Structure of PDB 4yvk Chain B Binding Site BS01

Receptor Information

>4yvk Chain B (length=249) Species: 71421 (Haemophilus influenzae Rd KW20)

GSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHK
TVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQG
GVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMT
LIDAVARFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLM
SGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS

Ligand information

>4yvk Chain C (length=71)

ugggaggucgucuaacgguaggacggcggacucucgauccgcugguggag
guucgaguccuccccucccag

.<<<<<<..<<<<.......>>>><<<<<<.......>>>>>>...<<<<
<.......>>>>>>>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4yvk Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
• Resolution: 3.002 Å
• Binding residue (original residue number in PDB): E18 G20 V21 R24 L160 K162 E167 D169 R183 S198 G199 H200 H201
• Binding residue (residue number reindexed from 1): E21 G23 V24 R27 L163 K165 E170 D172 R186 S201 G202 H203 H204

Enzymatic activity

• Catalytic site (original residue number in PDB): P89 E116 R154 D169
• Catalytic site (residue number reindexed from 1): P92 E119 R157 D172
• Enzyme Commision number: 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.

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

External links

• PDB: RCSB:4yvk, PDBe:4yvk, PDBj:4yvk
• PDBsum: 4yvk
• PubMed: 26183229
• UniProt: P43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)