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4YQA

Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds

Functional Information from GO Data
ChainGOidnamespacecontents
A0002939biological_processtRNA N1-guanine methylation
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0006400biological_processtRNA modification
A0008033biological_processtRNA processing
A0008168molecular_functionmethyltransferase activity
A0016740molecular_functiontransferase activity
A0032259biological_processmethylation
A0052906molecular_functiontRNA (guanine(37)-N1)-methyltransferase activity
Functional Information from PDB Data
site_idAC1
Number of Residues17
Detailsbinding site for residue 4GN A 301
ChainResidue
ATYR86
ASER132
AILE133
AGLY134
ATYR136
ALEU138
AGLY140
AGLY141
APRO144
ALEU87
ASER88
APRO89
AGLY113
AARG114
ATYR115
AGLU116
AGLY117

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsACT_SITE: Proton acceptor => ECO:0000255
ChainResidueDetails
AASP169

site_idSWS_FT_FI2
Number of Residues3
DetailsBINDING:
ChainResidueDetails
ATYR86
AGLY113
AILE133

Catalytic Information from CSA
site_idMCSA1
Number of Residues3
DetailsM-CSA 332
ChainResidueDetails
APRO89increase nucleophilicity, steric role
AGLU116electrostatic stabiliser, hydrogen bond acceptor
AARG154activator, electrostatic stabiliser, hydrogen bond donor

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PDB entries from 2025-07-02

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