4YQ5
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0002939 | biological_process | tRNA N1-guanine methylation |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006400 | biological_process | tRNA modification |
| A | 0008033 | biological_process | tRNA processing |
| A | 0008168 | molecular_function | methyltransferase activity |
| A | 0016740 | molecular_function | transferase activity |
| A | 0032259 | biological_process | methylation |
| A | 0052906 | molecular_function | tRNA (guanine(37)-N1)-methyltransferase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 15 |
| Details | binding site for residue 4G0 A 301 |
| Chain | Residue |
| A | TYR86 |
| A | LEU138 |
| A | GLY140 |
| A | GLY141 |
| A | PRO144 |
| A | PHE171 |
| A | ASP177 |
| A | LEU87 |
| A | SER88 |
| A | GLY113 |
| A | GLU116 |
| A | SER132 |
| A | ILE133 |
| A | GLY134 |
| A | TYR136 |
| site_id | AC2 |
| Number of Residues | 10 |
| Details | binding site for residue FLC A 302 |
| Chain | Residue |
| A | GLY20 |
| A | VAL21 |
| A | ARG24 |
| A | ARG114 |
| A | TYR115 |
| A | THR230 |
| A | ASP231 |
| A | ARG234 |
| A | HOH419 |
| A | HOH425 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 1 |
| Details | ACT_SITE: Proton acceptor => ECO:0000255 |
| Chain | Residue | Details |
| A | ASP169 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 3 |
| Details | BINDING: |
| Chain | Residue | Details |
| A | TYR86 | |
| A | GLY113 | |
| A | ILE133 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 4 |
| Details | M-CSA 332 |
| Chain | Residue | Details |
| A | PRO89 | increase nucleophilicity, steric role |
| A | GLU116 | electrostatic stabiliser, hydrogen bond acceptor |
| A | ARG154 | activator, electrostatic stabiliser, hydrogen bond donor |
| A | ASP169 | activator, hydrogen bond acceptor, hydrogen bond donor, increase nucleophilicity, proton acceptor, proton donor |
