6JPL
The X-ray structure of yeast tRNA methyltransferase Trm7-Trm734 in complex with S-adenosyl-L-methionine
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000049 | molecular_function | tRNA binding |
| A | 0002128 | biological_process | tRNA nucleoside ribose methylation |
| A | 0002130 | biological_process | wobble position ribose methylation |
| A | 0003674 | molecular_function | molecular_function |
| A | 0005515 | molecular_function | protein binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005768 | cellular_component | endosome |
| A | 0008033 | biological_process | tRNA processing |
| A | 0030234 | molecular_function | enzyme regulator activity |
| A | 0030488 | biological_process | tRNA methylation |
| A | 0032456 | biological_process | endocytic recycling |
| B | 0001510 | biological_process | RNA methylation |
| B | 0002128 | biological_process | tRNA nucleoside ribose methylation |
| B | 0002130 | biological_process | wobble position ribose methylation |
| B | 0002181 | biological_process | cytoplasmic translation |
| B | 0005515 | molecular_function | protein binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0008033 | biological_process | tRNA processing |
| B | 0008168 | molecular_function | methyltransferase activity |
| B | 0008175 | molecular_function | tRNA methyltransferase activity |
| B | 0016423 | molecular_function | tRNA (guanine) methyltransferase activity |
| B | 0016740 | molecular_function | transferase activity |
| B | 0030488 | biological_process | tRNA methylation |
| B | 0032259 | biological_process | methylation |
| B | 0106050 | molecular_function | tRNA 2'-O-methyltransferase activity |
| B | 0106340 | molecular_function | tRNA (guanosine(34)-2'-O)-methyltransferase activity |
| B | 1904047 | molecular_function | S-adenosyl-L-methionine binding |
| C | 0000049 | molecular_function | tRNA binding |
| C | 0002128 | biological_process | tRNA nucleoside ribose methylation |
| C | 0002130 | biological_process | wobble position ribose methylation |
| C | 0003674 | molecular_function | molecular_function |
| C | 0005515 | molecular_function | protein binding |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005768 | cellular_component | endosome |
| C | 0008033 | biological_process | tRNA processing |
| C | 0030234 | molecular_function | enzyme regulator activity |
| C | 0030488 | biological_process | tRNA methylation |
| C | 0032456 | biological_process | endocytic recycling |
| D | 0001510 | biological_process | RNA methylation |
| D | 0002128 | biological_process | tRNA nucleoside ribose methylation |
| D | 0002130 | biological_process | wobble position ribose methylation |
| D | 0002181 | biological_process | cytoplasmic translation |
| D | 0005515 | molecular_function | protein binding |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005829 | cellular_component | cytosol |
| D | 0008033 | biological_process | tRNA processing |
| D | 0008168 | molecular_function | methyltransferase activity |
| D | 0008175 | molecular_function | tRNA methyltransferase activity |
| D | 0016423 | molecular_function | tRNA (guanine) methyltransferase activity |
| D | 0016740 | molecular_function | transferase activity |
| D | 0030488 | biological_process | tRNA methylation |
| D | 0032259 | biological_process | methylation |
| D | 0106050 | molecular_function | tRNA 2'-O-methyltransferase activity |
| D | 0106340 | molecular_function | tRNA (guanosine(34)-2'-O)-methyltransferase activity |
| D | 1904047 | molecular_function | S-adenosyl-L-methionine binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | binding site for residue EPE A 1101 |
| Chain | Residue |
| A | VAL521 |
| A | PHE576 |
| A | GLY580 |
| A | LYS745 |
| A | ARG746 |
| A | HOH1328 |
| site_id | AC2 |
| Number of Residues | 9 |
| Details | binding site for residue SO4 A 1102 |
| Chain | Residue |
| A | THR978 |
| A | THR979 |
| A | SER1009 |
| A | TRP1011 |
| A | HOH1246 |
| A | HOH1288 |
| A | ASP3 |
| A | HIS6 |
| A | ARG43 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 A 1103 |
| Chain | Residue |
| A | ASN577 |
| A | SER578 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 A 1104 |
| Chain | Residue |
| A | ILE945 |
| A | ASN946 |
| A | GLY947 |
| A | SER990 |
| A | LYS999 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 A 1105 |
| Chain | Residue |
| A | ASN90 |
| A | SER91 |
| A | ARG127 |
| A | LYS320 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 A 1106 |
| Chain | Residue |
| A | GLY609 |
| A | SER611 |
| A | ARG613 |
| A | LYS630 |
| A | ALA631 |
| site_id | AC7 |
| Number of Residues | 16 |
| Details | binding site for residue SAM B 401 |
| Chain | Residue |
| B | SER25 |
| B | CYS51 |
| B | ALA52 |
| B | ALA53 |
| B | PRO54 |
| B | GLY55 |
| B | SER56 |
| B | TRP57 |
| B | ASP83 |
| B | LEU84 |
| B | ILE100 |
| B | ASP124 |
| B | GLY125 |
| B | ALA126 |
| B | HOH501 |
| B | HOH514 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | binding site for residue EPE C 1101 |
| Chain | Residue |
| C | VAL521 |
| C | PHE576 |
| C | GLY580 |
| C | LYS745 |
| C | ARG746 |
| C | HOH1339 |
| site_id | AC9 |
| Number of Residues | 9 |
| Details | binding site for residue SO4 C 1102 |
| Chain | Residue |
| C | ASP3 |
| C | HIS6 |
| C | ARG43 |
| C | THR978 |
| C | THR979 |
| C | SER1009 |
| C | TRP1011 |
| C | HOH1266 |
| C | HOH1296 |
| site_id | AD1 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 C 1103 |
| Chain | Residue |
| C | ASN577 |
| C | SER578 |
| site_id | AD2 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 C 1104 |
| Chain | Residue |
| C | ASN946 |
| C | GLY947 |
| C | LYS999 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 C 1105 |
| Chain | Residue |
| C | ASN90 |
| C | SER91 |
| C | ARG127 |
| C | LYS320 |
| site_id | AD4 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 C 1106 |
| Chain | Residue |
| C | GLY609 |
| C | ALA631 |
| site_id | AD5 |
| Number of Residues | 17 |
| Details | binding site for residue SAM D 401 |
| Chain | Residue |
| D | SER25 |
| D | CYS51 |
| D | ALA52 |
| D | ALA53 |
| D | PRO54 |
| D | GLY55 |
| D | SER56 |
| D | TRP57 |
| D | ASP83 |
| D | LEU84 |
| D | GLN85 |
| D | ILE100 |
| D | ASP124 |
| D | GLY125 |
| D | ALA126 |
| D | HOH501 |
| D | HOH513 |
Functional Information from PROSITE/UniProt
| site_id | PS00678 |
| Number of Residues | 15 |
| Details | WD_REPEATS_1 Trp-Asp (WD) repeats signature. VASCsdDrSIRLWDL |
| Chain | Residue | Details |
| A | VAL194-LEU208 | |
| A | LEU236-ILE250 | |
| A | VAL951-ILE965 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 72 |
| Details | Repeat: {"description":"WD 1"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 78 |
| Details | Repeat: {"description":"WD 2"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 84 |
| Details | Repeat: {"description":"WD 3"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 78 |
| Details | Repeat: {"description":"WD 4"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 78 |
| Details | Repeat: {"description":"WD 5"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 78 |
| Details | Repeat: {"description":"WD 6"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 78 |
| Details | Repeat: {"description":"WD 7"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 78 |
| Details | Repeat: {"description":"WD 8"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 100 |
| Details | Repeat: {"description":"WD 9"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 76 |
| Details | Repeat: {"description":"WD 10"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 82 |
| Details | Repeat: {"description":"WD 12"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI12 |
| Number of Residues | 96 |
| Details | Repeat: {"description":"WD 13"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI13 |
| Number of Residues | 78 |
| Details | Repeat: {"description":"WD 14"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI14 |
| Number of Residues | 350 |
| Details | Region: {"description":"Interacts with TRM7","evidences":[{"source":"PubMed","id":"31586407","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6JP6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6JPL","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI15 |
| Number of Residues | 52 |
| Details | Region: {"description":"Required for interaction with RTT10/TRM734","evidences":[{"source":"PubMed","id":"31586407","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_03162","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI17 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"31586407","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6JPL","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI18 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_03162","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
