2C3M
Crystal Structure Of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio africanus
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
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) |
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) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
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) |
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) |
Domain Annotation: CATH CATH Database Homepage
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF01558 | Pyruvate ferredoxin/flavodoxin oxidoreductase (POR) | Pyruvate ferredoxin/flavodoxin oxidoreductase | - | Family | |
PF01855 | Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg (POR_N) | Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg | - | Family | |
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 ... | Domain | |
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 | |
PF02775 | Thiamine pyrophosphate enzyme, C-terminal TPP binding domain (TPP_enzyme_C) | Thiamine pyrophosphate enzyme, C-terminal TPP binding domain | - | Domain | |
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 | |
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
InterPro: Protein Family Classification InterPro Database Homepage
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
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] | EC: 1.2.7.1 (PDB Primary Data) |