2WVA

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

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2wvaa2	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)
A	d2wvaa1	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)
B	d2wvab2	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)
B	d2wvab1	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

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8044249	3001728	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044269	3001790	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044268	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044269	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044268	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8044249	3001728	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044269	3001790	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8044249	3001728	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044268	3001790	SCOP2B (2022-06-29)
D [auth F]	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8044249	3001728	SCOP2B (2022-06-29)
D [auth F]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044269	3001790	SCOP2B (2022-06-29)
D [auth F]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044268	3001790	SCOP2B (2022-06-29)
E [auth V]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044268	3001790	SCOP2B (2022-06-29)
E [auth V]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044269	3001790	SCOP2B (2022-06-29)
E [auth V]	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8044249	3001728	SCOP2B (2022-06-29)
F [auth X]	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8044249	3001728	SCOP2B (2022-06-29)
F [auth X]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044269	3001790	SCOP2B (2022-06-29)
F [auth X]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044268	3001790	SCOP2B (2022-06-29)
G [auth Y]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044269	3001790	SCOP2B (2022-06-29)
G [auth Y]	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8044249	3001728	SCOP2B (2022-06-29)
G [auth Y]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044268	3001790	SCOP2B (2022-06-29)
H [auth Z]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044269	3001790	SCOP2B (2022-06-29)
H [auth Z]	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8044249	3001728	SCOP2B (2022-06-29)
H [auth Z]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044268	3001790	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	PF00205	e2wvaA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: PF00205	ECOD (1.6)
A	PF02775	e2wvaA3	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: PF02775	ECOD (1.6)
A	PF02776	e2wvaA2	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: PF02776	ECOD (1.6)
B	PF00205	e2wvaB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: PF00205	ECOD (1.6)
B	PF02775	e2wvaB3	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: PF02775	ECOD (1.6)
B	PF02776	e2wvaB2	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: PF02776	ECOD (1.6)
C [auth E]	PF00205	e2wvaE1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: PF00205	ECOD (1.6)
C [auth E]	PF02775	e2wvaE3	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: PF02775	ECOD (1.6)
C [auth E]	PF02776	e2wvaE2	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: PF02776	ECOD (1.6)
D [auth F]	PF00205	e2wvaF1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: PF00205	ECOD (1.6)
D [auth F]	PF02775	e2wvaF3	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: PF02775	ECOD (1.6)
D [auth F]	PF02776	e2wvaF2	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: PF02776	ECOD (1.6)
E [auth V]	PF00205	e2wvaV1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: PF00205	ECOD (1.6)
E [auth V]	PF02775	e2wvaV3	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: PF02775	ECOD (1.6)
E [auth V]	PF02776	e2wvaV2	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: PF02776	ECOD (1.6)
F [auth X]	PF00205	e2wvaX1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: PF00205	ECOD (1.6)
F [auth X]	PF02775	e2wvaX3	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: PF02775	ECOD (1.6)
F [auth X]	PF02776	e2wvaX2	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: PF02776	ECOD (1.6)
G [auth Y]	PF00205	e2wvaY1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: PF00205	ECOD (1.6)
G [auth Y]	PF02775	e2wvaY3	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: PF02775	ECOD (1.6)
G [auth Y]	PF02776	e2wvaY2	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: PF02776	ECOD (1.6)
H [auth Z]	PF00205	e2wvaZ1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: PF00205	ECOD (1.6)
H [auth Z]	PF02775	e2wvaZ3	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: PF02775	ECOD (1.6)
H [auth Z]	PF02776	e2wvaZ2	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: PF02776	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	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	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	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (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 domains	CATH (4.3.0)
C [auth E]	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (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 domains	CATH (4.3.0)
D [auth F]	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (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 domains	CATH (4.3.0)
E [auth V]	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (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 domains	CATH (4.3.0)
F [auth X]	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (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 domains	CATH (4.3.0)
G [auth Y]	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (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 domains	CATH (4.3.0)
H [auth Z]	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C [auth E], D [auth F], E [auth V], A, B, C [auth E], D [auth F], E [auth V], F [auth X], G [auth Y], H [auth Z]	PF00205	Thiamine pyrophosphate enzyme, central domain (TPP_enzyme_M)	Thiamine pyrophosphate enzyme, central domain	The central domain of TPP enzymes contains a 2-fold Rossman fold.	Domain
A, B, C [auth E], D [auth F], E [auth V], A, B, C [auth E], D [auth F], E [auth V], F [auth X], G [auth Y], H [auth Z]	PF02775	Thiamine pyrophosphate enzyme, C-terminal TPP binding domain (TPP_enzyme_C)	Thiamine pyrophosphate enzyme, C-terminal TPP binding domain	-	Domain
A, B, C [auth E], D [auth F], E [auth V], A, B, C [auth E], D [auth F], E [auth V], F [auth X], G [auth Y], H [auth Z]	PF02776	Thiamine pyrophosphate enzyme, N-terminal TPP binding domain (TPP_enzyme_N)	Thiamine pyrophosphate enzyme, N-terminal TPP binding domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C [auth E], D [auth F], E [auth V], A, B, C [auth E], D [auth F], E [auth V], F [auth X], G [auth Y], H [auth Z]	PYRUVATE DECARBOXYLASE	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding pyruvate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity vitamin binding thiamine pyrophosphate binding organic cyclic compound binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding pyruvate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity vitamin binding thiamine pyrophosphate binding organic cyclic compound binding anion binding quaternary ammonium group binding heterocyclic compound binding sulfur compound binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C [auth E], D [auth F], E [auth V], A, B, C [auth E], D [auth F], E [auth V], F [auth X], G [auth Y], H [auth Z]	IPR012001	Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain	Domain
A, B, C [auth E], D [auth F], E [auth V], A, B, C [auth E], D [auth F], E [auth V], F [auth X], G [auth Y], H [auth Z]	IPR000399	TPP-binding enzyme, conserved site	Conserved Site
A, B, C [auth E], D [auth F], E [auth V], A, B, C [auth E], D [auth F], E [auth V], F [auth X], G [auth Y], H [auth Z]	IPR047214	Pyruvate decarboxylase/indolepyruvate decarboxylase-like, PP-binding domain	Domain
A, B, C [auth E], D [auth F], E [auth V], A, B, C [auth E], D [auth F], E [auth V], F [auth X], G [auth Y], H [auth Z]	IPR012000	Thiamine pyrophosphate enzyme, central domain	Domain
A, B, C [auth E], D [auth F], E [auth V], A, B, C [auth E], D [auth F], E [auth V], F [auth X], G [auth Y], H [auth Z]	IPR012110	Pyruvate decarboxylase/indolepyruvate decarboxylase-like	Family
A, B, C [auth E], D [auth F], E [auth V], A, B, C [auth E], D [auth F], E [auth V], F [auth X], G [auth Y], H [auth Z]	IPR047213	Pyruvate decarboxylase/indolepyruvate decarboxylase-like, pyrimidine-binding domain	Domain
A, B, C [auth E], D [auth F], E [auth V], A, B, C [auth E], D [auth F], E [auth V], F [auth X], G [auth Y], H [auth Z]	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily
A, B, C [auth E], D [auth F], E [auth V], A, B, C [auth E], D [auth F], E [auth V], F [auth X], G [auth Y], H [auth Z]	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A, B, C [auth E], D [auth F], E [auth V], A, B, C [auth E], D [auth F], E [auth V], F [auth X], G [auth Y], H [auth Z]	IPR011766	Thiamine pyrophosphate enzyme, TPP-binding	Domain