Structure of PDB 4yvk Chain B

Receptor sequence

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

GSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHK
TVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQG
GVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMT
LIDAVARFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLM
SGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS

3D structure

• PDB: 4yvk Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
• Chain: B
• Resolution: 3.002 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	E18 G20 V21 R24 L160 K162 E167 D169 R183 S198 G199 H200 H201	E21 G23 V24 R27 L163 K165 E170 D172 R186 S201 G202 H203 H204
BS02	SFG	B	D169 S170 D177	D172 S173 D180
BS03	SFG	B	Y86 L87 S88 P89 Q90 G113 Y115 E116 S132 I133 L138 G140 G141 P144	Y89 L90 S91 P92 Q93 G116 Y118 E119 S135 I136 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:4yvk, PDBe:4yvk, PDBj:4yvk
• PDBsum: 4yvk
• PubMed: 26183229
• UniProt: P43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)