2C3M

Crystal Structure Of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio africanus

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)
A	d2c3ma1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	PFOR Pyr module	Pyruvate-ferredoxin oxidoreductase, PFOR, domain I	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)
A	d2c3ma2	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	PFOR PP module	Pyruvate-ferredoxin oxidoreductase, PFOR, domains VI	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)
A	d2c3ma3	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	Pyruvate-ferredoxin oxidoreductase, PFOR, domain II	Pyruvate-ferredoxin oxidoreductase, PFOR, domain II	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)
A	d2c3ma4	Alpha and beta proteins (a/b)	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)
A	d2c3ma5	Alpha and beta proteins (a+b)	Ferredoxin-like	4Fe-4S ferredoxins	Ferredoxin domains from multidomain proteins	Pyruvate-ferredoxin oxidoreductase, PFOR, domain V	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)
B	d2c3mb1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	PFOR Pyr module	Pyruvate-ferredoxin oxidoreductase, PFOR, domain I	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)
B	d2c3mb2	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	PFOR PP module	Pyruvate-ferredoxin oxidoreductase, PFOR, domains VI	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)
B	d2c3mb3	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	Pyruvate-ferredoxin oxidoreductase, PFOR, domain II	Pyruvate-ferredoxin oxidoreductase, PFOR, domain II	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)
B	d2c3mb4	Alpha and beta proteins (a/b)	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)
B	d2c3mb5	Alpha and beta proteins (a+b)	Ferredoxin-like	4Fe-4S ferredoxins	Ferredoxin domains from multidomain proteins	Pyruvate-ferredoxin oxidoreductase, PFOR, domain V	(Desulfocurvibacter africanus ) [TaxId: 873 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8039273	3001790	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8039276	3001790	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	4Fe-4S ferredoxins	8039286	3000020	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	8039282	3000879	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TK C-terminal domain-like	8039278	3000424	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TK C-terminal domain-like	8039278	3000424	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8039273	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8039276	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	4Fe-4S ferredoxins	8039286	3000020	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	8039282	3000879	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	pyruv_ox_red	e2c3mA5	A: alpha bundles	X: Bromodomain-like	H: Four-helical bundle insertion domain in pyruvate-ferredoxin oxidoreductase (From Topology)	T: Four-helical bundle insertion domain in pyruvate-ferredoxin oxidoreductase	F: pyruv_ox_red	ECOD (1.6)
A	Fer4_21_1	e2c3mA1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_21_1	ECOD (1.6)
A	POR	e2c3mA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	F: POR	ECOD (1.6)
A	Transketolase_C	e2c3mA2	A: a/b three-layered sandwiches	X: TK C-terminal domain-like (From Topology)	H: TK C-terminal domain-like (From Topology)	T: TK C-terminal domain-like	F: Transketolase_C	ECOD (1.6)
A	POR_N	e2c3mA4	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: POR_N	ECOD (1.6)
A	TPP_enzyme_C	e2c3mA6	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_C	ECOD (1.6)
B	pyruv_ox_red	e2c3mB6	A: alpha bundles	X: Bromodomain-like	H: Four-helical bundle insertion domain in pyruvate-ferredoxin oxidoreductase (From Topology)	T: Four-helical bundle insertion domain in pyruvate-ferredoxin oxidoreductase	F: pyruv_ox_red	ECOD (1.6)
B	Fer4_21_1	e2c3mB1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_21_1	ECOD (1.6)
B	POR	e2c3mB3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	F: POR	ECOD (1.6)
B	Transketolase_C	e2c3mB2	A: a/b three-layered sandwiches	X: TK C-terminal domain-like (From Topology)	H: TK C-terminal domain-like (From Topology)	T: TK C-terminal domain-like	F: Transketolase_C	ECOD (1.6)
B	POR_N	e2c3mB4	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: POR_N	ECOD (1.6)
B	TPP_enzyme_C	e2c3mB5	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
A	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.40.920.10	Alpha Beta	3-Layer(aba) Sandwich	Pyruvate-ferredoxin Oxidoreductase	domain 3	CATH (4.3.0)
A	4.10.780.10	Few Secondary Structures	Irregular	Pyruvate-ferredoxin Oxidoreductase	domain 4	CATH (4.3.0)
A	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	4.10.790.10	Few Secondary Structures	Irregular	Pyruvate-ferredoxin Oxidoreductase	domain 7	CATH (4.3.0)
B	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
B	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.40.920.10	Alpha Beta	3-Layer(aba) Sandwich	Pyruvate-ferredoxin Oxidoreductase	domain 3	CATH (4.3.0)
B	4.10.780.10	Few Secondary Structures	Irregular	Pyruvate-ferredoxin Oxidoreductase	domain 4	CATH (4.3.0)
B	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	4.10.790.10	Few Secondary Structures	Irregular	Pyruvate-ferredoxin Oxidoreductase	domain 7	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01855	Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg (POR_N)	Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg	-	Family
A, B	PF01558	Pyruvate ferredoxin/flavodoxin oxidoreductase (POR)	Pyruvate ferredoxin/flavodoxin oxidoreductase	-	Family
A, B	PF10371	Domain of unknown function (EKR)	Domain of unknown function	EKR is a short, 33 residue, domain found in bacterial and some lower eukaryotic species which lies between a POR (pyruvate ferredoxin/flavodoxin oxidoreductase) Pfam:PF01558 and the 4Fe-4S binding domain Fer4 Pfam:PF00037. It contains a characteristi ...	EKR is a short, 33 residue, domain found in bacterial and some lower eukaryotic species which lies between a POR (pyruvate ferredoxin/flavodoxin oxidoreductase) Pfam:PF01558 and the 4Fe-4S binding domain Fer4 Pfam:PF00037. It contains a characteristic EKR sequence motif. The exact function of this domain is not known.	Domain
A, B	PF17147	Pyruvate:ferredoxin oxidoreductase core domain II (PFOR_II)	Pyruvate:ferredoxin oxidoreductase core domain II	PFOR_II is a core domain of the anaerobic enzyme pyruvate:ferredoxin oxidoreductase and is necessary for inter subunit contacts in conjunction with domains I and IV [1,2].	Domain
A, B	PF02775	Thiamine pyrophosphate enzyme, C-terminal TPP binding domain (TPP_enzyme_C)	Thiamine pyrophosphate enzyme, C-terminal TPP binding domain	-	Domain
A, B	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
A, B	PF22338	Pyruvate-ferredoxin oxidoreductase, insertion domain (Pyruv_OxRed_insertion)	Pyruvate-ferredoxin oxidoreductase, insertion domain	This entry represents the insertion domain of Pyruvate-flavodoxin oxidoreductases [1,2], which adopts a four helical bundle fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PYRUVATE-FERREDOXIN OXIDOREDUCTASE	cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding pyruvate synthase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding pyruvate synthase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding vitamin binding thiamine pyrophosphate binding organic cyclic compound binding anion binding quaternary ammonium group binding heterocyclic compound binding sulfur compound binding	cellular metabolic process electron transport chain metabolic process cellular process generation of precursor metabolites and energy response to oxidative stress response to stimulus response to stress	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR011895	Pyruvate-flavodoxin oxidoreductase	Family
A, B	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A, B	IPR009014	Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II	Homologous Superfamily
A, B	IPR019752	Pyruvate/ketoisovalerate oxidoreductase, catalytic domain	Domain
A, B	IPR050722	Pyruvate:ferredoxin/flavodoxin oxidoreductase	Family
A, B	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
A, B	IPR002869	Pyruvate-flavodoxin oxidoreductase, central domain	Homologous Superfamily
A, B	IPR033412	Pyruvate:ferredoxin oxidoreductase, core domain II	Domain
A, B	IPR019456	Pyruvate-flavodoxin oxidoreductase, EKR domain	Domain
A, B	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A, B	IPR037112	Pyruvate-flavodoxin oxidoreductase, EKR domain superfamily	Homologous Superfamily
A, B	IPR002880	Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain	Domain
A, B	IPR011766	Thiamine pyrophosphate enzyme, TPP-binding	Domain

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

Chains	Enzyme Name	Description	Catalytic Residues
A	pyruvate:ferredoxin oxidoreducatse M-CSA #119	Pyruvate:ferrodoxin/flavodoxin reductases (PFORs) catalyse the oxidative decarboxylation of pyruvate to acetyl-CoA in anaerobic organisms. PFORs can occur in both obligately and facultatively anaerobic bacteria and also some eukaryotic microorganisms. PFORs are single-chain enzymes containing a thiamin pyrophosphate cofactor for the cleavage of carbon-carbon bonds next to a carbonyl group, and iron-sulphur clusters for electron transfer. Ferredoxin I and ferredoxin II, which are single 4Fe-4S cluster ferredoxins are the most effective electron carriers for PFORs in Desulfovibrio africanus.	Defined by 4 residues: THR:A-30 [auth A-31]GLU:A-63 [auth A-64]ARG:A-113 [auth A-114]ASN:A-995 [auth A-996] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.2.7.1 (PDB Primary Data) Search M-CSA Motif + EC 1.2.7.1

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.