2QY6 | pdb_00002qy6

Crystal structure of the N-terminal domain of UPF0209 protein yfcK from Escherichia coli O157:H7

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	MnmC, N-terminal methyltransferase domain	8047190	4005497	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090686	3000118	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090686	3000118	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	PK_Tyr_Ser-Thr	e2qy6B1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: PK_Tyr_Ser-Thr	ECOD (develop294)
A	Asp_Glu_race	e2qy6A1	A: alpha bundles	X: Profilin-like	H: sensor domains	T: sensor domains	F: Asp_Glu_race	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF05430	S-adenosyl-L-methionine-dependent methyltransferase (Methyltransf_30)	S-adenosyl-L-methionine-dependent methyltransferase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	UPF0209 protein yfcK	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 (5-methylaminomethyl-2-thiouridylate)(34)-methyltransferase activity methyltransferase activity catalytic activity oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors 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 (5-methylaminomethyl-2-thiouridylate)(34)-methyltransferase activity methyltransferase activity catalytic activity oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding	tRNA modification RNA metabolic process primary metabolic process tRNA wobble uridine modification gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing tRNA modification RNA metabolic process primary metabolic process tRNA wobble uridine modification gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification tRNA wobble base modification metabolic process cellular process macromolecule metabolic process RNA processing methylation	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR008471	MnmC-like methyltransferase	Domain
A, B	IPR023032	tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC	Family
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B	IPR047785	tRNA mnm(5)s(2)U biosynthesis bifunctional protein MnmC, N-terminal	Domain
A, B	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR017610	tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC, C-terminal	Domain
A, B	IPR006076	FAD dependent oxidoreductase	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.