1JNR | pdb_00001jnr

Structure of adenylylsulfate reductase from the hyperthermophilic Archaeoglobus fulgidus at 1.6 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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d1jnrd_	Alpha and beta proteins (a+b)	Ferredoxin-like	4Fe-4S ferredoxins	Ferredoxin domains from multidomain proteins	Adenylylsulfate reductase B subunit	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
B	d1jnrb_	Alpha and beta proteins (a+b)	Ferredoxin-like	4Fe-4S ferredoxins	Ferredoxin domains from multidomain proteins	Adenylylsulfate reductase B subunit	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
C	d1jnrc1	All alpha proteins	Spectrin repeat-like	Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain	Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain	Adenylylsulfate reductase A subunit	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
C	d1jnrc2	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain	Adenylylsulfate reductase A subunit	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
C	d1jnrc3	Alpha and beta proteins (a+b)	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	Adenylylsulfate reductase A subunit	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
A	d1jnra1	All alpha proteins	Spectrin repeat-like	Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain	Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain	Adenylylsulfate reductase A subunit	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
A	d1jnra2	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain	Adenylylsulfate reductase A subunit	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
A	d1jnra3	Alpha and beta proteins (a+b)	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	Adenylylsulfate reductase A subunit	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	4Fe-4S ferredoxins	8037223	3000020	SCOP2B (2022-06-29)
B	SCOP2 Family	Ferredoxin domains from multidomain proteins	8024844	4000021	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	4Fe-4S ferredoxins	8037223	3000020	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Succinate dehydrogenase/fumarate reductase domain-like	8056070	3000054	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	L-aspartate oxidase C-terminal domain-like	8056071	3000021	SCOP2B (2022-06-29)
A	SCOP2 Family	L-aspartate oxidase-like	8056069	4000053	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Succinate dehydrogenase/fumarate reductase domain-like	8056070	3000054	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	L-aspartate oxidase C-terminal domain-like	8056071	3000021	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)
D	APS-reductase_C	e1jnrD1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: APS-reductase_C	ECOD (1.6)
B	APS-reductase_C	e1jnrB1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: APS-reductase_C	ECOD (1.6)
C	Succ_DH_flav_C	e1jnrC1	A: alpha bundles	X: Spectrin repeat-like	H: Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain (From Topology)	T: Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain	F: Succ_DH_flav_C	ECOD (1.6)
C	aprA	e1jnrC2	A: a+b complex topology	X: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain (From Topology)	H: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain (From Topology)	T: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	F: aprA	ECOD (1.6)
C	FAD_binding_3_1st	e1jnrC3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: FAD_binding_3_1st	ECOD (1.6)
A	Succ_DH_flav_C	e1jnrA1	A: alpha bundles	X: Spectrin repeat-like	H: Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain (From Topology)	T: Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain	F: Succ_DH_flav_C	ECOD (1.6)
A	aprA	e1jnrA2	A: a+b complex topology	X: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain (From Topology)	H: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain (From Topology)	T: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	F: aprA	ECOD (1.6)
A	FAD_binding_3_1st	e1jnrA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: FAD_binding_3_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
D	6.20.260.10	Special	Other non-globular	Signal recognition particle alu RNA binding heterodimer, srp9/1	Adenylylsulphate reductase, beta subunit, C-terminal domain	CATH (4.3.0)
B	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	6.20.260.10	Special	Other non-globular	Signal recognition particle alu RNA binding heterodimer, srp9/1	Adenylylsulphate reductase, beta subunit, C-terminal domain	CATH (4.3.0)
C	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
C	3.90.700.10	Alpha Beta	Alpha-Beta Complex	Flavocytochrome C3	Chain A, domain 1	CATH (4.3.0)
C	1.20.58.100	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
A	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
A	3.90.700.10	Alpha Beta	Alpha-Beta Complex	Flavocytochrome C3	Chain A, domain 1	CATH (4.3.0)
A	1.20.58.100	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF00037	4Fe-4S binding domain (Fer4)	4Fe-4S binding domain	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich.	Domain
B, D	PF12139	Adenosine-5'-phosphosulfate reductase beta subunit (APS-reductase_C)	Adenosine-5'-phosphosulfate reductase beta subunit	-	Family
A, C	PF02910	Fumarate reductase flavoprotein C-term (Succ_DH_flav_C)	Fumarate reductase flavoprotein C-term	This family contains fumarate reductases, succinate dehydrogenases and L-aspartate oxidases.	Domain
A, C	PF00890	FAD binding domain (FAD_binding_2)	FAD binding domain	This family includes members that bind FAD. This family includes the flavoprotein subunits from succinate and fumarate dehydrogenase, aspartate oxidase and the alpha subunit of adenylylsulphate reductase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	adenylylsulfate reductase	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	-	-
A, C	adenylylsulfate reductase	oxidoreductase activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity electron transfer activity flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding	cellular respiration energy derivation by oxidation of organic compounds metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
B, D	IPR050572	Iron-Sulfur Ferredoxin	Family
B, D	IPR038465	APS reductase, beta subunit, C-terminal domain superfamily	Homologous Superfamily
B, D	IPR022738	Adenylylsulphate reductase, beta subunit, C-terminal	Domain
B, D	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B, D	IPR011802	Adenylylsulphate reductase, beta subunit	Family
A, C	IPR030664	FAD-dependent oxidoreductase SdhA/FrdA/AprA	Family
A, C	IPR003953	FAD-dependent oxidoreductase 2, FAD-binding domain	Domain
A, C	IPR015939	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal	Domain
A, C	IPR037099	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily	Homologous Superfamily
A, C	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, C	IPR011803	Adenylylsulphate reductase, alpha subunit	Family
A, C	IPR027477	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A, B	adenylyl-sulfate reductase M-CSA #123	Adenylylsulfate (adenosine 5'-phosphosulfate) reductase (APS reductase) from Archaeoglobus fulgidus catalyses the reversible reduction of APS to sulfite and AMP. This pathway provides sulfate which serves as a terminal electron acceptor of an anaerobic respiratory electron transfer chain. Electrons are also provided for anoxygenic photosynthesis and denitrification.	Defined by 8 residues: ASN:A-74GLU:A-141TRP:A-234ARG:A-265ASP:A-361HIS:A-398SER:A-449TRP:B-48 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.8.99.2 (PDB Primary Data) Search M-CSA Motif + EC 1.8.99.2

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.