Structure of PDB 4yvi Chain A Binding Site BS01

Receptor Information

>4yvi Chain A (length=239) Species: 71421 (Haemophilus influenzae Rd KW20)

HMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTV
DDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGV
TELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLI
DAVARFIPGVLDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKW
RLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS

Ligand information

>4yvi Chain C (length=71)

ugggaggucgucuaacgguaggacggcggacucuggauccgcugguggag
guucgaguccuccccucccag

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4yvi Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
• Resolution: 3.01 Å
• Binding residue (original residue number in PDB): R39 K45 H46 T48 V49 D50 R52 Y54 P58 G59 M60 Y115
• Binding residue (residue number reindexed from 1): R40 K46 H47 T49 V50 D51 R53 Y55 P59 G60 M61 Y116

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.

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