5D0A

Crystal structure of epoxyqueuosine reductase with cleaved RNA stem loop

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)
A	SCOP2B Superfamily	FMN-dependent nitroreductase-like	8092574	3001947	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ARM repeat-like	8092576	3000116	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FMN-dependent nitroreductase-like	8092574	3001947	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ARM repeat-like	8092576	3000116	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ARM repeat-like	8092576	3000116	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	FMN-dependent nitroreductase-like	8092574	3001947	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ARM repeat-like	8092576	3000116	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	FMN-dependent nitroreductase-like	8092574	3001947	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)
A	HEAT_2_1	e5d0aA2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: HEAT_2_1	ECOD (1.6)
A	EUF08225	e5d0aA3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: EUF08225	ECOD (1.6)
A	DUF1730	e5d0aA1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: DUF1730	ECOD (1.6)
B	DUF1730,EUF08225	e5d0aB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: DUF1730,EUF08225	ECOD (1.6)
B	DUF1730	e5d0aB3	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: DUF1730	ECOD (1.6)
B	DUF1730	e5d0aB2	A: a+b two layers	X: Alpha-beta plaits	H: FMN-dependent nitroreductase-like (From Topology)	T: FMN-dependent nitroreductase-like	F: DUF1730	ECOD (1.6)
C	DUF1730,EUF08225	e5d0aC2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: DUF1730,EUF08225	ECOD (1.6)
C	DUF1730	e5d0aC1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: DUF1730	ECOD (1.6)
C	DUF1730	e5d0aC3	A: a+b two layers	X: Alpha-beta plaits	H: FMN-dependent nitroreductase-like (From Topology)	T: FMN-dependent nitroreductase-like	F: DUF1730	ECOD (1.6)
D	HEAT_2_1	e5d0aD2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: HEAT_2_1	ECOD (1.6)
D	EUF08225	e5d0aD3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: EUF08225	ECOD (1.6)
D	DUF1730	e5d0aD1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: DUF1730	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF03130	PBS lyase HEAT-like repeat (HEAT_PBS)	PBS lyase HEAT-like repeat	-	Repeat
A, B, C, D	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, C, D	Epoxyqueuosine reductase	epoxyqueuosine reductase activity oxidoreductase 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	tRNA modification RNA metabolic process primary metabolic process 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 modification RNA metabolic process primary metabolic process 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 metabolic process cellular process macromolecule metabolic process RNA processing carbohydrate derivative biosynthetic process glycosyl compound metabolic process glycosyl compound biosynthetic process small molecule biosynthetic process carbohydrate derivative metabolic process ribonucleoside biosynthetic process nucleoside biosynthetic process queuosine metabolic process nucleoside metabolic process nucleobase-containing small molecule biosynthetic process queuosine biosynthetic process nucleobase-containing small molecule metabolic process small molecule metabolic process ribonucleoside metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
E, F	RNA (5'-R(GCPAPGPAPCPUPGPUPAPAPAPUPCPUPGP*C)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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