Structure of PDB 4yvg Chain A

Receptor sequence
>4yvgA (length=239) Species: 71421 (Haemophilus influenzae Rd KW20) [Search protein sequence]
HMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTV
DDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGV
TELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLI
DAVARFIPGVLDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKW
RLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
3D structure
PDB4yvg Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
ChainA
Resolution1.549 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) P89 E116 R154 D169
Catalytic site (residue number reindexed from 1) P90 E117 R155 D162
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 SAM A Y86 L87 S88 P89 Q90 G113 Y115 E116 L138 G140 G141 P144 Y87 L88 S89 P90 Q91 G114 Y116 E117 L139 G141 G142 P145
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:4yvg, PDBe:4yvg, PDBj:4yvg
PDBsum4yvg
PubMed26183229
UniProtP43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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