2WVA | pdb_00002wva

Structural insights into the pre-reaction state of pyruvate decarboxylase from Zymomonas mobilis


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ad2wvaa2 Alpha and beta proteins (a/b) DHS-like NAD/FAD-binding domain DHS-like NAD/FAD-binding domain automated matches automated matches (Zymomonas mobilis ) [TaxId: 542 ], SCOPe (2.08)
Ad2wvaa1 Alpha and beta proteins (a/b) Thiamin diphosphate-binding fold (THDP-binding) Thiamin diphosphate-binding fold (THDP-binding) automated matches automated matches (Zymomonas mobilis ) [TaxId: 542 ], SCOPe (2.08)
Bd2wvab2 Alpha and beta proteins (a/b) DHS-like NAD/FAD-binding domain DHS-like NAD/FAD-binding domain automated matches automated matches (Zymomonas mobilis ) [TaxId: 542 ], SCOPe (2.08)
Bd2wvab1 Alpha and beta proteins (a/b) Thiamin diphosphate-binding fold (THDP-binding) Thiamin diphosphate-binding fold (THDP-binding) automated matches automated matches (Zymomonas mobilis ) [TaxId: 542 ], SCOPe (2.08)
C [auth E]d2wvae2 Alpha and beta proteins (a/b) DHS-like NAD/FAD-binding domain DHS-like NAD/FAD-binding domain automated matches automated matches (Zymomonas mobilis ) [TaxId: 542 ], SCOPe (2.08)
C [auth E]d2wvae1 Alpha and beta proteins (a/b) Thiamin diphosphate-binding fold (THDP-binding) Thiamin diphosphate-binding fold (THDP-binding) automated matches automated matches (Zymomonas mobilis ) [TaxId: 542 ], SCOPe (2.08)
D [auth F]d2wvaf2 Alpha and beta proteins (a/b) DHS-like NAD/FAD-binding domain DHS-like NAD/FAD-binding domain automated matches automated matches (Zymomonas mobilis ) [TaxId: 542 ], SCOPe (2.08)
D [auth F]d2wvaf1 Alpha and beta proteins (a/b) Thiamin diphosphate-binding fold (THDP-binding) Thiamin diphosphate-binding fold (THDP-binding) automated matches automated matches (Zymomonas mobilis ) [TaxId: 542 ], SCOPe (2.08)
E [auth V]d2wvav2 Alpha and beta proteins (a/b) DHS-like NAD/FAD-binding domain DHS-like NAD/FAD-binding domain automated matches automated matches (Zymomonas mobilis ) [TaxId: 542 ], SCOPe (2.08)
E [auth V]d2wvav1 Alpha and beta proteins (a/b) Thiamin diphosphate-binding fold (THDP-binding) Thiamin diphosphate-binding fold (THDP-binding) automated matches automated matches (Zymomonas mobilis ) [TaxId: 542 ], SCOPe (2.08)
F [auth X]d2wvax2 Alpha and beta proteins (a/b) DHS-like NAD/FAD-binding domain DHS-like NAD/FAD-binding domain automated matches automated matches (Zymomonas mobilis ) [TaxId: 542 ], SCOPe (2.08)
F [auth X]d2wvax1 Alpha and beta proteins (a/b) Thiamin diphosphate-binding fold (THDP-binding) Thiamin diphosphate-binding fold (THDP-binding) automated matches automated matches (Zymomonas mobilis ) [TaxId: 542 ], SCOPe (2.08)
G [auth Y]d2wvay2 Alpha and beta proteins (a/b) DHS-like NAD/FAD-binding domain DHS-like NAD/FAD-binding domain automated matches automated matches (Zymomonas mobilis ) [TaxId: 542 ], SCOPe (2.08)
G [auth Y]d2wvay1 Alpha and beta proteins (a/b) Thiamin diphosphate-binding fold (THDP-binding) Thiamin diphosphate-binding fold (THDP-binding) automated matches automated matches (Zymomonas mobilis ) [TaxId: 542 ], SCOPe (2.08)
H [auth Z]d2wvaz2 Alpha and beta proteins (a/b) DHS-like NAD/FAD-binding domain DHS-like NAD/FAD-binding domain automated matches automated matches (Zymomonas mobilis ) [TaxId: 542 ], SCOPe (2.08)
H [auth Z]d2wvaz1 Alpha and beta proteins (a/b) Thiamin diphosphate-binding fold (THDP-binding) Thiamin diphosphate-binding fold (THDP-binding) automated matches automated matches (Zymomonas mobilis ) [TaxId: 542 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyDHS-like NAD/FAD-binding domain 8044249 3001728 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyThiamin diphosphate-binding fold (THDP-binding) 8044269 3001790 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyThiamin diphosphate-binding fold (THDP-binding) 8044268 3001790 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyThiamin diphosphate-binding fold (THDP-binding) 8044269 3001790 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyThiamin diphosphate-binding fold (THDP-binding) 8044268 3001790 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyDHS-like NAD/FAD-binding domain 8044249 3001728 SCOP2B (2022-06-29)
C [auth E]SCOP2B SuperfamilyThiamin diphosphate-binding fold (THDP-binding) 8044269 3001790 SCOP2B (2022-06-29)
C [auth E]SCOP2B SuperfamilyDHS-like NAD/FAD-binding domain 8044249 3001728 SCOP2B (2022-06-29)
C [auth E]SCOP2B SuperfamilyThiamin diphosphate-binding fold (THDP-binding) 8044268 3001790 SCOP2B (2022-06-29)
D [auth F]SCOP2B SuperfamilyDHS-like NAD/FAD-binding domain 8044249 3001728 SCOP2B (2022-06-29)
D [auth F]SCOP2B SuperfamilyThiamin diphosphate-binding fold (THDP-binding) 8044269 3001790 SCOP2B (2022-06-29)
D [auth F]SCOP2B SuperfamilyThiamin diphosphate-binding fold (THDP-binding) 8044268 3001790 SCOP2B (2022-06-29)
E [auth V]SCOP2B SuperfamilyThiamin diphosphate-binding fold (THDP-binding) 8044268 3001790 SCOP2B (2022-06-29)
E [auth V]SCOP2B SuperfamilyThiamin diphosphate-binding fold (THDP-binding) 8044269 3001790 SCOP2B (2022-06-29)
E [auth V]SCOP2B SuperfamilyDHS-like NAD/FAD-binding domain 8044249 3001728 SCOP2B (2022-06-29)
F [auth X]SCOP2B SuperfamilyDHS-like NAD/FAD-binding domain 8044249 3001728 SCOP2B (2022-06-29)
F [auth X]SCOP2B SuperfamilyThiamin diphosphate-binding fold (THDP-binding) 8044269 3001790 SCOP2B (2022-06-29)
F [auth X]SCOP2B SuperfamilyThiamin diphosphate-binding fold (THDP-binding) 8044268 3001790 SCOP2B (2022-06-29)
G [auth Y]SCOP2B SuperfamilyThiamin diphosphate-binding fold (THDP-binding) 8044269 3001790 SCOP2B (2022-06-29)
G [auth Y]SCOP2B SuperfamilyDHS-like NAD/FAD-binding domain 8044249 3001728 SCOP2B (2022-06-29)
G [auth Y]SCOP2B SuperfamilyThiamin diphosphate-binding fold (THDP-binding) 8044268 3001790 SCOP2B (2022-06-29)
H [auth Z]SCOP2B SuperfamilyThiamin diphosphate-binding fold (THDP-binding) 8044269 3001790 SCOP2B (2022-06-29)
H [auth Z]SCOP2B SuperfamilyDHS-like NAD/FAD-binding domain 8044249 3001728 SCOP2B (2022-06-29)
H [auth Z]SCOP2B SuperfamilyThiamin diphosphate-binding fold (THDP-binding) 8044268 3001790 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ATPP_enzyme_Me2wvaA1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: DHS-like NAD/FAD-binding domainF: TPP_enzyme_MECOD (1.6)
ATPP_enzyme_Ce2wvaA3 A: a/b three-layered sandwichesX: 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_CECOD (1.6)
ATPP_enzyme_Ne2wvaA2 A: a/b three-layered sandwichesX: 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_NECOD (1.6)
BTPP_enzyme_Me2wvaB1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: DHS-like NAD/FAD-binding domainF: TPP_enzyme_MECOD (1.6)
BTPP_enzyme_Ce2wvaB3 A: a/b three-layered sandwichesX: 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_CECOD (1.6)
BTPP_enzyme_Ne2wvaB2 A: a/b three-layered sandwichesX: 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_NECOD (1.6)
C [auth E]TPP_enzyme_Me2wvaE1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: DHS-like NAD/FAD-binding domainF: TPP_enzyme_MECOD (1.6)
C [auth E]TPP_enzyme_Ce2wvaE3 A: a/b three-layered sandwichesX: 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_CECOD (1.6)
C [auth E]TPP_enzyme_Ne2wvaE2 A: a/b three-layered sandwichesX: 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_NECOD (1.6)
D [auth F]TPP_enzyme_Me2wvaF1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: DHS-like NAD/FAD-binding domainF: TPP_enzyme_MECOD (1.6)
D [auth F]TPP_enzyme_Ce2wvaF3 A: a/b three-layered sandwichesX: 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_CECOD (1.6)
D [auth F]TPP_enzyme_Ne2wvaF2 A: a/b three-layered sandwichesX: 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_NECOD (1.6)
E [auth V]TPP_enzyme_Me2wvaV1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: DHS-like NAD/FAD-binding domainF: TPP_enzyme_MECOD (1.6)
E [auth V]TPP_enzyme_Ce2wvaV3 A: a/b three-layered sandwichesX: 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_CECOD (1.6)
E [auth V]TPP_enzyme_Ne2wvaV2 A: a/b three-layered sandwichesX: 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_NECOD (1.6)
F [auth X]TPP_enzyme_Me2wvaX1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: DHS-like NAD/FAD-binding domainF: TPP_enzyme_MECOD (1.6)
F [auth X]TPP_enzyme_Ce2wvaX3 A: a/b three-layered sandwichesX: 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_CECOD (1.6)
F [auth X]TPP_enzyme_Ne2wvaX2 A: a/b three-layered sandwichesX: 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_NECOD (1.6)
G [auth Y]TPP_enzyme_Me2wvaY1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: DHS-like NAD/FAD-binding domainF: TPP_enzyme_MECOD (1.6)
G [auth Y]TPP_enzyme_Ce2wvaY3 A: a/b three-layered sandwichesX: 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_CECOD (1.6)
G [auth Y]TPP_enzyme_Ne2wvaY2 A: a/b three-layered sandwichesX: 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_NECOD (1.6)
H [auth Z]TPP_enzyme_Me2wvaZ1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: DHS-like NAD/FAD-binding domainF: TPP_enzyme_MECOD (1.6)
H [auth Z]TPP_enzyme_Ce2wvaZ3 A: a/b three-layered sandwichesX: 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_CECOD (1.6)
H [auth Z]TPP_enzyme_Ne2wvaZ2 A: a/b three-layered sandwichesX: 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_NECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.40.50.970 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domainsCATH (4.3.0)
A3.40.50.1220 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold TPP-binding domainCATH (4.3.0)
B3.40.50.970 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domainsCATH (4.3.0)
B3.40.50.1220 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold TPP-binding domainCATH (4.3.0)
C [auth E]3.40.50.970 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domainsCATH (4.3.0)
C [auth E]3.40.50.1220 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold TPP-binding domainCATH (4.3.0)
D [auth F]3.40.50.970 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domainsCATH (4.3.0)
D [auth F]3.40.50.1220 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold TPP-binding domainCATH (4.3.0)
E [auth V]3.40.50.970 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domainsCATH (4.3.0)
E [auth V]3.40.50.1220 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold TPP-binding domainCATH (4.3.0)
F [auth X]3.40.50.970 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domainsCATH (4.3.0)
F [auth X]3.40.50.1220 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold TPP-binding domainCATH (4.3.0)
G [auth Y]3.40.50.970 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domainsCATH (4.3.0)
G [auth Y]3.40.50.1220 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold TPP-binding domainCATH (4.3.0)
H [auth Z]3.40.50.970 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domainsCATH (4.3.0)
H [auth Z]3.40.50.1220 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold TPP-binding domainCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF00205Thiamine pyrophosphate enzyme, central domain (TPP_enzyme_M)Thiamine pyrophosphate enzyme, central domainThe central domain of TPP enzymes contains a 2-fold Rossman fold. Domain
PF02775Thiamine pyrophosphate enzyme, C-terminal TPP binding domain (TPP_enzyme_C)Thiamine pyrophosphate enzyme, C-terminal TPP binding domainDomain
PF02776Thiamine pyrophosphate enzyme, N-terminal TPP binding domain (TPP_enzyme_N)Thiamine pyrophosphate enzyme, N-terminal TPP binding domainDomain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
PYRUVATE DECARBOXYLASE

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR012001Thiamine pyrophosphate enzyme, N-terminal TPP-binding domainDomain
IPR000399TPP-binding enzyme, conserved siteConserved Site
IPR047214Pyruvate decarboxylase/indolepyruvate decarboxylase-like, PP-binding domainDomain
IPR012000Thiamine pyrophosphate enzyme, central domainDomain
IPR029061Thiamin diphosphate-binding foldHomologous Superfamily
IPR012110Pyruvate decarboxylase/indolepyruvate decarboxylase-likeFamily
IPR047213Pyruvate decarboxylase/indolepyruvate decarboxylase-like, pyrimidine-binding domainDomain
IPR029035DHS-like NAD/FAD-binding domain superfamilyHomologous Superfamily
IPR011766Thiamine pyrophosphate enzyme, TPP-bindingDomain