3RFA
X-ray structure of RlmN from Escherichia coli in complex with S-adenosylmethionine
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000049 | molecular_function | tRNA binding |
| A | 0002935 | molecular_function | tRNA (adenine(37)-C2)-methyltransferase activity |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006364 | biological_process | rRNA processing |
| A | 0008033 | biological_process | tRNA processing |
| A | 0008168 | molecular_function | methyltransferase activity |
| A | 0008173 | molecular_function | RNA methyltransferase activity |
| A | 0016740 | molecular_function | transferase activity |
| A | 0019843 | molecular_function | rRNA binding |
| A | 0030488 | biological_process | tRNA methylation |
| A | 0032259 | biological_process | methylation |
| A | 0046677 | biological_process | response to antibiotic |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0051536 | molecular_function | iron-sulfur cluster binding |
| A | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
| A | 0070040 | molecular_function | rRNA (adenine(2503)-C2-)-methyltransferase activity |
| A | 0070475 | biological_process | rRNA base methylation |
| B | 0000049 | molecular_function | tRNA binding |
| B | 0002935 | molecular_function | tRNA (adenine(37)-C2)-methyltransferase activity |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006364 | biological_process | rRNA processing |
| B | 0008033 | biological_process | tRNA processing |
| B | 0008168 | molecular_function | methyltransferase activity |
| B | 0008173 | molecular_function | RNA methyltransferase activity |
| B | 0016740 | molecular_function | transferase activity |
| B | 0019843 | molecular_function | rRNA binding |
| B | 0030488 | biological_process | tRNA methylation |
| B | 0032259 | biological_process | methylation |
| B | 0046677 | biological_process | response to antibiotic |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0051536 | molecular_function | iron-sulfur cluster binding |
| B | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
| B | 0070040 | molecular_function | rRNA (adenine(2503)-C2-)-methyltransferase activity |
| B | 0070475 | biological_process | rRNA base methylation |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SF4 B 405 |
| Chain | Residue |
| B | CYS125 |
| B | LEU127 |
| B | CYS129 |
| B | CYS132 |
| B | ALA135 |
| B | GLY179 |
| B | SER213 |
| B | SAM406 |
| site_id | AC2 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE SAM B 406 |
| Chain | Residue |
| B | MET175 |
| B | MET176 |
| B | GLY177 |
| B | GLY179 |
| B | GLU180 |
| B | SER211 |
| B | THR212 |
| B | SER233 |
| B | HIS235 |
| B | TRP311 |
| B | ASN312 |
| B | SMC355 |
| B | SF4405 |
| B | HOH427 |
| B | HOH456 |
| B | HOH494 |
| B | PHE131 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SF4 A 405 |
| Chain | Residue |
| A | CYS125 |
| A | CYS129 |
| A | CYS132 |
| A | GLY179 |
| A | SER213 |
| A | SAM406 |
| site_id | AC4 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE SAM A 406 |
| Chain | Residue |
| A | PHE131 |
| A | MET176 |
| A | GLY177 |
| A | GLY179 |
| A | GLU180 |
| A | SER211 |
| A | THR212 |
| A | SER233 |
| A | HIS235 |
| A | VAL280 |
| A | ILE309 |
| A | TRP311 |
| A | ASN312 |
| A | SF4405 |
| A | HOH446 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 16 |
| Details | Binding site: {} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 239 |
| Details | Domain: {"description":"Radical SAM core","evidences":[{"source":"PROSITE-ProRule","id":"PRU01266","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | Active site: {"description":"S-methylcysteine intermediate","evidences":[{"source":"PubMed","id":"21415317","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21527678","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 5 |
| Details | M-CSA 938 |
| Chain | Residue | Details |
| A | GLU105 | proton shuttle (general acid/base) |
| A | CYS118 | covalent catalysis |
| A | CYS125 | activator, metal ligand |
| A | CYS129 | metal ligand |
| A | CYS132 | metal ligand |
| site_id | MCSA2 |
| Number of Residues | 6 |
| Details | M-CSA 938 |
| Chain | Residue | Details |
| B | GLU105 | proton shuttle (general acid/base) |
| B | CYS118 | covalent catalysis |
| B | CYS125 | activator, metal ligand |
| B | CYS129 | metal ligand |
| B | CYS132 | metal ligand |
| B | LEU358 | covalent catalysis |
