2V3W | pdb_00002v3w

Crystal structure of the benzoylformate decarboxylase variant L461A from Pseudomonas putida

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	d2v3wd1	Alpha and beta proteins (a/b)	DHS-like NAD/FAD-binding domain	DHS-like NAD/FAD-binding domain	automated matches	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
D	d2v3wd2	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
C	d2v3wc1	Alpha and beta proteins (a/b)	DHS-like NAD/FAD-binding domain	DHS-like NAD/FAD-binding domain	automated matches	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
C	d2v3wc2	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
B	d2v3wb1	Alpha and beta proteins (a/b)	DHS-like NAD/FAD-binding domain	DHS-like NAD/FAD-binding domain	automated matches	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
B	d2v3wb2	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
A	d2v3wa1	Alpha and beta proteins (a/b)	DHS-like NAD/FAD-binding domain	DHS-like NAD/FAD-binding domain	automated matches	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
A	d2v3wa2	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8042169	3001790	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8042168	3001728	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8042170	3001790	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8042168	3001728	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8042169	3001790	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8042170	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8042168	3001728	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8042169	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8042170	3001790	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8042169	3001790	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8042168	3001728	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8042170	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)
D	Methyltransf_2	e2v3wD1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Methyltransf_2	ECOD (v294.1)
D	E1_dh	e2v3wD2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: E1_dh	ECOD (v294.1)
C	Methyltransf_2	e2v3wC1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Methyltransf_2	ECOD (v294.1)
C	E1_dh	e2v3wC2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: E1_dh	ECOD (v294.1)
B	Methyltransf_2	e2v3wB1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Methyltransf_2	ECOD (v294.1)
B	E1_dh	e2v3wB2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: E1_dh	ECOD (v294.1)
A	Methyltransf_2	e2v3wA1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Methyltransf_2	ECOD (v294.1)
A	E1_dh	e2v3wA2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: E1_dh	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	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	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
C	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	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)
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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	BENZOYLFORMATE DECARBOXYLASE	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding flavin adenine dinucleotide binding nucleoside phosphate binding anion binding nucleotide binding heterocyclic compound binding benzoylformate decarboxylase activity carboxy-lyase activity lyase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding flavin adenine dinucleotide binding nucleoside phosphate binding anion binding nucleotide binding heterocyclic compound binding benzoylformate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity transketolase or transaldolase activity transferase activity acetolactate synthase activity vitamin binding thiamine pyrophosphate binding quaternary ammonium group binding sulfur compound binding	catabolic process benzene-containing compound metabolic process oxoacid metabolic process mandelate metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process mandelate catabolic process metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process catabolic process benzene-containing compound metabolic process oxoacid metabolic process mandelate metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process mandelate catabolic process metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process small molecule catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR045229	Thiamine pyrophosphate enzyme	Family
A, B, C, D	IPR012001	Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain	Domain
A, B, C, D	IPR000399	TPP-binding enzyme, conserved site	Conserved Site
A, B, C, D	IPR012000	Thiamine pyrophosphate enzyme, central domain	Domain
A, B, C, D	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A, B, C, D	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR011766	Thiamine pyrophosphate enzyme, TPP-binding	Domain

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.