5D08 | pdb_00005d08

Crystal structure of selenomethionine-labeled epoxyqueuosine reductase

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	SCOP2B Superfamily	ARM repeat-like	8092576	3000116	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FMN-dependent nitroreductase-like	8092574	3001947	SCOP2B (2022-06-29)
A	SCOP2 Family	Epoxyqueuosine reductase catalytic domain-like	8050756	4007034	SCOP2 (2022-06-29)
A	SCOP2 Family	Epoxyqueuosine reductase tRNA-binding domain-like	8092573	4007775	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FMN-dependent nitroreductase-like	8092574	3001947	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ARM repeat-like	8092576	3000116	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)
B	PemK_toxin	e5d08B1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PemK_toxin	ECOD (develop294)
A	HEAT_PBS, HEAT_2	e5d08A1	A: alpha bundles	X: Repetitive alpha hairpins	H: ARM repeat	T: ARM repeat	F: HEAT_PBS, HEAT_2	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03130	PBS lyase HEAT-like repeat (HEAT_PBS)	PBS lyase HEAT-like repeat	-	Repeat
A, B	PF08331	Epoxyqueuosine reductase QueG, DUF1730 (QueG_DUF1730)	Epoxyqueuosine reductase QueG, DUF1730	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Epoxyqueuosine reductase	epoxyqueuosine reductase activity oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups 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	tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA queuosine(34) biosynthetic 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 modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA queuosine(34) biosynthetic 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 metabolic process cellular process tRNA wobble base modification macromolecule metabolic process RNA processing	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
A, B	IPR011989	Armadillo-like helical	Homologous Superfamily
A, B	IPR004453	Epoxyqueuosine reductase QueG	Family
A, B	IPR016024	Armadillo-type fold	Homologous Superfamily
A, B	IPR013542	Epoxyqueuosine reductase QueG, DUF1730	Domain
A, B	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A, B	IPR004155	PBS lyase HEAT-like repeat	Repeat

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.