2DW6 | pdb_00002dw6

Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate

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)
D	d2dw6d1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	automated matches	(Bradyrhizobium japonicum ) [TaxId: 375 ],	SCOPe (2.08)
D	d2dw6d2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Bradyrhizobium japonicum ) [TaxId: 375 ],	SCOPe (2.08)
C	d2dw6c1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	automated matches	(Bradyrhizobium japonicum ) [TaxId: 375 ],	SCOPe (2.08)
C	d2dw6c2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Bradyrhizobium japonicum ) [TaxId: 375 ],	SCOPe (2.08)
B	d2dw6b1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	automated matches	(Bradyrhizobium japonicum ) [TaxId: 375 ],	SCOPe (2.08)
B	d2dw6b2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Bradyrhizobium japonicum ) [TaxId: 375 ],	SCOPe (2.08)
A	d2dw6a1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	automated matches	(Bradyrhizobium japonicum ) [TaxId: 375 ],	SCOPe (2.08)
A	d2dw6a2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Bradyrhizobium japonicum ) [TaxId: 375 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Enolase C-terminal domain-like	8039949	3000476	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Enolase N-terminal domain-like	8039950	3001064	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Enolase N-terminal domain-like	8039950	3001064	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Enolase C-terminal domain-like	8039949	3000476	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Enolase N-terminal domain-like	8039950	3001064	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Enolase C-terminal domain-like	8039949	3000476	SCOP2B (2022-06-29)
A	SCOP2 Family	D-glucarate dehydratase-like	8027570	4003246	SCOP2 (2022-06-29)
A	SCOP2 Family	Enolase N-terminal domain-like	8027571	4001209	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Enolase C-terminal domain-like	8039949	3000476	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Enolase N-terminal domain-like	8039950	3001064	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)
D	OsmC	e2dw6D1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: OsmC	ECOD (develop294)
D	Meth_synt_2	e2dw6D2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Meth_synt_2	ECOD (develop294)
C	OsmC	e2dw6C1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: OsmC	ECOD (develop294)
C	Meth_synt_2	e2dw6C2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Meth_synt_2	ECOD (develop294)
B	OsmC	e2dw6B1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: OsmC	ECOD (develop294)
B	Meth_synt_2	e2dw6B2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Meth_synt_2	ECOD (develop294)
A	OsmC	e2dw6A1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: OsmC	ECOD (develop294)
A	Meth_synt_2	e2dw6A2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Meth_synt_2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
D	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
C	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
C	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
B	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
B	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
A	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
A	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF13378	Enolase C-terminal domain-like (MR_MLE_C)	Enolase C-terminal domain-like	This domain appears at the C-terminus of many of the proteins that carry the MR_MLE_N Pfam:PF02746 domain. EC:4.2.1.40.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Bll6730 protein	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity D(-)-tartrate dehydratase activity	carbohydrate metabolic process catabolic process oxoacid metabolic process carbohydrate catabolic process aldonic acid catabolic process carboxylic acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process monocarboxylic acid catabolic process galactonate catabolic process carboxylic acid catabolic process D-galactonate catabolic process metabolic process carbohydrate metabolic process catabolic process oxoacid metabolic process carbohydrate catabolic process aldonic acid catabolic process carboxylic acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process monocarboxylic acid catabolic process galactonate catabolic process carboxylic acid catabolic process D-galactonate catabolic process metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process small molecule catabolic process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR034593	D-galactonate dehydratase DgoD-like	Family
A, B, C, D	IPR029065	Enolase_C-like	Unknown
A, B, C, D	IPR013342	Mandelate racemase, C-terminal domain	Domain
A, B, C, D	IPR029017	Enolase-like, N-terminal	Homologous Superfamily
A, B, C, D	IPR034611	D-tartrate dehydratase	Family
A, B, C, D	IPR036849	Enolase-like, C-terminal 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.