Structure of PDB 4yvi Chain A

Receptor sequence
>4yviA (length=239) Species: 71421 (Haemophilus influenzae Rd KW20) [Search protein sequence]
HMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTV
DDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGV
TELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLI
DAVARFIPGVLDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKW
RLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
3D structure
PDB4yvi Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
ChainA
Resolution3.01 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 rna A R39 K45 H46 T48 V49 D50 R52 Y54 P58 G59 M60 Y115 R40 K46 H47 T49 V50 D51 R53 Y55 P59 G60 M61 Y116
BS02 SFG A L87 S88 P89 Q90 G113 Y115 E116 S132 L138 T139 G140 G141 P144 L88 S89 P90 Q91 G114 Y116 E117 S133 L139 T140 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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Cellular Component
External links
PDB RCSB:4yvi, PDBe:4yvi, PDBj:4yvi
PDBsum4yvi
PubMed26183229
UniProtP43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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