5HR6
X-ray crystal structure of C118A RlmN with cross-linked tRNA purified from Escherichia coli
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 | 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 | 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 | 10 |
| Details | binding site for residue MET A 501 |
| Chain | Residue |
| A | MET175 |
| A | 5AD503 |
| A | GLY177 |
| A | GLY179 |
| A | GLU180 |
| A | SER211 |
| A | THR212 |
| A | SER213 |
| A | SER233 |
| A | SF4502 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue SF4 A 502 |
| Chain | Residue |
| A | CYS125 |
| A | CYS129 |
| A | CYS132 |
| A | SER213 |
| A | MET501 |
| site_id | AC3 |
| Number of Residues | 12 |
| Details | binding site for residue 5AD A 503 |
| Chain | Residue |
| A | PHE131 |
| A | CYS132 |
| A | SER233 |
| A | HIS235 |
| A | GLU278 |
| A | VAL280 |
| A | ILE309 |
| A | TRP311 |
| A | ASN312 |
| A | SMC355 |
| A | GLY356 |
| A | MET501 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | binding site for residue MG A 504 |
| Chain | Residue |
| A | LEU196 |
| A | LEU203 |
| C | A26 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue MG C 101 |
| Chain | Residue |
| A | HOH610 |
| C | C38 |
| C | G39 |
| C | HOH202 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | binding site for residue MG C 102 |
| Chain | Residue |
| C | U7 |
| C | C8 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | binding site for residue MG C 103 |
| Chain | Residue |
| C | U7 |
| C | A13 |
| C | G14 |
| site_id | AC8 |
| Number of Residues | 9 |
| Details | binding site for residue MET B 501 |
| Chain | Residue |
| B | GLY177 |
| B | GLY179 |
| B | GLU180 |
| B | SER211 |
| B | THR212 |
| B | SER213 |
| B | SER233 |
| B | SF4502 |
| B | 5AD503 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | binding site for residue SF4 B 502 |
| Chain | Residue |
| B | CYS125 |
| B | LEU127 |
| B | CYS129 |
| B | CYS132 |
| B | ALA135 |
| B | SER213 |
| B | MET501 |
| site_id | AD1 |
| Number of Residues | 13 |
| Details | binding site for residue 5AD B 503 |
| Chain | Residue |
| B | PHE131 |
| B | CYS132 |
| B | SER233 |
| B | HIS235 |
| B | GLU278 |
| B | VAL280 |
| B | ILE309 |
| B | TRP311 |
| B | ASN312 |
| B | SMC355 |
| B | GLY356 |
| B | MET501 |
| B | HOH603 |
| site_id | AD2 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 504 |
| Chain | Residue |
| B | LEU196 |
| B | ASP198 |
| B | LEU203 |
| B | HOH607 |
| D | A26 |
| D | HOH201 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue MG D 101 |
| Chain | Residue |
| B | HOH614 |
| D | C38 |
| D | G39 |
| D | HOH203 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: Proton acceptor => ECO:0000255 |
| Chain | Residue | Details |
| A | GLU105 | |
| B | GLU105 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | ACT_SITE: S-methylcysteine intermediate => ECO:0000269|PubMed:21415317, ECO:0000269|PubMed:21527678 |
| Chain | Residue | Details |
| A | SMC355 | |
| B | SMC355 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 14 |
| Details | BINDING: |
| Chain | Residue | Details |
| A | CYS125 | |
| B | CYS132 | |
| B | GLY179 | |
| B | SER211 | |
| B | SER233 | |
| B | ASN312 | |
| A | CYS129 | |
| A | CYS132 | |
| A | GLY179 | |
| A | SER211 | |
| A | SER233 | |
| A | ASN312 | |
| B | CYS125 | |
| B | CYS129 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 6 |
| Details | M-CSA 938 |
| Chain | Residue | Details |
| A | GLU105 | proton shuttle (general acid/base) |
| A | ALA118 | covalent catalysis |
| A | CYS125 | activator, metal ligand |
| A | CYS129 | metal ligand |
| A | CYS132 | metal ligand |
| A | SMC355 | covalent catalysis |
| site_id | MCSA2 |
| Number of Residues | 6 |
| Details | M-CSA 938 |
| Chain | Residue | Details |
| B | GLU105 | proton shuttle (general acid/base) |
| B | ALA118 | covalent catalysis |
| B | CYS125 | activator, metal ligand |
| B | CYS129 | metal ligand |
| B | CYS132 | metal ligand |
| B | SMC355 | covalent catalysis |
