Structure of PDB 4yvk Chain A

Receptor sequence

>4yvkA (length=239) Species: 71421 (Haemophilus influenzae Rd KW20)

SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKT
VDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGG
VTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTL
IDAVARFIPGVDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKW
RLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS

3D structure

• PDB: 4yvk Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
• Chain: A
• Resolution: 3.002 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): P89 E116 R154 D169
• Catalytic site (residue number reindexed from 1): P91 E118 R156 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	F9 R39 H46 Y54 G56 G59 M60 Y115	F11 R41 H48 Y56 G58 G61 M62 Y117
BS02	SFG	A	L87 S88 P89 Q90 G113 R114 Y115 E116 S132 L138 G140 G141 P144	L89 S90 P91 Q92 G115 R116 Y117 E118 S134 L140 G142 G143 P146

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)