 58 hydrogen-bonded bond_interaction The O atom on the S213 side chain was also hydrogen-bonded to the phosphate moiety of G57 of the tRNA (Fig. 2). RESULTS | |
| 66 75 phosphate chemical The O atom on the S213 side chain was also hydrogen-bonded to the phosphate moiety of G57 of the tRNA (Fig. 2). RESULTS | |
| 86 89 G57 residue_name_number The O atom on the S213 side chain was also hydrogen-bonded to the phosphate moiety of G57 of the tRNA (Fig. 2). RESULTS | |
| 97 101 tRNA chemical The O atom on the S213 side chain was also hydrogen-bonded to the phosphate moiety of G57 of the tRNA (Fig. 2). RESULTS | |
| 5 14 β-hairpin structure_element This β-hairpin region was disordered in the crystal structure of the CaThg1-tRNA complex. RESULTS | |
| 26 36 disordered protein_state This β-hairpin region was disordered in the crystal structure of the CaThg1-tRNA complex. RESULTS | |
| 44 61 crystal structure evidence This β-hairpin region was disordered in the crystal structure of the CaThg1-tRNA complex. RESULTS | |
| 69 80 CaThg1-tRNA complex_assembly This β-hairpin region was disordered in the crystal structure of the CaThg1-tRNA complex. RESULTS | |
| 4 17 accepter stem structure_element The accepter stem of the tRNA substrate was recognized by molecule A of MaTLP. RESULTS | |
| 25 29 tRNA chemical The accepter stem of the tRNA substrate was recognized by molecule A of MaTLP. RESULTS | |
| 72 77 MaTLP protein The accepter stem of the tRNA substrate was recognized by molecule A of MaTLP. RESULTS | |
| 15 17 G2 residue_name_number The N7 atom of G2 at the 5′-end was hydrogen-bonded to the N atom of the R136 side chain, whereas the α-phosphate was bonded to the N137 side chain (Fig. 2). RESULTS | |
| 36 51 hydrogen-bonded bond_interaction The N7 atom of G2 at the 5′-end was hydrogen-bonded to the N atom of the R136 side chain, whereas the α-phosphate was bonded to the N137 side chain (Fig. 2). RESULTS | |
| 73 77 R136 residue_name_number The N7 atom of G2 at the 5′-end was hydrogen-bonded to the N atom of the R136 side chain, whereas the α-phosphate was bonded to the N137 side chain (Fig. 2). RESULTS | |
| 104 113 phosphate chemical The N7 atom of G2 at the 5′-end was hydrogen-bonded to the N atom of the R136 side chain, whereas the α-phosphate was bonded to the N137 side chain (Fig. 2). RESULTS | |
| 132 136 N137 residue_name_number The N7 atom of G2 at the 5′-end was hydrogen-bonded to the N atom of the R136 side chain, whereas the α-phosphate was bonded to the N137 side chain (Fig. 2). RESULTS | |
| 0 4 R136 residue_name_number R136 was also hydrogen-bonded to the base of C72 (the Watson-Crick bond partner of ΔG1). RESULTS | |
| 14 29 hydrogen-bonded bond_interaction R136 was also hydrogen-bonded to the base of C72 (the Watson-Crick bond partner of ΔG1). RESULTS | |
| 45 48 C72 residue_name_number R136 was also hydrogen-bonded to the base of C72 (the Watson-Crick bond partner of ΔG1). RESULTS | |
| 4 16 triphosphate chemical The triphosphate moiety at the 5′-end of the tRNA was bonded to the D21-K26 region. RESULTS | |
| 45 49 tRNA chemical The triphosphate moiety at the 5′-end of the tRNA was bonded to the D21-K26 region. RESULTS | |
| 68 75 D21-K26 residue_range The triphosphate moiety at the 5′-end of the tRNA was bonded to the D21-K26 region. RESULTS | |
| 6 16 phosphates chemical These phosphates were also coordinated to two metal ions, presumably Mg2+ (Mg2+A and Mg2+B) because they were observed at the same positions (figs. S3 and S4) previously identified by CaThg1 and HsThg1 structures. RESULTS | |
| 27 41 coordinated to bond_interaction These phosphates were also coordinated to two metal ions, presumably Mg2+ (Mg2+A and Mg2+B) because they were observed at the same positions (figs. S3 and S4) previously identified by CaThg1 and HsThg1 structures. RESULTS | |
| 69 73 Mg2+ chemical These phosphates were also coordinated to two metal ions, presumably Mg2+ (Mg2+A and Mg2+B) because they were observed at the same positions (figs. S3 and S4) previously identified by CaThg1 and HsThg1 structures. RESULTS | |
| 75 79 Mg2+ chemical These phosphates were also coordinated to two metal ions, presumably Mg2+ (Mg2+A and Mg2+B) because they were observed at the same positions (figs. S3 and S4) previously identified by CaThg1 and HsThg1 structures. RESULTS | |
| 85 89 Mg2+ chemical These phosphates were also coordinated to two metal ions, presumably Mg2+ (Mg2+A and Mg2+B) because they were observed at the same positions (figs. S3 and S4) previously identified by CaThg1 and HsThg1 structures. RESULTS | |
| 184 190 CaThg1 protein These phosphates were also coordinated to two metal ions, presumably Mg2+ (Mg2+A and Mg2+B) because they were observed at the same positions (figs. S3 and S4) previously identified by CaThg1 and HsThg1 structures. RESULTS | |
| 195 201 HsThg1 protein These phosphates were also coordinated to two metal ions, presumably Mg2+ (Mg2+A and Mg2+B) because they were observed at the same positions (figs. S3 and S4) previously identified by CaThg1 and HsThg1 structures. RESULTS | |
| 202 212 structures evidence These phosphates were also coordinated to two metal ions, presumably Mg2+ (Mg2+A and Mg2+B) because they were observed at the same positions (figs. S3 and S4) previously identified by CaThg1 and HsThg1 structures. RESULTS | |
| 24 38 coordinated by bond_interaction These ions were in turn coordinated by the O atoms of the side chains of D21 and D69 and the main-chain O of G22 (fig. S3A). RESULTS | |
| 73 76 D21 residue_name_number These ions were in turn coordinated by the O atoms of the side chains of D21 and D69 and the main-chain O of G22 (fig. S3A). RESULTS | |
| 81 84 D69 residue_name_number These ions were in turn coordinated by the O atoms of the side chains of D21 and D69 and the main-chain O of G22 (fig. S3A). RESULTS | |
| 109 112 G22 residue_name_number These ions were in turn coordinated by the O atoms of the side chains of D21 and D69 and the main-chain O of G22 (fig. S3A). RESULTS | |
| 0 8 Mutation experimental_method Mutation of D29 and D76 in HsThg1 (corresponding to D21 and D69 of MaTLP) has been shown to markedly decrease G−1 addition activity. RESULTS | |
| 12 15 D29 residue_name_number Mutation of D29 and D76 in HsThg1 (corresponding to D21 and D69 of MaTLP) has been shown to markedly decrease G−1 addition activity. RESULTS | |
| 20 23 D76 residue_name_number Mutation of D29 and D76 in HsThg1 (corresponding to D21 and D69 of MaTLP) has been shown to markedly decrease G−1 addition activity. RESULTS | |
| 27 33 HsThg1 protein Mutation of D29 and D76 in HsThg1 (corresponding to D21 and D69 of MaTLP) has been shown to markedly decrease G−1 addition activity. RESULTS | |
| 52 55 D21 residue_name_number Mutation of D29 and D76 in HsThg1 (corresponding to D21 and D69 of MaTLP) has been shown to markedly decrease G−1 addition activity. RESULTS | |
| 60 63 D69 residue_name_number Mutation of D29 and D76 in HsThg1 (corresponding to D21 and D69 of MaTLP) has been shown to markedly decrease G−1 addition activity. RESULTS | |
| 67 72 MaTLP protein Mutation of D29 and D76 in HsThg1 (corresponding to D21 and D69 of MaTLP) has been shown to markedly decrease G−1 addition activity. RESULTS | |
| 110 113 G−1 residue_name_number Mutation of D29 and D76 in HsThg1 (corresponding to D21 and D69 of MaTLP) has been shown to markedly decrease G−1 addition activity. RESULTS | |
| 34 37 GTP chemical Template-dependent binding of the GTP analog to the MaTLP-ppptRNAPheΔ1 complex RESULTS | |
| 52 70 MaTLP-ppptRNAPheΔ1 complex_assembly Template-dependent binding of the GTP analog to the MaTLP-ppptRNAPheΔ1 complex RESULTS | |
| 35 44 structure evidence Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP. RESULTS | |
| 71 76 MaTLP protein Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP. RESULTS | |
| 91 95 tRNA chemical Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP. RESULTS | |
| 97 109 ppptRNAPheΔ1 chemical Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP. RESULTS | |
| 120 123 GTP chemical Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP. RESULTS | |
| 132 137 GDPNP chemical Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP. RESULTS | |
| 163 170 soaking experimental_method Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP. RESULTS | |
| 175 193 MaTLP-ppptRNAPheΔ1 complex_assembly Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP. RESULTS | |
| 202 209 crystal evidence Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP. RESULTS | |
| 235 240 GDPNP chemical Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP. RESULTS | |
| 13 22 structure evidence The obtained structure showed that the guanine base of the incoming GDPNP formed Watson-Crick hydrogen bonds with C72 and accompanied base-stacking interactions with G2 of the tRNA (Fig. 3B), whereas no interaction was observed between the guanine base and the enzyme. RESULTS | |
| 39 46 guanine chemical The obtained structure showed that the guanine base of the incoming GDPNP formed Watson-Crick hydrogen bonds with C72 and accompanied base-stacking interactions with G2 of the tRNA (Fig. 3B), whereas no interaction was observed between the guanine base and the enzyme. RESULTS | |
| 68 73 GDPNP chemical The obtained structure showed that the guanine base of the incoming GDPNP formed Watson-Crick hydrogen bonds with C72 and accompanied base-stacking interactions with G2 of the tRNA (Fig. 3B), whereas no interaction was observed between the guanine base and the enzyme. RESULTS | |
| 81 108 Watson-Crick hydrogen bonds bond_interaction The obtained structure showed that the guanine base of the incoming GDPNP formed Watson-Crick hydrogen bonds with C72 and accompanied base-stacking interactions with G2 of the tRNA (Fig. 3B), whereas no interaction was observed between the guanine base and the enzyme. RESULTS | |
| 114 117 C72 residue_name_number The obtained structure showed that the guanine base of the incoming GDPNP formed Watson-Crick hydrogen bonds with C72 and accompanied base-stacking interactions with G2 of the tRNA (Fig. 3B), whereas no interaction was observed between the guanine base and the enzyme. RESULTS | |
| 134 160 base-stacking interactions bond_interaction The obtained structure showed that the guanine base of the incoming GDPNP formed Watson-Crick hydrogen bonds with C72 and accompanied base-stacking interactions with G2 of the tRNA (Fig. 3B), whereas no interaction was observed between the guanine base and the enzyme. RESULTS | |
| 166 168 G2 residue_name_number The obtained structure showed that the guanine base of the incoming GDPNP formed Watson-Crick hydrogen bonds with C72 and accompanied base-stacking interactions with G2 of the tRNA (Fig. 3B), whereas no interaction was observed between the guanine base and the enzyme. RESULTS | |
| 176 180 tRNA chemical The obtained structure showed that the guanine base of the incoming GDPNP formed Watson-Crick hydrogen bonds with C72 and accompanied base-stacking interactions with G2 of the tRNA (Fig. 3B), whereas no interaction was observed between the guanine base and the enzyme. RESULTS | |
| 240 247 guanine chemical The obtained structure showed that the guanine base of the incoming GDPNP formed Watson-Crick hydrogen bonds with C72 and accompanied base-stacking interactions with G2 of the tRNA (Fig. 3B), whereas no interaction was observed between the guanine base and the enzyme. RESULTS | |
| 31 35 tRNA chemical The 5′-end (position 2) of the tRNA moved significantly (Fig. 3C) due to the insertion of GDPNP. RESULTS | |
| 90 95 GDPNP chemical The 5′-end (position 2) of the tRNA moved significantly (Fig. 3C) due to the insertion of GDPNP. RESULTS | |
| 18 33 5′-triphosphate chemical Surprisingly, the 5′-triphosphate moiety after movement occupied the GTP/ATP triphosphate position during the activation step (Fig. 3D). RESULTS | |
| 69 72 GTP chemical Surprisingly, the 5′-triphosphate moiety after movement occupied the GTP/ATP triphosphate position during the activation step (Fig. 3D). RESULTS | |
| 73 76 ATP chemical Surprisingly, the 5′-triphosphate moiety after movement occupied the GTP/ATP triphosphate position during the activation step (Fig. 3D). RESULTS | |
| 77 89 triphosphate chemical Surprisingly, the 5′-triphosphate moiety after movement occupied the GTP/ATP triphosphate position during the activation step (Fig. 3D). RESULTS | |
| 61 64 GTP chemical Together with the observation that the 3′-OH of the incoming GTP analog was within coordination distance (2.8 Å) to Mg2+A (fig. S3B) and was able to execute a nucleophilic attack on the α-phosphate of the 5′-end, this structure indicates that the elongation reaction (second reaction) takes place at the same reaction center where the activation reaction (first reaction) occurs. RESULTS | |
| 116 120 Mg2+ chemical Together with the observation that the 3′-OH of the incoming GTP analog was within coordination distance (2.8 Å) to Mg2+A (fig. S3B) and was able to execute a nucleophilic attack on the α-phosphate of the 5′-end, this structure indicates that the elongation reaction (second reaction) takes place at the same reaction center where the activation reaction (first reaction) occurs. RESULTS | |
| 188 197 phosphate chemical Together with the observation that the 3′-OH of the incoming GTP analog was within coordination distance (2.8 Å) to Mg2+A (fig. S3B) and was able to execute a nucleophilic attack on the α-phosphate of the 5′-end, this structure indicates that the elongation reaction (second reaction) takes place at the same reaction center where the activation reaction (first reaction) occurs. RESULTS | |
| 218 227 structure evidence Together with the observation that the 3′-OH of the incoming GTP analog was within coordination distance (2.8 Å) to Mg2+A (fig. S3B) and was able to execute a nucleophilic attack on the α-phosphate of the 5′-end, this structure indicates that the elongation reaction (second reaction) takes place at the same reaction center where the activation reaction (first reaction) occurs. RESULTS | |
| 309 324 reaction center site Together with the observation that the 3′-OH of the incoming GTP analog was within coordination distance (2.8 Å) to Mg2+A (fig. S3B) and was able to execute a nucleophilic attack on the α-phosphate of the 5′-end, this structure indicates that the elongation reaction (second reaction) takes place at the same reaction center where the activation reaction (first reaction) occurs. RESULTS | |
| 25 29 tRNA chemical Structural change of the tRNA (ppptRNAPheΔ1). FIG | |
| 31 43 ppptRNAPheΔ1 chemical Structural change of the tRNA (ppptRNAPheΔ1). FIG | |
| 25 29 tRNA chemical Structural change of the tRNA (ppptRNAPheΔ1) accepter stem in MaTLP caused by insertion of GDPNP. (A) Structure before GDPNP binding. FIG | |
| 31 43 ppptRNAPheΔ1 chemical Structural change of the tRNA (ppptRNAPheΔ1) accepter stem in MaTLP caused by insertion of GDPNP. (A) Structure before GDPNP binding. FIG | |
| 45 58 accepter stem structure_element Structural change of the tRNA (ppptRNAPheΔ1) accepter stem in MaTLP caused by insertion of GDPNP. (A) Structure before GDPNP binding. FIG | |
| 62 67 MaTLP protein Structural change of the tRNA (ppptRNAPheΔ1) accepter stem in MaTLP caused by insertion of GDPNP. (A) Structure before GDPNP binding. FIG | |
| 91 96 GDPNP chemical Structural change of the tRNA (ppptRNAPheΔ1) accepter stem in MaTLP caused by insertion of GDPNP. (A) Structure before GDPNP binding. FIG | |
| 102 111 Structure evidence Structural change of the tRNA (ppptRNAPheΔ1) accepter stem in MaTLP caused by insertion of GDPNP. (A) Structure before GDPNP binding. FIG | |
| 119 124 GDPNP chemical Structural change of the tRNA (ppptRNAPheΔ1) accepter stem in MaTLP caused by insertion of GDPNP. (A) Structure before GDPNP binding. FIG | |
| 4 13 Structure evidence (B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well. FIG | |
| 20 25 GDPNP chemical (B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well. FIG | |
| 39 52 Superposition experimental_method (B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well. FIG | |
| 64 74 structures evidence (B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well. FIG | |
| 113 117 tRNA chemical (B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well. FIG | |
| 161 166 GDPNP chemical (B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well. FIG | |
| 172 185 Superposition experimental_method (B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well. FIG | |
| 207 211 tRNA chemical (B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well. FIG | |
| 218 223 GDPNP chemical (B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well. FIG | |
| 245 248 GTP chemical (B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well. FIG | |
| 299 311 triphosphate chemical (B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well. FIG | |
| 4 16 triphosphate chemical The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B). RESULTS | |
| 27 32 GDPNP chemical The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B). RESULTS | |
| 44 53 interface site The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B). RESULTS | |
| 72 73 A structure_element The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B). RESULTS | |
| 78 79 B structure_element The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B). RESULTS | |
| 147 150 R19 residue_name_number The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B). RESULTS | |
| 161 162 A structure_element The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B). RESULTS | |
| 165 168 R83 residue_name_number The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B). RESULTS | |
| 179 180 B structure_element The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B). RESULTS | |
| 183 186 K86 residue_name_number The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B). RESULTS | |
| 197 198 B structure_element The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B). RESULTS | |
| 205 209 R114 residue_name_number The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B). RESULTS | |
| 220 221 A structure_element The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B). RESULTS | |
| 26 40 well conserved protein_state All of these residues are well conserved (fig. S5), and mutation of corresponding residues in ScThg1 (R27, R93, K96, and R133) decreased the catalytic efficiency of G−1 addition. RESULTS | |
| 56 64 mutation experimental_method All of these residues are well conserved (fig. S5), and mutation of corresponding residues in ScThg1 (R27, R93, K96, and R133) decreased the catalytic efficiency of G−1 addition. RESULTS | |
| 94 100 ScThg1 protein All of these residues are well conserved (fig. S5), and mutation of corresponding residues in ScThg1 (R27, R93, K96, and R133) decreased the catalytic efficiency of G−1 addition. RESULTS | |
| 102 105 R27 residue_name_number All of these residues are well conserved (fig. S5), and mutation of corresponding residues in ScThg1 (R27, R93, K96, and R133) decreased the catalytic efficiency of G−1 addition. RESULTS | |
| 107 110 R93 residue_name_number All of these residues are well conserved (fig. S5), and mutation of corresponding residues in ScThg1 (R27, R93, K96, and R133) decreased the catalytic efficiency of G−1 addition. RESULTS | |
| 112 115 K96 residue_name_number All of these residues are well conserved (fig. S5), and mutation of corresponding residues in ScThg1 (R27, R93, K96, and R133) decreased the catalytic efficiency of G−1 addition. RESULTS | |
| 121 125 R133 residue_name_number All of these residues are well conserved (fig. S5), and mutation of corresponding residues in ScThg1 (R27, R93, K96, and R133) decreased the catalytic efficiency of G−1 addition. RESULTS | |
| 165 168 G−1 residue_name_number All of these residues are well conserved (fig. S5), and mutation of corresponding residues in ScThg1 (R27, R93, K96, and R133) decreased the catalytic efficiency of G−1 addition. RESULTS | |
| 4 16 triphosphate chemical The triphosphate of the GDPNP was also bonded to the third Mg2+ (Mg2+C), which, unlike Mg2+A and Mg2+B, is not coordinated by the TLP molecule (fig. S3B). RESULTS | |
| 24 29 GDPNP chemical The triphosphate of the GDPNP was also bonded to the third Mg2+ (Mg2+C), which, unlike Mg2+A and Mg2+B, is not coordinated by the TLP molecule (fig. S3B). RESULTS | |
| 59 63 Mg2+ chemical The triphosphate of the GDPNP was also bonded to the third Mg2+ (Mg2+C), which, unlike Mg2+A and Mg2+B, is not coordinated by the TLP molecule (fig. S3B). RESULTS | |
| 65 69 Mg2+ chemical The triphosphate of the GDPNP was also bonded to the third Mg2+ (Mg2+C), which, unlike Mg2+A and Mg2+B, is not coordinated by the TLP molecule (fig. S3B). RESULTS | |
| 87 91 Mg2+ chemical The triphosphate of the GDPNP was also bonded to the third Mg2+ (Mg2+C), which, unlike Mg2+A and Mg2+B, is not coordinated by the TLP molecule (fig. S3B). RESULTS | |
| 97 101 Mg2+ chemical The triphosphate of the GDPNP was also bonded to the third Mg2+ (Mg2+C), which, unlike Mg2+A and Mg2+B, is not coordinated by the TLP molecule (fig. S3B). RESULTS | |
| 111 125 coordinated by bond_interaction The triphosphate of the GDPNP was also bonded to the third Mg2+ (Mg2+C), which, unlike Mg2+A and Mg2+B, is not coordinated by the TLP molecule (fig. S3B). RESULTS | |
| 130 133 TLP protein_type The triphosphate of the GDPNP was also bonded to the third Mg2+ (Mg2+C), which, unlike Mg2+A and Mg2+B, is not coordinated by the TLP molecule (fig. S3B). RESULTS | |
| 5 17 triphosphate chemical This triphosphate binding mode is the same as that for the second nucleotide binding site in Thg1. RESULTS | |
| 59 89 second nucleotide binding site site This triphosphate binding mode is the same as that for the second nucleotide binding site in Thg1. RESULTS | |
| 93 97 Thg1 protein This triphosphate binding mode is the same as that for the second nucleotide binding site in Thg1. RESULTS | |
| 54 65 second site site However, in previous analyses, the base moiety at the second site was either invisible or far beyond the reaction distance of the phosphate, and therefore, flipping of the base was expected to occur. RESULTS | |
| 130 139 phosphate chemical However, in previous analyses, the base moiety at the second site was either invisible or far beyond the reaction distance of the phosphate, and therefore, flipping of the base was expected to occur. RESULTS | |
| 0 35 tRNA binding and repair experiments experimental_method tRNA binding and repair experiments of the β-hairpin mutants RESULTS | |
| 43 52 β-hairpin structure_element tRNA binding and repair experiments of the β-hairpin mutants RESULTS | |
| 53 60 mutants protein_state tRNA binding and repair experiments of the β-hairpin mutants RESULTS | |
| 11 15 tRNA chemical To confirm tRNA recognition by the β-hairpin, we created mutation variants with altered residues in the β-hairpin region. RESULTS | |
| 35 44 β-hairpin structure_element To confirm tRNA recognition by the β-hairpin, we created mutation variants with altered residues in the β-hairpin region. RESULTS | |
| 49 74 created mutation variants experimental_method To confirm tRNA recognition by the β-hairpin, we created mutation variants with altered residues in the β-hairpin region. RESULTS | |
| 104 113 β-hairpin structure_element To confirm tRNA recognition by the β-hairpin, we created mutation variants with altered residues in the β-hairpin region. RESULTS | |
| 6 57 tRNA binding and enzymatic activities were measured experimental_method Then, tRNA binding and enzymatic activities were measured. RESULTS | |
| 0 9 β-Hairpin structure_element β-Hairpin deletion variant delR198-R215 almost completely abolished the binding of tRNAPheΔ1 (fig. S6). RESULTS | |
| 10 26 deletion variant protein_state β-Hairpin deletion variant delR198-R215 almost completely abolished the binding of tRNAPheΔ1 (fig. S6). RESULTS | |
| 27 39 delR198-R215 mutant β-Hairpin deletion variant delR198-R215 almost completely abolished the binding of tRNAPheΔ1 (fig. S6). RESULTS | |
| 83 92 tRNAPheΔ1 chemical β-Hairpin deletion variant delR198-R215 almost completely abolished the binding of tRNAPheΔ1 (fig. S6). RESULTS | |
| 41 53 delR198-R215 mutant Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A). RESULTS | |
| 58 70 delG202-E210 mutant Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A). RESULTS | |
| 130 139 wild type protein_state Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A). RESULTS | |
| 149 158 mutations experimental_method Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A). RESULTS | |
| 160 165 N179A mutant Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A). RESULTS | |
| 170 175 F174A mutant Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A). RESULTS | |
| 176 181 N179A mutant Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A). RESULTS | |
| 182 187 R188A mutant Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A). RESULTS | |
| 196 222 anticodon recognition site site Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A). RESULTS | |
| 241 253 Thg1-tRNAHis complex_assembly Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A). RESULTS | |
| 262 271 structure evidence Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A). RESULTS | |
| 22 31 tRNAHisΔ1 chemical Experiments using the tRNAHisΔ1 substrate gave similar results (Fig. 4A). RESULTS | |
| 42 59 crystal structure evidence All these results are consistent with the crystal structure and suggest that the β-hairpin plays an important role in anticodon-independent binding of the tRNA substrate. RESULTS | |
| 81 90 β-hairpin structure_element All these results are consistent with the crystal structure and suggest that the β-hairpin plays an important role in anticodon-independent binding of the tRNA substrate. RESULTS | |
| 155 159 tRNA chemical All these results are consistent with the crystal structure and suggest that the β-hairpin plays an important role in anticodon-independent binding of the tRNA substrate. RESULTS | |
| 16 25 β-hairpin structure_element Residues in the β-hairpin are not well conserved, except for R215 (fig. S5). RESULTS | |
| 30 48 not well conserved protein_state Residues in the β-hairpin are not well conserved, except for R215 (fig. S5). RESULTS | |
| 61 65 R215 residue_name_number Residues in the β-hairpin are not well conserved, except for R215 (fig. S5). RESULTS | |
| 0 7 Mutants protein_state Mutants R215A and R215A/S213A, in which the completely conserved R215 was changed to alanine, showed a moderate effect on the activity (27.3 and 16.3%, respectively). RESULTS | |
| 8 13 R215A mutant Mutants R215A and R215A/S213A, in which the completely conserved R215 was changed to alanine, showed a moderate effect on the activity (27.3 and 16.3%, respectively). RESULTS | |
| 18 23 R215A mutant Mutants R215A and R215A/S213A, in which the completely conserved R215 was changed to alanine, showed a moderate effect on the activity (27.3 and 16.3%, respectively). RESULTS | |
| 24 29 S213A mutant Mutants R215A and R215A/S213A, in which the completely conserved R215 was changed to alanine, showed a moderate effect on the activity (27.3 and 16.3%, respectively). RESULTS | |
| 44 64 completely conserved protein_state Mutants R215A and R215A/S213A, in which the completely conserved R215 was changed to alanine, showed a moderate effect on the activity (27.3 and 16.3%, respectively). RESULTS | |
| 65 69 R215 residue_name_number Mutants R215A and R215A/S213A, in which the completely conserved R215 was changed to alanine, showed a moderate effect on the activity (27.3 and 16.3%, respectively). RESULTS | |
| 74 81 changed experimental_method Mutants R215A and R215A/S213A, in which the completely conserved R215 was changed to alanine, showed a moderate effect on the activity (27.3 and 16.3%, respectively). RESULTS | |
| 85 92 alanine residue_name Mutants R215A and R215A/S213A, in which the completely conserved R215 was changed to alanine, showed a moderate effect on the activity (27.3 and 16.3%, respectively). RESULTS | |
| 37 46 conserved protein_state Thus, specific interactions with the conserved R215 and van der Waals contacts to residues in the β-hairpin would be important for tRNA recognition. RESULTS | |
| 47 51 R215 residue_name_number Thus, specific interactions with the conserved R215 and van der Waals contacts to residues in the β-hairpin would be important for tRNA recognition. RESULTS | |
| 56 78 van der Waals contacts bond_interaction Thus, specific interactions with the conserved R215 and van der Waals contacts to residues in the β-hairpin would be important for tRNA recognition. RESULTS | |
| 98 107 β-hairpin structure_element Thus, specific interactions with the conserved R215 and van der Waals contacts to residues in the β-hairpin would be important for tRNA recognition. RESULTS | |
| 131 135 tRNA chemical Thus, specific interactions with the conserved R215 and van der Waals contacts to residues in the β-hairpin would be important for tRNA recognition. RESULTS | |
| 0 19 Mutational analysis experimental_method Mutational analysis of the β-hairpin and anticodon binding region. FIG | |
| 27 36 β-hairpin structure_element Mutational analysis of the β-hairpin and anticodon binding region. FIG | |
| 41 65 anticodon binding region site Mutational analysis of the β-hairpin and anticodon binding region. FIG | |
| 21 33 ppptRNAPheΔ1 chemical (A) Guanylylation of ppptRNAPheΔ1 and ppptRNAHisΔ1 by various TLP mutants. FIG | |
| 38 50 ppptRNAHisΔ1 chemical (A) Guanylylation of ppptRNAPheΔ1 and ppptRNAHisΔ1 by various TLP mutants. FIG | |
| 62 65 TLP protein_type (A) Guanylylation of ppptRNAPheΔ1 and ppptRNAHisΔ1 by various TLP mutants. FIG | |
| 66 73 mutants protein_state (A) Guanylylation of ppptRNAPheΔ1 and ppptRNAHisΔ1 by various TLP mutants. FIG | |
| 19 29 [α-32P]GTP chemical The activity using [α-32P]GTP, wild-type MaTLP, and ppptRNAPheΔ1 is denoted as 100. (B) Guanylylation of tRNAPheΔ1, tRNAPhe, and tRNAHisΔ−1 by various TLP mutants. FIG | |
| 31 40 wild-type protein_state The activity using [α-32P]GTP, wild-type MaTLP, and ppptRNAPheΔ1 is denoted as 100. (B) Guanylylation of tRNAPheΔ1, tRNAPhe, and tRNAHisΔ−1 by various TLP mutants. FIG | |
| 41 46 MaTLP protein The activity using [α-32P]GTP, wild-type MaTLP, and ppptRNAPheΔ1 is denoted as 100. (B) Guanylylation of tRNAPheΔ1, tRNAPhe, and tRNAHisΔ−1 by various TLP mutants. FIG | |
| 52 64 ppptRNAPheΔ1 chemical The activity using [α-32P]GTP, wild-type MaTLP, and ppptRNAPheΔ1 is denoted as 100. (B) Guanylylation of tRNAPheΔ1, tRNAPhe, and tRNAHisΔ−1 by various TLP mutants. FIG | |
| 105 114 tRNAPheΔ1 chemical The activity using [α-32P]GTP, wild-type MaTLP, and ppptRNAPheΔ1 is denoted as 100. (B) Guanylylation of tRNAPheΔ1, tRNAPhe, and tRNAHisΔ−1 by various TLP mutants. FIG | |
| 116 123 tRNAPhe chemical The activity using [α-32P]GTP, wild-type MaTLP, and ppptRNAPheΔ1 is denoted as 100. (B) Guanylylation of tRNAPheΔ1, tRNAPhe, and tRNAHisΔ−1 by various TLP mutants. FIG | |
| 129 139 tRNAHisΔ−1 chemical The activity using [α-32P]GTP, wild-type MaTLP, and ppptRNAPheΔ1 is denoted as 100. (B) Guanylylation of tRNAPheΔ1, tRNAPhe, and tRNAHisΔ−1 by various TLP mutants. FIG | |
| 151 154 TLP protein_type The activity using [α-32P]GTP, wild-type MaTLP, and ppptRNAPheΔ1 is denoted as 100. (B) Guanylylation of tRNAPheΔ1, tRNAPhe, and tRNAHisΔ−1 by various TLP mutants. FIG | |
| 155 162 mutants protein_state The activity using [α-32P]GTP, wild-type MaTLP, and ppptRNAPheΔ1 is denoted as 100. (B) Guanylylation of tRNAPheΔ1, tRNAPhe, and tRNAHisΔ−1 by various TLP mutants. FIG | |
| 16 25 tRNAPheΔ1 chemical The activity to tRNAPheΔ1 is about 10% of ppptRNAPheΔ1. FIG | |
| 42 54 ppptRNAPheΔ1 chemical The activity to tRNAPheΔ1 is about 10% of ppptRNAPheΔ1. FIG | |
| 56 69 accepter stem structure_element Termination of the elongation reaction by measuring the accepter stem RESULTS | |
| 0 4 TLPs protein_type TLPs catalyze the Watson-Crick template–dependent elongation or repair reaction for 5′-end truncated tRNAPhe substrates lacking G1 only (tRNAPheΔ1), or lacking both G1 and G2 (tRNAPheΔ1,2), whereas they do not show any activity with intact tRNAPhe (thus, repair is unnecessary). RESULTS | |
| 101 108 tRNAPhe chemical TLPs catalyze the Watson-Crick template–dependent elongation or repair reaction for 5′-end truncated tRNAPhe substrates lacking G1 only (tRNAPheΔ1), or lacking both G1 and G2 (tRNAPheΔ1,2), whereas they do not show any activity with intact tRNAPhe (thus, repair is unnecessary). RESULTS | |
| 128 130 G1 residue_name_number TLPs catalyze the Watson-Crick template–dependent elongation or repair reaction for 5′-end truncated tRNAPhe substrates lacking G1 only (tRNAPheΔ1), or lacking both G1 and G2 (tRNAPheΔ1,2), whereas they do not show any activity with intact tRNAPhe (thus, repair is unnecessary). RESULTS | |
| 137 146 tRNAPheΔ1 chemical TLPs catalyze the Watson-Crick template–dependent elongation or repair reaction for 5′-end truncated tRNAPhe substrates lacking G1 only (tRNAPheΔ1), or lacking both G1 and G2 (tRNAPheΔ1,2), whereas they do not show any activity with intact tRNAPhe (thus, repair is unnecessary). RESULTS | |
| 165 167 G1 residue_name_number TLPs catalyze the Watson-Crick template–dependent elongation or repair reaction for 5′-end truncated tRNAPhe substrates lacking G1 only (tRNAPheΔ1), or lacking both G1 and G2 (tRNAPheΔ1,2), whereas they do not show any activity with intact tRNAPhe (thus, repair is unnecessary). RESULTS | |
| 172 174 G2 residue_name_number TLPs catalyze the Watson-Crick template–dependent elongation or repair reaction for 5′-end truncated tRNAPhe substrates lacking G1 only (tRNAPheΔ1), or lacking both G1 and G2 (tRNAPheΔ1,2), whereas they do not show any activity with intact tRNAPhe (thus, repair is unnecessary). RESULTS | |
| 176 187 tRNAPheΔ1,2 chemical TLPs catalyze the Watson-Crick template–dependent elongation or repair reaction for 5′-end truncated tRNAPhe substrates lacking G1 only (tRNAPheΔ1), or lacking both G1 and G2 (tRNAPheΔ1,2), whereas they do not show any activity with intact tRNAPhe (thus, repair is unnecessary). RESULTS | |
| 240 247 tRNAPhe chemical TLPs catalyze the Watson-Crick template–dependent elongation or repair reaction for 5′-end truncated tRNAPhe substrates lacking G1 only (tRNAPheΔ1), or lacking both G1 and G2 (tRNAPheΔ1,2), whereas they do not show any activity with intact tRNAPhe (thus, repair is unnecessary). RESULTS | |
| 4 7 TLP protein_type How TLP distinguishes between tRNAs that need 5′-end repair from ones that do not, or in other words, how the elongation reaction is properly terminated, remains unknown. RESULTS | |
| 30 35 tRNAs chemical How TLP distinguishes between tRNAs that need 5′-end repair from ones that do not, or in other words, how the elongation reaction is properly terminated, remains unknown. RESULTS | |
| 12 21 structure evidence The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths. RESULTS | |
| 29 47 MaTLP-ppptRNAPheΔ1 complex_assembly The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths. RESULTS | |
| 75 79 Thg1 protein The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths. RESULTS | |
| 85 88 TLP protein_type The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths. RESULTS | |
| 89 94 dimer oligomeric_state The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths. RESULTS | |
| 117 121 tRNA chemical The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths. RESULTS | |
| 141 153 elbow region structure_element The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths. RESULTS | |
| 161 170 β-hairpin structure_element The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths. RESULTS | |
| 183 184 B structure_element The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths. RESULTS | |
| 212 213 A structure_element The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths. RESULTS | |
| 249 257 flexible protein_state The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths. RESULTS | |
| 272 281 β-hairpin structure_element The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths. RESULTS | |
| 309 313 tRNA chemical The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths. RESULTS | |
| 340 353 accepter stem structure_element The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths. RESULTS | |
| 32 65 used computer graphics to examine experimental_method To confirm this speculation, we used computer graphics to examine whether the β-hairpin region was able to bind tRNA substrates with different accepter stem lengths when the 5′-end was properly placed in the reaction site. RESULTS | |
| 78 87 β-hairpin structure_element To confirm this speculation, we used computer graphics to examine whether the β-hairpin region was able to bind tRNA substrates with different accepter stem lengths when the 5′-end was properly placed in the reaction site. RESULTS | |
| 112 116 tRNA chemical To confirm this speculation, we used computer graphics to examine whether the β-hairpin region was able to bind tRNA substrates with different accepter stem lengths when the 5′-end was properly placed in the reaction site. RESULTS | |
| 143 156 accepter stem structure_element To confirm this speculation, we used computer graphics to examine whether the β-hairpin region was able to bind tRNA substrates with different accepter stem lengths when the 5′-end was properly placed in the reaction site. RESULTS | |
| 208 221 reaction site site To confirm this speculation, we used computer graphics to examine whether the β-hairpin region was able to bind tRNA substrates with different accepter stem lengths when the 5′-end was properly placed in the reaction site. RESULTS | |
| 65 69 tRNA chemical When the 5′-end was placed in the reaction site, the body of the tRNA molecule shifted in a manner dependent on the accepter stem length. RESULTS | |
| 116 129 accepter stem structure_element When the 5′-end was placed in the reaction site, the body of the tRNA molecule shifted in a manner dependent on the accepter stem length. RESULTS | |
| 4 8 tRNA chemical The tRNA body also rotated because of the helical nature of the accepter stem (fig. S7). RESULTS | |
| 64 77 accepter stem structure_element The tRNA body also rotated because of the helical nature of the accepter stem (fig. S7). RESULTS | |
| 11 20 structure evidence This model structure showed that the accepter stem of intact tRNAPhe was too long for the β-hairpin to recognize its elbow region, whereas tRNAPheΔ1 and tRNAPheΔ1,2 were recognized by the β-hairpin region (fig. S7), which is consistent with previous experiments. RESULTS | |
| 37 50 accepter stem structure_element This model structure showed that the accepter stem of intact tRNAPhe was too long for the β-hairpin to recognize its elbow region, whereas tRNAPheΔ1 and tRNAPheΔ1,2 were recognized by the β-hairpin region (fig. S7), which is consistent with previous experiments. RESULTS | |
| 61 68 tRNAPhe chemical This model structure showed that the accepter stem of intact tRNAPhe was too long for the β-hairpin to recognize its elbow region, whereas tRNAPheΔ1 and tRNAPheΔ1,2 were recognized by the β-hairpin region (fig. S7), which is consistent with previous experiments. RESULTS | |
| 90 99 β-hairpin structure_element This model structure showed that the accepter stem of intact tRNAPhe was too long for the β-hairpin to recognize its elbow region, whereas tRNAPheΔ1 and tRNAPheΔ1,2 were recognized by the β-hairpin region (fig. S7), which is consistent with previous experiments. RESULTS | |
| 117 129 elbow region structure_element This model structure showed that the accepter stem of intact tRNAPhe was too long for the β-hairpin to recognize its elbow region, whereas tRNAPheΔ1 and tRNAPheΔ1,2 were recognized by the β-hairpin region (fig. S7), which is consistent with previous experiments. RESULTS | |
| 139 148 tRNAPheΔ1 chemical This model structure showed that the accepter stem of intact tRNAPhe was too long for the β-hairpin to recognize its elbow region, whereas tRNAPheΔ1 and tRNAPheΔ1,2 were recognized by the β-hairpin region (fig. S7), which is consistent with previous experiments. RESULTS | |
| 153 164 tRNAPheΔ1,2 chemical This model structure showed that the accepter stem of intact tRNAPhe was too long for the β-hairpin to recognize its elbow region, whereas tRNAPheΔ1 and tRNAPheΔ1,2 were recognized by the β-hairpin region (fig. S7), which is consistent with previous experiments. RESULTS | |
| 188 197 β-hairpin structure_element This model structure showed that the accepter stem of intact tRNAPhe was too long for the β-hairpin to recognize its elbow region, whereas tRNAPheΔ1 and tRNAPheΔ1,2 were recognized by the β-hairpin region (fig. S7), which is consistent with previous experiments. RESULTS | |
| 28 38 structures evidence On the basis of these model structures, we concluded that the TLP molecule can properly terminate elongation by measuring the accepter stem length of tRNA substrates. RESULTS | |
| 62 65 TLP protein_type On the basis of these model structures, we concluded that the TLP molecule can properly terminate elongation by measuring the accepter stem length of tRNA substrates. RESULTS | |
| 126 139 accepter stem structure_element On the basis of these model structures, we concluded that the TLP molecule can properly terminate elongation by measuring the accepter stem length of tRNA substrates. RESULTS | |
| 150 154 tRNA chemical On the basis of these model structures, we concluded that the TLP molecule can properly terminate elongation by measuring the accepter stem length of tRNA substrates. RESULTS | |
| 22 26 tRNA chemical Dual binding mode for tRNA repair RESULTS | |
| 12 31 structural analysis experimental_method The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer. RESULTS | |
| 55 58 TLP protein_type The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer. RESULTS | |
| 63 67 Thg1 protein The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer. RESULTS | |
| 83 93 tetrameric oligomeric_state The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer. RESULTS | |
| 146 151 tRNAs chemical The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer. RESULTS | |
| 153 157 Thg1 protein The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer. RESULTS | |
| 161 169 bound to protein_state The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer. RESULTS | |
| 170 177 tRNAHis chemical The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer. RESULTS | |
| 183 191 tetramer oligomeric_state The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer. RESULTS | |
| 201 204 TLP protein_type The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer. RESULTS | |
| 208 216 bound to protein_state The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer. RESULTS | |
| 217 224 tRNAPhe chemical The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer. RESULTS | |
| 230 235 dimer oligomeric_state The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer. RESULTS | |
| 23 27 tRNA chemical This difference in the tRNA binding modes is closely related to their enzymatic functions. RESULTS | |
| 4 40 tRNAHis-specific G−1 addition enzyme protein_type The tRNAHis-specific G−1 addition enzyme Thg1 needs to recognize both the accepter stem and anticodon of tRNAHis. RESULTS | |
| 41 45 Thg1 protein The tRNAHis-specific G−1 addition enzyme Thg1 needs to recognize both the accepter stem and anticodon of tRNAHis. RESULTS | |
| 74 87 accepter stem structure_element The tRNAHis-specific G−1 addition enzyme Thg1 needs to recognize both the accepter stem and anticodon of tRNAHis. RESULTS | |
| 92 101 anticodon structure_element The tRNAHis-specific G−1 addition enzyme Thg1 needs to recognize both the accepter stem and anticodon of tRNAHis. RESULTS | |
| 105 112 tRNAHis chemical The tRNAHis-specific G−1 addition enzyme Thg1 needs to recognize both the accepter stem and anticodon of tRNAHis. RESULTS | |
| 4 14 tetrameric oligomeric_state The tetrameric architecture of the Thg1 molecule allows it to access both regions located at the opposite side of the tRNA molecule [the AB dimer recognizes the accepter stem and CD dimer anticodon ]. RESULTS | |
| 35 39 Thg1 protein The tetrameric architecture of the Thg1 molecule allows it to access both regions located at the opposite side of the tRNA molecule [the AB dimer recognizes the accepter stem and CD dimer anticodon ]. RESULTS | |
| 118 122 tRNA chemical The tetrameric architecture of the Thg1 molecule allows it to access both regions located at the opposite side of the tRNA molecule [the AB dimer recognizes the accepter stem and CD dimer anticodon ]. RESULTS | |
| 137 139 AB structure_element The tetrameric architecture of the Thg1 molecule allows it to access both regions located at the opposite side of the tRNA molecule [the AB dimer recognizes the accepter stem and CD dimer anticodon ]. RESULTS | |
| 140 145 dimer oligomeric_state The tetrameric architecture of the Thg1 molecule allows it to access both regions located at the opposite side of the tRNA molecule [the AB dimer recognizes the accepter stem and CD dimer anticodon ]. RESULTS | |
| 161 174 accepter stem structure_element The tetrameric architecture of the Thg1 molecule allows it to access both regions located at the opposite side of the tRNA molecule [the AB dimer recognizes the accepter stem and CD dimer anticodon ]. RESULTS | |
| 179 181 CD structure_element The tetrameric architecture of the Thg1 molecule allows it to access both regions located at the opposite side of the tRNA molecule [the AB dimer recognizes the accepter stem and CD dimer anticodon ]. RESULTS | |
| 182 187 dimer oligomeric_state The tetrameric architecture of the Thg1 molecule allows it to access both regions located at the opposite side of the tRNA molecule [the AB dimer recognizes the accepter stem and CD dimer anticodon ]. RESULTS | |
| 33 36 TLP protein_type In contrast, the binding mode of TLP corresponds to the anticodon-independent repair reactions of 5′-truncated general tRNAs. RESULTS | |
| 119 124 tRNAs chemical In contrast, the binding mode of TLP corresponds to the anticodon-independent repair reactions of 5′-truncated general tRNAs. RESULTS | |
| 131 144 accepter stem structure_element This binding mode is also suitable for the correct termination of the elongation or repair reaction by measuring the length of the accepter stem by the flexible β-hairpin. RESULTS | |
| 152 160 flexible protein_state This binding mode is also suitable for the correct termination of the elongation or repair reaction by measuring the length of the accepter stem by the flexible β-hairpin. RESULTS | |
| 161 170 β-hairpin structure_element This binding mode is also suitable for the correct termination of the elongation or repair reaction by measuring the length of the accepter stem by the flexible β-hairpin. RESULTS | |
| 8 15 tRNAHis chemical Because tRNAHis requires an extra guanosine (G−1) at the 5′-end, the repair enzyme has to extend the 5′-end by one more nucleotide than other tRNAs. RESULTS | |
| 34 43 guanosine chemical Because tRNAHis requires an extra guanosine (G−1) at the 5′-end, the repair enzyme has to extend the 5′-end by one more nucleotide than other tRNAs. RESULTS | |
| 45 48 G−1 residue_name_number Because tRNAHis requires an extra guanosine (G−1) at the 5′-end, the repair enzyme has to extend the 5′-end by one more nucleotide than other tRNAs. RESULTS | |
| 142 147 tRNAs chemical Because tRNAHis requires an extra guanosine (G−1) at the 5′-end, the repair enzyme has to extend the 5′-end by one more nucleotide than other tRNAs. RESULTS | |
| 0 3 TLP protein_type TLP has been shown to confer such catalytic activity on tRNAHisΔ−1 (Fig. 4B). RESULTS | |
| 56 66 tRNAHisΔ−1 chemical TLP has been shown to confer such catalytic activity on tRNAHisΔ−1 (Fig. 4B). RESULTS | |
| 25 28 TLP protein_type Here, we showed that the TLP mutants, wherein the β-hairpin is truncated and tRNAPheΔ1 binding ability is lost, can still bind to tRNAPhe (GUG) whose anticodon is changed to that for His (fig. S6, C, H, and I). RESULTS | |
| 29 36 mutants protein_state Here, we showed that the TLP mutants, wherein the β-hairpin is truncated and tRNAPheΔ1 binding ability is lost, can still bind to tRNAPhe (GUG) whose anticodon is changed to that for His (fig. S6, C, H, and I). RESULTS | |
| 50 59 β-hairpin structure_element Here, we showed that the TLP mutants, wherein the β-hairpin is truncated and tRNAPheΔ1 binding ability is lost, can still bind to tRNAPhe (GUG) whose anticodon is changed to that for His (fig. S6, C, H, and I). RESULTS | |
| 63 72 truncated protein_state Here, we showed that the TLP mutants, wherein the β-hairpin is truncated and tRNAPheΔ1 binding ability is lost, can still bind to tRNAPhe (GUG) whose anticodon is changed to that for His (fig. S6, C, H, and I). RESULTS | |
| 77 86 tRNAPheΔ1 chemical Here, we showed that the TLP mutants, wherein the β-hairpin is truncated and tRNAPheΔ1 binding ability is lost, can still bind to tRNAPhe (GUG) whose anticodon is changed to that for His (fig. S6, C, H, and I). RESULTS | |
| 130 137 tRNAPhe chemical Here, we showed that the TLP mutants, wherein the β-hairpin is truncated and tRNAPheΔ1 binding ability is lost, can still bind to tRNAPhe (GUG) whose anticodon is changed to that for His (fig. S6, C, H, and I). RESULTS | |
| 139 142 GUG chemical Here, we showed that the TLP mutants, wherein the β-hairpin is truncated and tRNAPheΔ1 binding ability is lost, can still bind to tRNAPhe (GUG) whose anticodon is changed to that for His (fig. S6, C, H, and I). RESULTS | |
| 183 186 His residue_name Here, we showed that the TLP mutants, wherein the β-hairpin is truncated and tRNAPheΔ1 binding ability is lost, can still bind to tRNAPhe (GUG) whose anticodon is changed to that for His (fig. S6, C, H, and I). RESULTS | |
| 17 24 tRNAPhe chemical Also, the intact tRNAPhe, which is not recognized by TLP (Fig. 4B and fig. S6E), can be recognized when its anticodon is changed to that for His (fig. S6D). RESULTS | |
| 53 56 TLP protein_type Also, the intact tRNAPhe, which is not recognized by TLP (Fig. 4B and fig. S6E), can be recognized when its anticodon is changed to that for His (fig. S6D). RESULTS | |
| 141 144 His residue_name Also, the intact tRNAPhe, which is not recognized by TLP (Fig. 4B and fig. S6E), can be recognized when its anticodon is changed to that for His (fig. S6D). RESULTS | |
| 17 20 TLP protein_type Furthermore, the TLP variant (F174A/N179A/R188A) whose anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] is disrupted has been shown to have a reduced catalytic activity to tRNAHisΔ−1 (Fig. 4B). RESULTS | |
| 21 28 variant protein_state Furthermore, the TLP variant (F174A/N179A/R188A) whose anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] is disrupted has been shown to have a reduced catalytic activity to tRNAHisΔ−1 (Fig. 4B). RESULTS | |
| 30 35 F174A mutant Furthermore, the TLP variant (F174A/N179A/R188A) whose anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] is disrupted has been shown to have a reduced catalytic activity to tRNAHisΔ−1 (Fig. 4B). RESULTS | |
| 36 41 N179A mutant Furthermore, the TLP variant (F174A/N179A/R188A) whose anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] is disrupted has been shown to have a reduced catalytic activity to tRNAHisΔ−1 (Fig. 4B). RESULTS | |
| 42 47 R188A mutant Furthermore, the TLP variant (F174A/N179A/R188A) whose anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] is disrupted has been shown to have a reduced catalytic activity to tRNAHisΔ−1 (Fig. 4B). RESULTS | |
| 55 81 anticodon recognition site site Furthermore, the TLP variant (F174A/N179A/R188A) whose anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] is disrupted has been shown to have a reduced catalytic activity to tRNAHisΔ−1 (Fig. 4B). RESULTS | |
| 100 112 Thg1-tRNAHis complex_assembly Furthermore, the TLP variant (F174A/N179A/R188A) whose anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] is disrupted has been shown to have a reduced catalytic activity to tRNAHisΔ−1 (Fig. 4B). RESULTS | |
| 121 130 structure evidence Furthermore, the TLP variant (F174A/N179A/R188A) whose anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] is disrupted has been shown to have a reduced catalytic activity to tRNAHisΔ−1 (Fig. 4B). RESULTS | |
| 201 211 tRNAHisΔ−1 chemical Furthermore, the TLP variant (F174A/N179A/R188A) whose anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] is disrupted has been shown to have a reduced catalytic activity to tRNAHisΔ−1 (Fig. 4B). RESULTS | |
| 45 48 TLP protein_type All these experimental results indicate that TLP recognizes and binds tRNAs carrying the His anticodon in the same way that Thg1 recognizes tRNAHis. RESULTS | |
| 70 75 tRNAs chemical All these experimental results indicate that TLP recognizes and binds tRNAs carrying the His anticodon in the same way that Thg1 recognizes tRNAHis. RESULTS | |
| 89 92 His residue_name All these experimental results indicate that TLP recognizes and binds tRNAs carrying the His anticodon in the same way that Thg1 recognizes tRNAHis. RESULTS | |
| 124 128 Thg1 protein All these experimental results indicate that TLP recognizes and binds tRNAs carrying the His anticodon in the same way that Thg1 recognizes tRNAHis. RESULTS | |
| 140 147 tRNAHis chemical All these experimental results indicate that TLP recognizes and binds tRNAs carrying the His anticodon in the same way that Thg1 recognizes tRNAHis. RESULTS | |
| 24 27 TLP protein_type Thus, we concluded that TLP has two tRNA binding modes that are selectively used, depending on both the length of the accepter stem and the anticodon. RESULTS | |
| 36 40 tRNA chemical Thus, we concluded that TLP has two tRNA binding modes that are selectively used, depending on both the length of the accepter stem and the anticodon. RESULTS | |
| 118 131 accepter stem structure_element Thus, we concluded that TLP has two tRNA binding modes that are selectively used, depending on both the length of the accepter stem and the anticodon. RESULTS | |
| 140 149 anticodon structure_element Thus, we concluded that TLP has two tRNA binding modes that are selectively used, depending on both the length of the accepter stem and the anticodon. RESULTS | |
| 103 106 His residue_name The elongation or repair reaction normally terminates when the 5′-end reaches position 1, but when the His anticodon is present, TLP binds the tRNA in the second mode by recognizing the anticodon to execute the G−1 addition reaction. RESULTS | |
| 129 132 TLP protein_type The elongation or repair reaction normally terminates when the 5′-end reaches position 1, but when the His anticodon is present, TLP binds the tRNA in the second mode by recognizing the anticodon to execute the G−1 addition reaction. RESULTS | |
| 143 147 tRNA chemical The elongation or repair reaction normally terminates when the 5′-end reaches position 1, but when the His anticodon is present, TLP binds the tRNA in the second mode by recognizing the anticodon to execute the G−1 addition reaction. RESULTS | |
| 211 214 G−1 residue_name_number The elongation or repair reaction normally terminates when the 5′-end reaches position 1, but when the His anticodon is present, TLP binds the tRNA in the second mode by recognizing the anticodon to execute the G−1 addition reaction. RESULTS | |
| 39 42 TLP protein_type By having two different binding modes, TLP can manage this special feature of tRNAHis. RESULTS | |
| 78 85 tRNAHis chemical By having two different binding modes, TLP can manage this special feature of tRNAHis. RESULTS | |
| 4 8 Thg1 protein The Thg1/TLP family of proteins extends tRNA chains in the 3′-5′ direction. DISCUSS | |
| 9 12 TLP protein_type The Thg1/TLP family of proteins extends tRNA chains in the 3′-5′ direction. DISCUSS | |
| 40 44 tRNA chemical The Thg1/TLP family of proteins extends tRNA chains in the 3′-5′ direction. DISCUSS | |
| 11 23 5′-phosphate chemical First, the 5′-phosphate is activated by GTP/ATP. DISCUSS | |
| 40 43 GTP chemical First, the 5′-phosphate is activated by GTP/ATP. DISCUSS | |
| 44 47 ATP chemical First, the 5′-phosphate is activated by GTP/ATP. DISCUSS | |
| 20 29 phosphate chemical Then, the activated phosphate is attacked by the incoming nucleotide, resulting in an extension by one nucleotide at the 5′-end. DISCUSS | |
| 22 28 solved experimental_method Here, we successfully solved for the first time the intermediate structures of the template-dependent 3′-5′ elongation complex of MaTLP. DISCUSS | |
| 65 75 structures evidence Here, we successfully solved for the first time the intermediate structures of the template-dependent 3′-5′ elongation complex of MaTLP. DISCUSS | |
| 130 135 MaTLP protein Here, we successfully solved for the first time the intermediate structures of the template-dependent 3′-5′ elongation complex of MaTLP. DISCUSS | |
| 22 32 structures evidence On the basis of these structures, we will discuss the 3′-5′ addition reaction compared with canonical 5′-3′ elongation by DNA/RNA polymerases. DISCUSS | |
| 122 141 DNA/RNA polymerases protein_type On the basis of these structures, we will discuss the 3′-5′ addition reaction compared with canonical 5′-3′ elongation by DNA/RNA polymerases. DISCUSS | |
| 66 69 TLP protein_type Figure 5 is a schematic diagram of the 3′-5′ addition reaction of TLP. DISCUSS | |
| 20 46 triphosphate binding sites site This enzyme has two triphosphate binding sites and one reaction center at the position overlapping these two binding sites (Fig. 5A). DISCUSS | |
| 55 70 reaction center site This enzyme has two triphosphate binding sites and one reaction center at the position overlapping these two binding sites (Fig. 5A). DISCUSS | |
| 109 122 binding sites site This enzyme has two triphosphate binding sites and one reaction center at the position overlapping these two binding sites (Fig. 5A). DISCUSS | |
| 35 38 GTP chemical In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C). DISCUSS | |
| 39 42 ATP chemical In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C). DISCUSS | |
| 46 54 bound to protein_state In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C). DISCUSS | |
| 55 61 site 1 site In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C). DISCUSS | |
| 77 89 5′-phosphate chemical In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C). DISCUSS | |
| 97 101 tRNA chemical In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C). DISCUSS | |
| 121 125 Mg2+ chemical In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C). DISCUSS | |
| 145 154 phosphate chemical In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C). DISCUSS | |
| 162 165 GTP chemical In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C). DISCUSS | |
| 166 169 ATP chemical In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C). DISCUSS | |
| 4 13 structure evidence The structure of the MaTLP-ppptRNAPheΔ1 complex, wherein β- and γ-phosphates coordinate with Mg2+A and Mg2+B, respectively (Figs. 3A and 5C′), may represent this activated intermediate. DISCUSS | |
| 21 39 MaTLP-ppptRNAPheΔ1 complex_assembly The structure of the MaTLP-ppptRNAPheΔ1 complex, wherein β- and γ-phosphates coordinate with Mg2+A and Mg2+B, respectively (Figs. 3A and 5C′), may represent this activated intermediate. DISCUSS | |
| 66 76 phosphates chemical The structure of the MaTLP-ppptRNAPheΔ1 complex, wherein β- and γ-phosphates coordinate with Mg2+A and Mg2+B, respectively (Figs. 3A and 5C′), may represent this activated intermediate. DISCUSS | |
| 77 92 coordinate with bond_interaction The structure of the MaTLP-ppptRNAPheΔ1 complex, wherein β- and γ-phosphates coordinate with Mg2+A and Mg2+B, respectively (Figs. 3A and 5C′), may represent this activated intermediate. DISCUSS | |
| 93 97 Mg2+ chemical The structure of the MaTLP-ppptRNAPheΔ1 complex, wherein β- and γ-phosphates coordinate with Mg2+A and Mg2+B, respectively (Figs. 3A and 5C′), may represent this activated intermediate. DISCUSS | |
| 103 107 Mg2+ chemical The structure of the MaTLP-ppptRNAPheΔ1 complex, wherein β- and γ-phosphates coordinate with Mg2+A and Mg2+B, respectively (Figs. 3A and 5C′), may represent this activated intermediate. DISCUSS | |
| 34 44 nucleotide chemical Subsequent binding of an incoming nucleotide to site 2 followed by formation of the Watson-Crick base pair with a nucleotide in the template strand conveys the 3′-OH of the incoming nucleotide to the position of deprotonation by Mg2+A and the 5′-triphosphate of the tRNA to the reaction center (Figs. 3B and 5D). DISCUSS | |
| 48 54 site 2 site Subsequent binding of an incoming nucleotide to site 2 followed by formation of the Watson-Crick base pair with a nucleotide in the template strand conveys the 3′-OH of the incoming nucleotide to the position of deprotonation by Mg2+A and the 5′-triphosphate of the tRNA to the reaction center (Figs. 3B and 5D). DISCUSS | |
| 84 106 Watson-Crick base pair bond_interaction Subsequent binding of an incoming nucleotide to site 2 followed by formation of the Watson-Crick base pair with a nucleotide in the template strand conveys the 3′-OH of the incoming nucleotide to the position of deprotonation by Mg2+A and the 5′-triphosphate of the tRNA to the reaction center (Figs. 3B and 5D). DISCUSS | |
| 114 124 nucleotide chemical Subsequent binding of an incoming nucleotide to site 2 followed by formation of the Watson-Crick base pair with a nucleotide in the template strand conveys the 3′-OH of the incoming nucleotide to the position of deprotonation by Mg2+A and the 5′-triphosphate of the tRNA to the reaction center (Figs. 3B and 5D). DISCUSS | |
| 182 192 nucleotide chemical Subsequent binding of an incoming nucleotide to site 2 followed by formation of the Watson-Crick base pair with a nucleotide in the template strand conveys the 3′-OH of the incoming nucleotide to the position of deprotonation by Mg2+A and the 5′-triphosphate of the tRNA to the reaction center (Figs. 3B and 5D). DISCUSS | |
| 229 233 Mg2+ chemical Subsequent binding of an incoming nucleotide to site 2 followed by formation of the Watson-Crick base pair with a nucleotide in the template strand conveys the 3′-OH of the incoming nucleotide to the position of deprotonation by Mg2+A and the 5′-triphosphate of the tRNA to the reaction center (Figs. 3B and 5D). DISCUSS | |
| 243 258 5′-triphosphate chemical Subsequent binding of an incoming nucleotide to site 2 followed by formation of the Watson-Crick base pair with a nucleotide in the template strand conveys the 3′-OH of the incoming nucleotide to the position of deprotonation by Mg2+A and the 5′-triphosphate of the tRNA to the reaction center (Figs. 3B and 5D). DISCUSS | |
| 266 270 tRNA chemical Subsequent binding of an incoming nucleotide to site 2 followed by formation of the Watson-Crick base pair with a nucleotide in the template strand conveys the 3′-OH of the incoming nucleotide to the position of deprotonation by Mg2+A and the 5′-triphosphate of the tRNA to the reaction center (Figs. 3B and 5D). DISCUSS | |
| 278 293 reaction center site Subsequent binding of an incoming nucleotide to site 2 followed by formation of the Watson-Crick base pair with a nucleotide in the template strand conveys the 3′-OH of the incoming nucleotide to the position of deprotonation by Mg2+A and the 5′-triphosphate of the tRNA to the reaction center (Figs. 3B and 5D). DISCUSS | |
| 18 27 structure evidence Thus, the present structure shows that this 3′-5′ elongation enzyme utilizes a reaction center homologous to that of 5′-3′ elongation enzymes for both activation and elongation in a stepwise fashion. DISCUSS | |
| 44 67 3′-5′ elongation enzyme protein_type Thus, the present structure shows that this 3′-5′ elongation enzyme utilizes a reaction center homologous to that of 5′-3′ elongation enzymes for both activation and elongation in a stepwise fashion. DISCUSS | |
| 79 94 reaction center site Thus, the present structure shows that this 3′-5′ elongation enzyme utilizes a reaction center homologous to that of 5′-3′ elongation enzymes for both activation and elongation in a stepwise fashion. DISCUSS | |
| 117 141 5′-3′ elongation enzymes protein_type Thus, the present structure shows that this 3′-5′ elongation enzyme utilizes a reaction center homologous to that of 5′-3′ elongation enzymes for both activation and elongation in a stepwise fashion. DISCUSS | |
| 24 27 TLP protein_type It should be noted that TLP has evolved to allow the occurrence of these two elaborate reaction steps within one reaction center. DISCUSS | |
| 113 128 reaction center site It should be noted that TLP has evolved to allow the occurrence of these two elaborate reaction steps within one reaction center. DISCUSS | |
| 8 23 reaction center site (A) The reaction center overlapped with two triphosphate binding sites. FIG | |
| 44 70 triphosphate binding sites site (A) The reaction center overlapped with two triphosphate binding sites. FIG | |
| 33 46 binding sites site A, B, and C (in green) represent binding sites for Mg2+A, Mg2+B, and Mg2+C. P (in blue) represents the phosphate binding sites; O− (in red) is the binding site for the deprotonated OH group. FIG | |
| 51 55 Mg2+ chemical A, B, and C (in green) represent binding sites for Mg2+A, Mg2+B, and Mg2+C. P (in blue) represents the phosphate binding sites; O− (in red) is the binding site for the deprotonated OH group. FIG | |
| 58 62 Mg2+ chemical A, B, and C (in green) represent binding sites for Mg2+A, Mg2+B, and Mg2+C. P (in blue) represents the phosphate binding sites; O− (in red) is the binding site for the deprotonated OH group. FIG | |
| 69 73 Mg2+ chemical A, B, and C (in green) represent binding sites for Mg2+A, Mg2+B, and Mg2+C. P (in blue) represents the phosphate binding sites; O− (in red) is the binding site for the deprotonated OH group. FIG | |
| 76 77 P site A, B, and C (in green) represent binding sites for Mg2+A, Mg2+B, and Mg2+C. P (in blue) represents the phosphate binding sites; O− (in red) is the binding site for the deprotonated OH group. FIG | |
| 103 126 phosphate binding sites site A, B, and C (in green) represent binding sites for Mg2+A, Mg2+B, and Mg2+C. P (in blue) represents the phosphate binding sites; O− (in red) is the binding site for the deprotonated OH group. FIG | |
| 147 159 binding site site A, B, and C (in green) represent binding sites for Mg2+A, Mg2+B, and Mg2+C. P (in blue) represents the phosphate binding sites; O− (in red) is the binding site for the deprotonated OH group. FIG | |
| 10 13 TLP protein_type Important TLP residues for tRNA and Mg2+ binding are also shown. (B) Structure of the activation complex (corresponding to fig. S8). FIG | |
| 27 31 tRNA chemical Important TLP residues for tRNA and Mg2+ binding are also shown. (B) Structure of the activation complex (corresponding to fig. S8). FIG | |
| 36 40 Mg2+ chemical Important TLP residues for tRNA and Mg2+ binding are also shown. (B) Structure of the activation complex (corresponding to fig. S8). FIG | |
| 69 78 Structure evidence Important TLP residues for tRNA and Mg2+ binding are also shown. (B) Structure of the activation complex (corresponding to fig. S8). FIG | |
| 0 3 GTP chemical GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′). FIG | |
| 4 7 ATP chemical GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′). FIG | |
| 17 44 triphosphate binding site 1 site GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′). FIG | |
| 79 91 5′-phosphate chemical GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′). FIG | |
| 106 115 phosphate chemical GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′). FIG | |
| 119 122 GTP chemical GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′). FIG | |
| 123 126 ATP chemical GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′). FIG | |
| 132 135 PPi chemical GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′). FIG | |
| 137 160 inorganic pyrophosphate chemical GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′). FIG | |
| 188 197 structure evidence GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′). FIG | |
| 246 255 structure evidence GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′). FIG | |
| 5 14 Structure evidence (C′) Structure before the elongation reaction (corresponding to Fig. 3A). FIG | |
| 4 19 5′-triphosphate chemical The 5′-triphosphate of the tRNA binds to the same site as for activation of the 5′-terminus of the tRNA in (B). FIG | |
| 27 31 tRNA chemical The 5′-triphosphate of the tRNA binds to the same site as for activation of the 5′-terminus of the tRNA in (B). FIG | |
| 99 103 tRNA chemical The 5′-triphosphate of the tRNA binds to the same site as for activation of the 5′-terminus of the tRNA in (B). FIG | |
| 4 13 Structure evidence (D) Structure of initiation of the elongation reaction (corresponding to Fig. 3B). FIG | |
| 25 28 GTP chemical The base of the incoming GTP forms a Watson-Crick hydrogen bond with the nucleotide at position 72 in the template chain and a base-stacking interaction with a neighboring base (G2). FIG | |
| 37 63 Watson-Crick hydrogen bond bond_interaction The base of the incoming GTP forms a Watson-Crick hydrogen bond with the nucleotide at position 72 in the template chain and a base-stacking interaction with a neighboring base (G2). FIG | |
| 73 83 nucleotide chemical The base of the incoming GTP forms a Watson-Crick hydrogen bond with the nucleotide at position 72 in the template chain and a base-stacking interaction with a neighboring base (G2). FIG | |
| 96 98 72 residue_number The base of the incoming GTP forms a Watson-Crick hydrogen bond with the nucleotide at position 72 in the template chain and a base-stacking interaction with a neighboring base (G2). FIG | |
| 127 152 base-stacking interaction bond_interaction The base of the incoming GTP forms a Watson-Crick hydrogen bond with the nucleotide at position 72 in the template chain and a base-stacking interaction with a neighboring base (G2). FIG | |
| 178 180 G2 residue_name_number The base of the incoming GTP forms a Watson-Crick hydrogen bond with the nucleotide at position 72 in the template chain and a base-stacking interaction with a neighboring base (G2). FIG | |
| 45 60 5′-triphosphate chemical Movement of the 5′-terminal chain leaves the 5′-triphosphate of the tRNA in the same site as the activation step in (B). FIG | |
| 68 72 tRNA chemical Movement of the 5′-terminal chain leaves the 5′-triphosphate of the tRNA in the same site as the activation step in (B). FIG | |
| 26 29 GTP chemical The 3′-OH of the incoming GTP is deprotonated by Mg2+A and attacks the α-phosphate to form a covalent bond. (E) After the elongation reaction, the triphosphate of the new nucleotide is placed on site 1, as in (C′), and is ready for the next reaction. FIG | |
| 49 53 Mg2+ chemical The 3′-OH of the incoming GTP is deprotonated by Mg2+A and attacks the α-phosphate to form a covalent bond. (E) After the elongation reaction, the triphosphate of the new nucleotide is placed on site 1, as in (C′), and is ready for the next reaction. FIG | |
| 73 82 phosphate chemical The 3′-OH of the incoming GTP is deprotonated by Mg2+A and attacks the α-phosphate to form a covalent bond. (E) After the elongation reaction, the triphosphate of the new nucleotide is placed on site 1, as in (C′), and is ready for the next reaction. FIG | |
| 147 159 triphosphate chemical The 3′-OH of the incoming GTP is deprotonated by Mg2+A and attacks the α-phosphate to form a covalent bond. (E) After the elongation reaction, the triphosphate of the new nucleotide is placed on site 1, as in (C′), and is ready for the next reaction. FIG | |
| 171 181 nucleotide chemical The 3′-OH of the incoming GTP is deprotonated by Mg2+A and attacks the α-phosphate to form a covalent bond. (E) After the elongation reaction, the triphosphate of the new nucleotide is placed on site 1, as in (C′), and is ready for the next reaction. FIG | |
| 195 201 site 1 site The 3′-OH of the incoming GTP is deprotonated by Mg2+A and attacks the α-phosphate to form a covalent bond. (E) After the elongation reaction, the triphosphate of the new nucleotide is placed on site 1, as in (C′), and is ready for the next reaction. FIG | |
| 137 152 reaction center site Figure 6 compares the 3′-5′ and 5′-3′ elongation mechanisms, showing the symmetrical nature of both elongation reactions using a similar reaction center composed of Mg2+A and Mg2+B in the conserved catalytic core. DISCUSS | |
| 165 169 Mg2+ chemical Figure 6 compares the 3′-5′ and 5′-3′ elongation mechanisms, showing the symmetrical nature of both elongation reactions using a similar reaction center composed of Mg2+A and Mg2+B in the conserved catalytic core. DISCUSS | |
| 175 179 Mg2+ chemical Figure 6 compares the 3′-5′ and 5′-3′ elongation mechanisms, showing the symmetrical nature of both elongation reactions using a similar reaction center composed of Mg2+A and Mg2+B in the conserved catalytic core. DISCUSS | |
| 188 197 conserved protein_state Figure 6 compares the 3′-5′ and 5′-3′ elongation mechanisms, showing the symmetrical nature of both elongation reactions using a similar reaction center composed of Mg2+A and Mg2+B in the conserved catalytic core. DISCUSS | |
| 198 212 catalytic core site Figure 6 compares the 3′-5′ and 5′-3′ elongation mechanisms, showing the symmetrical nature of both elongation reactions using a similar reaction center composed of Mg2+A and Mg2+B in the conserved catalytic core. DISCUSS | |
| 3 6 TLP protein_type In TLP, which carries out 3′-5′ elongation, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the T7 RNA polymerase, a representative 5′-3′ DNA/RNA polymerase, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond. DISCUSS | |
| 106 115 phosphate chemical In TLP, which carries out 3′-5′ elongation, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the T7 RNA polymerase, a representative 5′-3′ DNA/RNA polymerase, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond. DISCUSS | |
| 123 127 tRNA chemical In TLP, which carries out 3′-5′ elongation, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the T7 RNA polymerase, a representative 5′-3′ DNA/RNA polymerase, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond. DISCUSS | |
| 174 191 T7 RNA polymerase protein In TLP, which carries out 3′-5′ elongation, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the T7 RNA polymerase, a representative 5′-3′ DNA/RNA polymerase, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond. DISCUSS | |
| 210 234 5′-3′ DNA/RNA polymerase protein_type In TLP, which carries out 3′-5′ elongation, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the T7 RNA polymerase, a representative 5′-3′ DNA/RNA polymerase, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond. DISCUSS | |
| 283 286 RNA chemical In TLP, which carries out 3′-5′ elongation, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the T7 RNA polymerase, a representative 5′-3′ DNA/RNA polymerase, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond. DISCUSS | |
| 309 318 phosphate chemical In TLP, which carries out 3′-5′ elongation, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the T7 RNA polymerase, a representative 5′-3′ DNA/RNA polymerase, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond. DISCUSS | |
| 41 43 Mg chemical In these reactions, the roles of the two Mg ions are identical. DISCUSS | |
| 0 4 Mg2+ chemical Mg2+A activates the 3′-OH of the incoming nucleotide in TLP and the 3′-OH of the 3′-end of the RNA chain in T7 RNA polymerase. DISCUSS | |
| 56 59 TLP protein_type Mg2+A activates the 3′-OH of the incoming nucleotide in TLP and the 3′-OH of the 3′-end of the RNA chain in T7 RNA polymerase. DISCUSS | |
| 95 98 RNA chemical Mg2+A activates the 3′-OH of the incoming nucleotide in TLP and the 3′-OH of the 3′-end of the RNA chain in T7 RNA polymerase. DISCUSS | |
| 108 125 T7 RNA polymerase protein Mg2+A activates the 3′-OH of the incoming nucleotide in TLP and the 3′-OH of the 3′-end of the RNA chain in T7 RNA polymerase. DISCUSS | |
| 12 16 Mg2+ chemical The role of Mg2+B is to position the 5′-triphosphate of the tRNA in TLP and the incoming nucleotide in T7 RNA polymerase. DISCUSS | |
| 37 52 5′-triphosphate chemical The role of Mg2+B is to position the 5′-triphosphate of the tRNA in TLP and the incoming nucleotide in T7 RNA polymerase. DISCUSS | |
| 60 64 tRNA chemical The role of Mg2+B is to position the 5′-triphosphate of the tRNA in TLP and the incoming nucleotide in T7 RNA polymerase. DISCUSS | |
| 68 71 TLP protein_type The role of Mg2+B is to position the 5′-triphosphate of the tRNA in TLP and the incoming nucleotide in T7 RNA polymerase. DISCUSS | |
| 103 120 T7 RNA polymerase protein The role of Mg2+B is to position the 5′-triphosphate of the tRNA in TLP and the incoming nucleotide in T7 RNA polymerase. DISCUSS | |
| 10 14 Mg2+ chemical These two Mg2+ ions are coordinated by a conserved Asp (D21 and D69 in TLP) in the conserved catalytic core. DISCUSS | |
| 24 38 coordinated by bond_interaction These two Mg2+ ions are coordinated by a conserved Asp (D21 and D69 in TLP) in the conserved catalytic core. DISCUSS | |
| 41 50 conserved protein_state These two Mg2+ ions are coordinated by a conserved Asp (D21 and D69 in TLP) in the conserved catalytic core. DISCUSS | |
| 51 54 Asp residue_name These two Mg2+ ions are coordinated by a conserved Asp (D21 and D69 in TLP) in the conserved catalytic core. DISCUSS | |
| 56 59 D21 residue_name_number These two Mg2+ ions are coordinated by a conserved Asp (D21 and D69 in TLP) in the conserved catalytic core. DISCUSS | |
| 64 67 D69 residue_name_number These two Mg2+ ions are coordinated by a conserved Asp (D21 and D69 in TLP) in the conserved catalytic core. DISCUSS | |
| 71 74 TLP protein_type These two Mg2+ ions are coordinated by a conserved Asp (D21 and D69 in TLP) in the conserved catalytic core. DISCUSS | |
| 83 92 conserved protein_state These two Mg2+ ions are coordinated by a conserved Asp (D21 and D69 in TLP) in the conserved catalytic core. DISCUSS | |
| 93 107 catalytic core site These two Mg2+ ions are coordinated by a conserved Asp (D21 and D69 in TLP) in the conserved catalytic core. DISCUSS | |
| 0 10 Structures evidence Structures of template-dependent nucleotide elongation in the 3′-5′ and 5′-3′ directions. FIG | |
| 53 56 TLP protein_type Symmetrical relationship between 3′-5′ elongation by TLP (this study) (left) and 5′-3′ elongation by T7 RNA polymerase [Protein Data Bank (PDB) ID: 1S76] (right). FIG | |
| 101 118 T7 RNA polymerase protein Symmetrical relationship between 3′-5′ elongation by TLP (this study) (left) and 5′-3′ elongation by T7 RNA polymerase [Protein Data Bank (PDB) ID: 1S76] (right). FIG | |
| 96 105 phosphate chemical In the 3′-5′ elongation reaction, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the 5′-3′ elongation reaction, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond. FIG | |
| 113 117 tRNA chemical In the 3′-5′ elongation reaction, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the 5′-3′ elongation reaction, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond. FIG | |
| 238 241 RNA chemical In the 3′-5′ elongation reaction, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the 5′-3′ elongation reaction, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond. FIG | |
| 264 273 phosphate chemical In the 3′-5′ elongation reaction, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the 5′-3′ elongation reaction, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond. FIG | |
| 24 28 Mg2+ chemical Green spheres represent Mg2+ ions. FIG | |
| 30 34 tRNA chemical Because the chemical roles of tRNA and the incoming nucleotide are reversed in these two reactions, these two substrates are inserted into a similar reaction center from opposite directions (Fig. 6). DISCUSS | |
| 149 164 reaction center site Because the chemical roles of tRNA and the incoming nucleotide are reversed in these two reactions, these two substrates are inserted into a similar reaction center from opposite directions (Fig. 6). DISCUSS | |
| 164 183 DNA/RNA polymerases protein_type However, from an energetic viewpoint, these two reactions are clearly different: Whereas the high energy of the incoming nucleotide is used for its own addition in DNA/RNA polymerases, the high energy of the incoming nucleotide is used for subsequent addition in TLP. DISCUSS | |
| 263 266 TLP protein_type However, from an energetic viewpoint, these two reactions are clearly different: Whereas the high energy of the incoming nucleotide is used for its own addition in DNA/RNA polymerases, the high energy of the incoming nucleotide is used for subsequent addition in TLP. DISCUSS | |
| 17 20 TLP protein_type For this reason, TLP requires a mechanism that activates the 5′-terminus of the tRNA during the initial step of the reaction. DISCUSS | |
| 80 84 tRNA chemical For this reason, TLP requires a mechanism that activates the 5′-terminus of the tRNA during the initial step of the reaction. DISCUSS | |
| 110 125 reaction center site Our analysis showed that the initial activation and subsequent elongation reactions occur sequentially at one reaction center. DISCUSS | |
| 45 68 substrate binding sites site In this case, the enzyme needs to create two substrate binding sites for two different reactions in the vicinities of one reaction center. DISCUSS | |
| 122 137 reaction center site In this case, the enzyme needs to create two substrate binding sites for two different reactions in the vicinities of one reaction center. DISCUSS | |
| 0 3 TLP protein_type TLP has successfully created such sites by utilizing a conformational change in the tRNA through Watson-Crick base pairing (Fig. 3). DISCUSS | |
| 84 88 tRNA chemical TLP has successfully created such sites by utilizing a conformational change in the tRNA through Watson-Crick base pairing (Fig. 3). DISCUSS | |
| 97 122 Watson-Crick base pairing bond_interaction TLP has successfully created such sites by utilizing a conformational change in the tRNA through Watson-Crick base pairing (Fig. 3). DISCUSS | |
| 33 36 TLP protein_type These structural features of the TLP molecule suggest that development of an activation reaction site is a prerequisite for developing the 3′-5′ elongation enzyme. DISCUSS | |
| 77 101 activation reaction site site These structural features of the TLP molecule suggest that development of an activation reaction site is a prerequisite for developing the 3′-5′ elongation enzyme. DISCUSS | |
| 139 162 3′-5′ elongation enzyme protein_type These structural features of the TLP molecule suggest that development of an activation reaction site is a prerequisite for developing the 3′-5′ elongation enzyme. DISCUSS | |
| 51 74 5′-3′ elongation enzyme protein_type This is clearly more difficult than developing the 5′-3′ elongation enzyme, wherein the activation reaction site is not necessary, and which may be the primary reason why the 5′-3′ elongation enzyme has been exclusively developed. DISCUSS | |
| 88 112 activation reaction site site This is clearly more difficult than developing the 5′-3′ elongation enzyme, wherein the activation reaction site is not necessary, and which may be the primary reason why the 5′-3′ elongation enzyme has been exclusively developed. DISCUSS | |
| 175 198 5′-3′ elongation enzyme protein_type This is clearly more difficult than developing the 5′-3′ elongation enzyme, wherein the activation reaction site is not necessary, and which may be the primary reason why the 5′-3′ elongation enzyme has been exclusively developed. DISCUSS | |
| 88 91 TLP protein_type Here, we established a structural basis for 3′-5′ nucleotide elongation and showed that TLP has evolved to acquire a two-step Watson-Crick template–dependent 3′-5′ elongation reaction using the catalytic center homologous to 5′-3′ elongation enzymes. DISCUSS | |
| 194 210 catalytic center site Here, we established a structural basis for 3′-5′ nucleotide elongation and showed that TLP has evolved to acquire a two-step Watson-Crick template–dependent 3′-5′ elongation reaction using the catalytic center homologous to 5′-3′ elongation enzymes. DISCUSS | |
| 225 249 5′-3′ elongation enzymes protein_type Here, we established a structural basis for 3′-5′ nucleotide elongation and showed that TLP has evolved to acquire a two-step Watson-Crick template–dependent 3′-5′ elongation reaction using the catalytic center homologous to 5′-3′ elongation enzymes. DISCUSS | |
| 4 15 active site site The active site of this enzyme is created at the dimerization interface. DISCUSS | |
| 49 71 dimerization interface site The active site of this enzyme is created at the dimerization interface. DISCUSS | |
| 88 101 accepter stem structure_element The dimerization also endows this protein with the ability to measure the length of the accepter stem of the tRNA substrate, so that the enzyme can properly terminate the elongation reaction. DISCUSS | |
| 109 113 tRNA chemical The dimerization also endows this protein with the ability to measure the length of the accepter stem of the tRNA substrate, so that the enzyme can properly terminate the elongation reaction. DISCUSS | |
| 97 100 G−1 residue_name_number Furthermore, the dual binding mode of this protein suggests that it has further evolved to cover G−1 addition of tRNAHis by additional dimerization (dimer of dimers). DISCUSS | |
| 113 120 tRNAHis chemical Furthermore, the dual binding mode of this protein suggests that it has further evolved to cover G−1 addition of tRNAHis by additional dimerization (dimer of dimers). DISCUSS | |
| 149 154 dimer oligomeric_state Furthermore, the dual binding mode of this protein suggests that it has further evolved to cover G−1 addition of tRNAHis by additional dimerization (dimer of dimers). DISCUSS | |
| 158 164 dimers oligomeric_state Furthermore, the dual binding mode of this protein suggests that it has further evolved to cover G−1 addition of tRNAHis by additional dimerization (dimer of dimers). DISCUSS | |
| 18 37 structural analysis experimental_method Thus, the present structural analysis is consistent with the scenario in which TLP began as a 5′-end repair enzyme and evolved into a tRNAHis-specific G−1 addition enzyme. DISCUSS | |
| 79 82 TLP protein_type Thus, the present structural analysis is consistent with the scenario in which TLP began as a 5′-end repair enzyme and evolved into a tRNAHis-specific G−1 addition enzyme. DISCUSS | |
| 134 170 tRNAHis-specific G−1 addition enzyme protein_type Thus, the present structural analysis is consistent with the scenario in which TLP began as a 5′-end repair enzyme and evolved into a tRNAHis-specific G−1 addition enzyme. DISCUSS | |
| 40 44 Thg1 protein The detailed molecular mechanism of the Thg1/TLP family established by our analysis will open up new perspectives in our understanding of 3′-5′ versus 5′-3′ polymerization and the molecular evolution of template-dependent polymerases. DISCUSS | |
| 45 48 TLP protein_type The detailed molecular mechanism of the Thg1/TLP family established by our analysis will open up new perspectives in our understanding of 3′-5′ versus 5′-3′ polymerization and the molecular evolution of template-dependent polymerases. DISCUSS | |
| 203 233 template-dependent polymerases protein_type The detailed molecular mechanism of the Thg1/TLP family established by our analysis will open up new perspectives in our understanding of 3′-5′ versus 5′-3′ polymerization and the molecular evolution of template-dependent polymerases. DISCUSS | |
| 12 17 tRNAs chemical Transcribed tRNAs were purified by a HiTrap DEAE FF column (GE Healthcare) as previously described. METHODS | |
| 7 12 tRNAs chemical Pooled tRNAs were precipitated with isopropanol and dissolved in buffer E [20 mM Hepes-NaOH (pH 7.5), 100 mM NaCl, and 10 mM MgCl2]. METHODS | |
| 49 54 Thg1p protein The highly conserved tRNAHis guanylyltransferase Thg1p interacts with the origin recognition complex and is required for the G2/M phase transition in the yeast Saccharomyces cerevisiae REF | |