Structure of PDB 4yvh Chain A

Receptor sequence
>4yvhA (length=240) Species: 71421 (Haemophilus influenzae Rd KW20) [Search protein sequence]
SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKT
VDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGG
VTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTL
IDAVARFIPGVLDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRK
WRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
3D structure
PDB4yvh Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
ChainA
Resolution1.6 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) P89 E116 R154 D169
Catalytic site (residue number reindexed from 1) P91 E118 R156 D163
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 SFG A Y86 L87 S88 P89 Q90 G113 Y115 E116 S132 L138 G140 G141 P144 Y88 L89 S90 P91 Q92 G115 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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4yvh, PDBe:4yvh, PDBj:4yvh
PDBsum4yvh
PubMed26183229
UniProtP43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

[Back to BioLiP]