1VKY | pdb_00001vky

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
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	QueA-like	8029042	4002968	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	QueA-like	8041421	3001952	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	QueA-like	8041421	3001952	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	Peptidase_S46, Trypsin_2	e1vkyB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: LigT-related	T: LigT-related	F: Peptidase_S46, Trypsin_2	ECOD (v294.1)
B	RecU	e1vkyB2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (v294.1)
A	Queuosine_synth	e1vkyA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: barrel domain in QueA-like proteins	F: Queuosine_synth	ECOD (v294.1)
A	Queuosine_synth	e1vkyA2	A: a/b three-layered sandwiches	X: a/b domain in QueA-like proteins (Pfam 02547)	H: a/b domain in QueA-like proteins (Pfam 02547)	T: a/b domain in QueA-like proteins (Pfam 02547)	F: Queuosine_synth	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

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	tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA wobble guanine modification 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 gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA wobble guanine modification 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 tRNA queuosine(34) biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm

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 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.