3VAV | pdb_00003vav

Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from Burkholderia thailandensis

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)
J	d3vavj_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Ketopantoate hydroxymethyltransferase PanB	automated matches	(Burkholderia thailandensis E264 ) [TaxId: 271848 ],	SCOPe (2.08)
I	d3vavi_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Ketopantoate hydroxymethyltransferase PanB	automated matches	(Burkholderia thailandensis E264 ) [TaxId: 271848 ],	SCOPe (2.08)
H	d3vavh_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Ketopantoate hydroxymethyltransferase PanB	automated matches	(Burkholderia thailandensis E264 ) [TaxId: 271848 ],	SCOPe (2.08)
G	d3vavg_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Ketopantoate hydroxymethyltransferase PanB	automated matches	(Burkholderia thailandensis E264 ) [TaxId: 271848 ],	SCOPe (2.08)
F	d3vavf_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Ketopantoate hydroxymethyltransferase PanB	automated matches	(Burkholderia thailandensis E264 ) [TaxId: 271848 ],	SCOPe (2.08)
E	d3vave_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Ketopantoate hydroxymethyltransferase PanB	automated matches	(Burkholderia thailandensis E264 ) [TaxId: 271848 ],	SCOPe (2.08)
D	d3vavd_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Ketopantoate hydroxymethyltransferase PanB	automated matches	(Burkholderia thailandensis E264 ) [TaxId: 271848 ],	SCOPe (2.08)
C	d3vavc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Ketopantoate hydroxymethyltransferase PanB	automated matches	(Burkholderia thailandensis E264 ) [TaxId: 271848 ],	SCOPe (2.08)
B	d3vavb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Ketopantoate hydroxymethyltransferase PanB	automated matches	(Burkholderia thailandensis E264 ) [TaxId: 271848 ],	SCOPe (2.08)
A	d3vava_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Ketopantoate hydroxymethyltransferase PanB	automated matches	(Burkholderia thailandensis E264 ) [TaxId: 271848 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8079897	3000510	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8079897	3000510	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8079897	3000510	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8079897	3000510	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8079897	3000510	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8079897	3000510	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8079897	3000510	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8079897	3000510	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8079897	3000510	SCOP2B (2022-06-29)
A	SCOP2 Family	PanB-like	8079896	4000413	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Phosphoenolpyruvate/pyruvate domain	8079897	3000510	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
J	V-set	e3vavJ1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (v294.1)
I	PI3K_C2	e3vavI2	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: PI3K_C2	ECOD (v294.1)
H	V-set	e3vavH1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (v294.1)
G	Glycolytic	e3vavG1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: Glycolytic	ECOD (v294.1)
F	V-set	e3vavF1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (v294.1)
E	V-set	e3vavE1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (v294.1)
D	V-set	e3vavD1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (v294.1)
C	Glycolytic	e3vavC1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: Glycolytic	ECOD (v294.1)
B	V-set	e3vavB1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (v294.1)
A	Eno-Rase_FAD_bd,Enoyl_reductase,Eno-Rase_NADH_b	e3vavA1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Eno-Rase_FAD_bd,Enoyl_reductase,Eno-Rase_NADH_b	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
I	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
H	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
G	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
F	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
E	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
D	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
C	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
B	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
A	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	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, E A, B, C, D, E, F, G, H, I, J	3-methyl-2-oxobutanoate hydroxymethyltransferase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding 3-methyl-2-oxobutanoate hydroxymethyltransferase activity transferase activity, transferring one-carbon groups transferase activity hydroxymethyl-, formyl- and related transferase activity catalytic activity	pantothenate metabolic process water-soluble vitamin biosynthetic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process modified amino acid biosynthetic process carboxylic acid metabolic process modified amino acid metabolic process vitamin biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process vitamin metabolic process biosynthetic process pantothenate biosynthetic process pantothenate metabolic process water-soluble vitamin biosynthetic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process modified amino acid biosynthetic process carboxylic acid metabolic process modified amino acid metabolic process vitamin biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process vitamin metabolic process biosynthetic process pantothenate biosynthetic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR015813	Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR003700	Ketopantoate hydroxymethyltransferase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR040442	Pyruvate kinase-like domain superfamily	Homologous Superfamily

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.