Structure of PDB 5wyr Chain A

Receptor sequence
>5wyrA (length=242) Species: 208963 (Pseudomonas aeruginosa UCBPP-PA14) [Search protein sequence]
SMLWVGVVSIFPEMFRAISDYGITSRAVKQGLLTLTCWNPRVYTEDRHQT
VDDRPFGGGPGMVMKIKPLEGALADARQAAGGRKAKVIYLSPQGRQLTQA
GVRELAEEEALILIAGRYEGIDERFIEEHVDEEWSIGDYVLSGGELPAMV
LVDAVTRLLPGALGEDSFTDGLLDCPHYTRPEVYADKRVPEVLLSGNHEH
IRRWRLQQALGRTWERRADLLDSRSLSGEEQKLLAEYIRQRD
3D structure
PDB5wyr Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD fromPseudomonas aeruginosa.
ChainA
Resolution2.45 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) P94 E121 R159 D174
Catalytic site (residue number reindexed from 1) P92 E119 R157 D166
Enzyme Commision number 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 SFG A Y91 L92 S93 P94 Q95 G118 Y120 E121 S137 I138 L143 G145 G146 P149 Y89 L90 S91 P92 Q93 G116 Y118 E119 S135 I136 L141 G143 G144 P147 PDBbind-CN: -logKd/Ki=6.39,Kd=0.41uM
BS02 SFG A S175 D182 S167 D174 PDBbind-CN: -logKd/Ki=6.39,Kd=0.41uM
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0052906 tRNA (guanine(37)-N1)-methyltransferase activity
Biological Process
GO:0002939 tRNA N1-guanine methylation
GO:0006400 tRNA modification
GO:0008033 tRNA processing
GO:0032259 methylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5wyr, PDBe:5wyr, PDBj:5wyr
PDBsum5wyr
PubMed31399541
UniProtQ02RL6|TRMD_PSEAB tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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