2VS1

The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)- methyltransferase in complex with S-adenosyl-L-homocysteine

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	TrmA	e2vs1A1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: TrmA	ECOD (1.6)
A	Methyltransf_11_2	e2vs1A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
A	2.40.50.1070	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF05958	tRNA (Uracil-5-)-methyltransferase (tRNA_U5-meth_tr)	tRNA (Uracil-5-)-methyltransferase	-	Family
A	PF21579	tRNA (uracil(54)-C(5))-methyltransferase, TRAM domain (PabTrmU54_TRAM_dom)	tRNA (uracil(54)-C(5))-methyltransferase, TRAM domain	This domain is found at the N-terminal end of tRNA (uracil(54)-C(5))- methyltransferase from Pyrococcus abyssi (PabTrmU54), which catalyses the formation of 5-methyl-uridine at position 54 (m5U54) in tRNA. This domain, a TRAM domain, adopts a five-st ...	This domain is found at the N-terminal end of tRNA (uracil(54)-C(5))- methyltransferase from Pyrococcus abyssi (PabTrmU54), which catalyses the formation of 5-methyl-uridine at position 54 (m5U54) in tRNA. This domain, a TRAM domain, adopts a five-stranded beta barrel architecture characteristic of an oligosaccharide/ oligonucleotide-binding fold (OB-fold) [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	UNCHARACTERIZED RNA METHYLTRANSFERASE PYRAB10780	tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups tRNA (uridine) methyltransferase activity catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity tRNA (uracil(54)-C5)-methyltransferase activity, S-adenosyl methionine-dependent methyltransferase activity catalytic activity iron-sulfur cluster binding binding tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups tRNA (uridine) methyltransferase activity catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity tRNA (uracil(54)-C5)-methyltransferase activity, S-adenosyl methionine-dependent methyltransferase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing cellular metabolic process tRNA modification primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing cellular metabolic process tRNA modification primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process organic cyclic compound metabolic process RNA modification biosynthetic process methylation macromolecule modification ncRNA metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA methylation tRNA methylation	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR010280	(Uracil-5)-methyltransferase family	Family
A	IPR048845	tRNA (uracil(54)-C(5))/23S rRNA (uracil(747)-C(5))-methyltransferase, TRAM domain	Domain
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	IPR030391	RNA methyltransferase TrmA, conserved site	Conserved Site
A	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A	IPR030390	RNA methyltransferase TrmA, active site	Active Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	CSS	Parent Component: CYS RESID: AA0269 PSI-MOD : L-cysteine persulfide MOD:00274

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.