1VKY

Crystal structure of S-adenosylmethionine tRNA ribosyltransferase (TM0574) from Thermotoga maritima at 2.00 A resolution

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1vkya_	Multi-domain proteins (alpha and beta)	QueA-like	QueA-like	QueA-like	Queuosine biosynthesis protein queA	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d1vkyb_	Multi-domain proteins (alpha and beta)	QueA-like	QueA-like	QueA-like	Queuosine biosynthesis protein queA	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	QueA-like	8041421	3001952	SCOP2B (2022-06-29)
B	SCOP2 Family	QueA-like	8029042	4002968	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	QueA-like	8041421	3001952	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF02547	e1vkyA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: barrel domain in QueA-like proteins	F: PF02547	ECOD (1.6)
A	PF02547	e1vkyA2	A: a/b three-layered sandwiches	X: a/b domain in QueA-like proteins (Pfam 02547) (From Topology)	H: a/b domain in QueA-like proteins (Pfam 02547) (From Topology)	T: a/b domain in QueA-like proteins (Pfam 02547)	F: PF02547	ECOD (1.6)
B	PF02547	e1vkyB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: barrel domain in QueA-like proteins	F: PF02547	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1780.10	Alpha Beta	3-Layer(aba) Sandwich	QueA-like	QueA-like	CATH (4.3.0)
A	2.40.10.240	Mainly Beta	Beta Barrel	Thrombin, subunit H	QueA-like	CATH (4.3.0)
B	3.40.1780.10	Alpha Beta	3-Layer(aba) Sandwich	QueA-like	QueA-like	CATH (4.3.0)
B	2.40.10.240	Mainly Beta	Beta Barrel	Thrombin, subunit H	QueA-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02547	Queuosine biosynthesis protein (Queuosine_synth)	Queuosine biosynthesis protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	S-adenosylmethionine:tRNA ribosyltransferase-isomerase	isomerase activity glycosyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine:tRNA ribosyltransferase-isomerase activity catalytic activity	glycosyl compound metabolic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process nucleoside biosynthetic process queuosine metabolic process nucleobase-containing compound metabolic process queuosine biosynthetic process organic substance metabolic process nucleobase-containing small molecule metabolic process organic substance biosynthetic process small molecule metabolic process carbohydrate derivative biosynthetic process organonitrogen compound metabolic process glycosyl compound biosynthetic process glycosyl compound metabolic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process nucleoside biosynthetic process queuosine metabolic process nucleobase-containing compound metabolic process queuosine biosynthetic process organic substance metabolic process nucleobase-containing small molecule metabolic process organic substance biosynthetic process small molecule metabolic process carbohydrate derivative biosynthetic process organonitrogen compound metabolic process glycosyl compound biosynthetic process small molecule biosynthetic process primary metabolic process ribonucleoside biosynthetic process nucleobase-containing compound biosynthetic process nucleoside metabolic process nucleobase-containing small molecule biosynthetic process organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process metabolic process ribonucleoside metabolic process cellular biosynthetic process RNA metabolic process tRNA wobble guanine modification tRNA processing tRNA wobble base modification RNA processing cellular metabolic process tRNA modification gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process RNA modification ncRNA metabolic process macromolecule modification nucleic acid catabolic process cellular process macromolecule metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR003699	S-adenosylmethionine:tRNA ribosyltransferase-isomerase, QueA	Family
A, B	IPR042118	QueA, domain 1	Homologous Superfamily
A, B	IPR036100	S-adenosylmethionine:tRNA ribosyltransferase-isomerase, QueA superfamily	Homologous Superfamily
A, B	IPR042119	QueA, domain 2	Homologous Superfamily

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.