2GP4 | pdb_00002gp4

Structure of [FeS]cluster-free Apo Form of 6-Phosphogluconate Dehydratase from Shewanella oneidensis

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)
B	d2gp4b1	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	LeuD/IlvD-like	IlvD/EDD C-terminal domain-like	6-phosphogluconate dehydratase EDD	(Shewanella oneidensis MR-1 ) [TaxId: 211586 ],	SCOPe (2.08)
B	d2gp4b2	Alpha and beta proteins (a+b)	IlvD/EDD N-terminal domain-like	IlvD/EDD N-terminal domain-like	lvD/EDD N-terminal domain-like	6-phosphogluconate dehydratase EDD	(Shewanella oneidensis MR-1 ) [TaxId: 211586 ],	SCOPe (2.08)
B	d2gp4b3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Shewanella oneidensis MR-1 ) [TaxId: 211586 ],	SCOPe (2.08)
A	d2gp4a1	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	LeuD/IlvD-like	IlvD/EDD C-terminal domain-like	6-phosphogluconate dehydratase EDD	(Shewanella oneidensis MR-1 ) [TaxId: 211586 ],	SCOPe (2.08)
A	d2gp4a2	Alpha and beta proteins (a+b)	IlvD/EDD N-terminal domain-like	IlvD/EDD N-terminal domain-like	lvD/EDD N-terminal domain-like	6-phosphogluconate dehydratase EDD	(Shewanella oneidensis MR-1 ) [TaxId: 211586 ],	SCOPe (2.08)
A	d2gp4a3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Shewanella oneidensis MR-1 ) [TaxId: 211586 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	LeuD/IlvD-like	8041984	3000947	SCOP2B (2022-06-29)
A	SCOP2 Family	IlvD/EDD C-terminal domain-like	8029605	4002536	SCOP2 (2022-06-29)
A	SCOP2 Family	lvD/EDD N-terminal domain-like	8029606	4000460	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	LeuD/IlvD-like	8041984	3000947	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	IlvD/EDD N-terminal domain-like	8041985	3000347	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)
B		e2gp4B1	A: alpha bundles	X: EGF-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F:	ECOD (develop294)
B	Glyco_hydro_20b	e2gp4B2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Glyco_hydro_20b	ECOD (develop294)
A	ILVD_EDD	e2gp4A1	A: alpha arrays	X: lvD/EDD N-terminal domain-like	H: lvD/EDD N-terminal domain-like	T: lvD/EDD N-terminal domain-like	F: ILVD_EDD	ECOD (develop294)
A	ILV_EDD_C	e2gp4A2	A: alpha bundles	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain	T: The swivelling beta/beta/alpha domain	F: ILV_EDD_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.50.30.80	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)
A	3.50.30.80	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF24877	Dihydroxy-acid/6-phosphogluconate dehydratase C-terminal (ILV_EDD_C)	Dihydroxy-acid/6-phosphogluconate dehydratase C-terminal	This is the C-terminal domain of Ilv/ED dehydratase protein family which includes dihydroxy-acid/6-phosphogluconate dehydratases, and pentonate dehydratases [1]. Members of this entry are involved in various biosynthetic and carbohydrate metabolic p ...	This is the C-terminal domain of Ilv/ED dehydratase protein family which includes dihydroxy-acid/6-phosphogluconate dehydratases, and pentonate dehydratases [1]. Members of this entry are involved in various biosynthetic and carbohydrate metabolic pathways [2]. Dihydroxy-acid dehydratase catalyses the fourth step in the biosynthesis of isoleucine and valine, the dehydration of 2,3-dihydroxy-isovaleic acid into alpha-ketoisovaleric acid. 6-Phosphogluconate dehydratase catalyses the first step in the Entner-Doudoroff pathway, the dehydration of 6-phospho-D-gluconate into 6-phospho-2-dehydro-3-deoxy-D-gluconate. They consist of two domains, N- and C-terminal, the latter contains residues (Ser490 and Thr492) that participate in the formation of the substrate binding site. This domain is composed of a beta-sheet consisting of six parallel and two anti-parallel beta-strands that are arranged like a beta-barrel [2,3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	6-phosphogluconate dehydratase	hydro-lyase activity lyase activity catalytic activity phosphogluconate dehydratase activity carbon-oxygen lyase activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	Entner-Doudoroff pathway through 6-phosphogluconate carbohydrate metabolic process pyruvate metabolic process catabolic process oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process carboxylic acid metabolic process primary metabolic process glyceraldehyde-3-phosphate metabolic process organic acid metabolic process aldehyde metabolic process organophosphate metabolic process phosphate-containing compound metabolic process Entner-Doudoroff pathway through 6-phosphogluconate carbohydrate metabolic process pyruvate metabolic process catabolic process oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process carboxylic acid metabolic process primary metabolic process glyceraldehyde-3-phosphate metabolic process organic acid metabolic process aldehyde metabolic process organophosphate metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process Entner-Doudoroff pathway monocarboxylic acid metabolic process phosphorus metabolic process D-gluconate metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004786	6-phosphogluconate dehydratase	Family
A, B	IPR000581	Dihydroxy-acid/6-phosphogluconate dehydratase, N-terminal	Domain
A, B	IPR037237	IlvD/EDD, N-terminal domain	Homologous Superfamily
A, B	IPR042096	Dihydroxy-acid dehydratase, C-terminal	Homologous Superfamily
A, B	IPR020558	Dihydroxy-acid/6-phosphogluconate dehydratase, conserved site	Conserved Site
A, B	IPR056740	Dihydroxy-acid/6-phosphogluconate dehydratase, C-terminal	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.