2VPX

Polysulfide reductase with bound quinone (UQ1)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	4Fe-4S ferredoxins	8087201	3000020	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	4Fe-4S ferredoxins	8087201	3000020	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	Molydop_binding	e2vpxA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: Molydop_binding	ECOD (1.6)
A	Molybdop_Fe4S4	e2vpxA3	A: a+b two layers	X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domain 1	F: Molybdop_Fe4S4	ECOD (1.6)
A	Molybdopterin_2nd	e2vpxA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_2nd	ECOD (1.6)
A	Molybdopterin_1st_1	e2vpxA4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_1st_1	ECOD (1.6)
D [auth E]	Molydop_binding	e2vpxE1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: Molydop_binding	ECOD (1.6)
D [auth E]	Molybdop_Fe4S4	e2vpxE3	A: a+b two layers	X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domain 1	F: Molybdop_Fe4S4	ECOD (1.6)
D [auth E]	Molybdopterin_2nd	e2vpxE4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_2nd	ECOD (1.6)
D [auth E]	Molybdopterin_1st_1	e2vpxE2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_1st_1	ECOD (1.6)
B	Fer4_11	e2vpxB1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_11	ECOD (1.6)
B	Fer4_11_1	e2vpxB2	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_11_1	ECOD (1.6)
E [auth F]	Fer4_11	e2vpxF2	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_11	ECOD (1.6)
E [auth F]	Fer4_11_1	e2vpxF1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_11_1	ECOD (1.6)
C	NrfD_2_C	e2vpxC2	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle (From Homology)	H: Transmembrane heme-binding four-helical bundle	T: Transmembrane di-heme cytochromes	F: NrfD_2_C	ECOD (1.6)
C	NrfD_2	e2vpxC1	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle (From Homology)	H: Transmembrane heme-binding four-helical bundle	T: Transmembrane di-heme cytochromes	F: NrfD_2	ECOD (1.6)
F [auth G]	NrfD_2_C	e2vpxG2	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle (From Homology)	H: Transmembrane heme-binding four-helical bundle	T: Transmembrane di-heme cytochromes	F: NrfD_2_C	ECOD (1.6)
F [auth G]	NrfD_2	e2vpxG1	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle (From Homology)	H: Transmembrane heme-binding four-helical bundle	T: Transmembrane di-heme cytochromes	F: NrfD_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.20.25.90	Mainly Beta	Single Sheet	N-terminal domain of TfIIb	ADC-like domains	CATH (4.3.0)
A	3.40.50.740	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.40.228.10	Alpha Beta	3-Layer(aba) Sandwich	Dimethylsulfoxide Reductase	domain 2	CATH (4.3.0)
A	3.30.2070.10	Alpha Beta	2-Layer Sandwich	Formate dehydrogenase/DMSO reductase,	Formate dehydrogenase/DMSO reductase,	CATH (4.3.0)
A	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
D [auth E]	2.20.25.90	Mainly Beta	Single Sheet	N-terminal domain of TfIIb	ADC-like domains	CATH (4.3.0)
D [auth E]	3.40.50.740	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D [auth E]	3.40.228.10	Alpha Beta	3-Layer(aba) Sandwich	Dimethylsulfoxide Reductase	domain 2	CATH (4.3.0)
D [auth E]	3.30.2070.10	Alpha Beta	2-Layer Sandwich	Formate dehydrogenase/DMSO reductase,	Formate dehydrogenase/DMSO reductase,	CATH (4.3.0)
D [auth E]	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
B	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
E [auth F]	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
C	1.20.1630.10	Mainly Alpha	Up-down Bundle	Formate dehydrogenase/DMSO reductase fold	Formate dehydrogenase/DMSO reductase domain	CATH (4.3.0)
F [auth G]	1.20.1630.10	Mainly Alpha	Up-down Bundle	Formate dehydrogenase/DMSO reductase fold	Formate dehydrogenase/DMSO reductase domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth E]	PF01568	Molydopterin dinucleotide binding domain (Molydop_binding)	Molydopterin dinucleotide binding domain	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entir ...	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor [1]. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [2].	Domain
A, D [auth E]	PF04879	Molybdopterin oxidoreductase Fe4S4 domain (Molybdop_Fe4S4)	Molybdopterin oxidoreductase Fe4S4 domain	This domain is found in formate dehydrogenase H for which the structure is known. This first domain (residues 1 to 60) of PDB:1aa6 is an Fe4S4 cluster just below the protein surface [1].	Domain
A, D [auth E]	PF00384	Molybdopterin oxidoreductase (Molybdopterin)	Molybdopterin oxidoreductase	-	Family
B, E [auth F]	PF13247	4Fe-4S dicluster domain (Fer4_11)	4Fe-4S dicluster 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 contai ...	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 contains two 4Fe4S clusters.	Domain
B, E [auth F]	PF12800	4Fe-4S binding domain (Fer4_4)	4Fe-4S binding domain	This 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
C, F [auth G]	PF14589	Polysulfide reductase (NrfD_2)	Polysulfide reductase	Bacterial polysulfide reductase is an integral membrane protein complex responsible for quinone-coupled reduction of polysulfide, a process important in extreme environments such as deep-sea vents and hot springs. Polysulfides are a class of compound ...	Bacterial polysulfide reductase is an integral membrane protein complex responsible for quinone-coupled reduction of polysulfide, a process important in extreme environments such as deep-sea vents and hot springs. Polysulfides are a class of compounds composed of chains of sulfur atoms, which in their simplest form are present as an anion with general formula Sn(2-). In nature, polysulfides are found in particularly high concentrations in extreme volcanic or geothermically active environments. Here, the reduction and oxidation of polysulfides are vital processes for many bacteria and are essential steps in the global sulfur cycle. In particular, the reduction of polysulfide to hydrogen sulfide in these environments is usually linked to energy-generating respiratory processes, supporting growth of many microorganisms, particularly hyperthermophiles.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth E]	THIOSULFATE REDUCTASE	oxidoreductase activity catalytic activity binding organic cyclic compound binding molybdopterin cofactor binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	-
B, E [auth F]	NRFC PROTEIN	iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding electron transfer activity cation binding ion binding metal ion binding	-	-
C, F [auth G]	HYPOTHETICAL MEMBRANE SPANNING PROTEIN	-	-	membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth E]	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
A, D [auth E]	IPR006657	Molybdopterin dinucleotide-binding domain	Domain
A, D [auth E]	IPR006656	Molybdopterin oxidoreductase	Domain
A, D [auth E]	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A, D [auth E]	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A, D [auth E]	IPR019546	Twin-arginine translocation pathway, signal sequence, bacterial/archaeal	Conserved Site
B, E [auth F]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
B, E [auth F]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B, E [auth F]	IPR000813	7Fe ferredoxin	Family
C, F [auth G]	IPR032796	Polysulfide reductase	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
C, F [auth G]	OPM	Transmembrane	Alpha-helical polytopic	Electron transport chain complex II superfamily	Polysulfide reductase

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
C, F [auth G]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
C, F [auth G]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Mo/Wbis-MGD Oxidoreductases	Polysulfide Reductase PsrABC (native)

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.