Structure of PDB 4yvj Chain B

Receptor sequence

>4yvjB (length=249) Species: 71421 (Haemophilus influenzae Rd KW20)

GSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHK
TVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQG
GVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMT
LIDAVARFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLM
SGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS

3D structure

• PDB: 4yvj Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
• Chain: B
• Resolution: 2.9 Å

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.

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	B	G20 V21 R24 L160 K162 E167 D169 R183 S198 G199 H200 H201	G23 V24 R27 L163 K165 E170 D172 R186 S201 G202 H203 H204
BS02	SFG	B	D169 S170 D177	D172 S173 D180
BS03	SFG	B	L87 S88 P89 Q90 G113 R114 Y115 E116 S132 L138 G140 G141 P144	L90 S91 P92 Q93 G116 R117 Y118 E119 S135 L141 G143 G144 P147

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