8EJ0 | pdb_00008ej0

Crystal structure of Fe-S cluster-dependent dehydratase from Paralcaligenes ureilyticus in complex with Mg

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth G]	Polyketide_cyc2	e8ej0G1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (v294.1)
C [auth E]	Polyketide_cyc2	e8ej0E1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (v294.1)
B [auth C]	Polyketide_cyc2	e8ej0C1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (v294.1)
A	V-set	e8ej0A1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: V-set	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth E], D [auth G]	PF00920	Dihydroxy-acid/6-phosphogluconate dehydratase N-terminal (ILVD_EDD_N)	Dihydroxy-acid/6-phosphogluconate dehydratase N-terminal	This is the N-terminal domain of Ilv/ED dehydratase protein family which includes dihydroxy-acid/6-phosphogluconate dehydratases, and pentonate dehydratases [3]. Members of this entry are involved in various biosynthetic and carbohydrate metabolic pa ...	This is the N-terminal domain of Ilv/ED dehydratase protein family which includes dihydroxy-acid/6-phosphogluconate dehydratases, and pentonate dehydratases [3]. 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. This domain is composed of a beta-sheet with four parallel beta-strands surrounded by four alpha-helices and forms a binding site for a [2Fe-2S] cluster and a Mg2+ ion [1,2].	Domain
A, B [auth C], C [auth E], D [auth G]	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 [auth C], C [auth E], D [auth G]	Dihydroxyacid dehydratase	hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth E], D [auth G]	IPR000581	Dihydroxy-acid/6-phosphogluconate dehydratase, N-terminal	Domain
A, B [auth C], C [auth E], D [auth G]	IPR037237	IlvD/EDD, N-terminal domain	Homologous Superfamily
A, B [auth C], C [auth E], D [auth G]	IPR042096	Dihydroxy-acid dehydratase, C-terminal	Homologous Superfamily
A, B [auth C], C [auth E], D [auth G]	IPR056740	Dihydroxy-acid/6-phosphogluconate dehydratase, C-terminal	Domain
A, B [auth C], C [auth E], D [auth G]	IPR052352	Sugar Degradation Dehydratases	Family

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.