5J84 | pdb_00005j84

Crystal structure of L-arabinonate dehydratase in holo-form

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)
H	ILVD_EDD_1st	e5j84H2	A: alpha arrays	X: lvD/EDD N-terminal domain-like (From Topology)	H: lvD/EDD N-terminal domain-like (From Topology)	T: lvD/EDD N-terminal domain-like	F: ILVD_EDD_1st	ECOD (1.6)
H	ILVD_EDD_2nd	e5j84H1	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: ILVD_EDD_2nd	ECOD (1.6)
G	ILVD_EDD_1st	e5j84G2	A: alpha arrays	X: lvD/EDD N-terminal domain-like (From Topology)	H: lvD/EDD N-terminal domain-like (From Topology)	T: lvD/EDD N-terminal domain-like	F: ILVD_EDD_1st	ECOD (1.6)
G	ILVD_EDD_2nd	e5j84G1	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: ILVD_EDD_2nd	ECOD (1.6)
F	ILVD_EDD_1st	e5j84F2	A: alpha arrays	X: lvD/EDD N-terminal domain-like (From Topology)	H: lvD/EDD N-terminal domain-like (From Topology)	T: lvD/EDD N-terminal domain-like	F: ILVD_EDD_1st	ECOD (1.6)
F	ILVD_EDD_2nd	e5j84F1	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: ILVD_EDD_2nd	ECOD (1.6)
E	ILVD_EDD_1st	e5j84E2	A: alpha arrays	X: lvD/EDD N-terminal domain-like (From Topology)	H: lvD/EDD N-terminal domain-like (From Topology)	T: lvD/EDD N-terminal domain-like	F: ILVD_EDD_1st	ECOD (1.6)
E	ILVD_EDD_2nd	e5j84E1	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: ILVD_EDD_2nd	ECOD (1.6)
D	ILVD_EDD_1st	e5j84D2	A: alpha arrays	X: lvD/EDD N-terminal domain-like (From Topology)	H: lvD/EDD N-terminal domain-like (From Topology)	T: lvD/EDD N-terminal domain-like	F: ILVD_EDD_1st	ECOD (1.6)
D	ILVD_EDD_2nd	e5j84D1	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: ILVD_EDD_2nd	ECOD (1.6)
C	ILVD_EDD_1st	e5j84C2	A: alpha arrays	X: lvD/EDD N-terminal domain-like (From Topology)	H: lvD/EDD N-terminal domain-like (From Topology)	T: lvD/EDD N-terminal domain-like	F: ILVD_EDD_1st	ECOD (1.6)
C	ILVD_EDD_2nd	e5j84C1	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: ILVD_EDD_2nd	ECOD (1.6)
B	ILVD_EDD_1st	e5j84B1	A: alpha arrays	X: lvD/EDD N-terminal domain-like (From Topology)	H: lvD/EDD N-terminal domain-like (From Topology)	T: lvD/EDD N-terminal domain-like	F: ILVD_EDD_1st	ECOD (1.6)
B	ILVD_EDD_2nd	e5j84B2	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: ILVD_EDD_2nd	ECOD (1.6)
A	ILVD_EDD_1st	e5j84A1	A: alpha arrays	X: lvD/EDD N-terminal domain-like (From Topology)	H: lvD/EDD N-terminal domain-like (From Topology)	T: lvD/EDD N-terminal domain-like	F: ILVD_EDD_1st	ECOD (1.6)
A	ILVD_EDD_2nd	e5j84A2	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: ILVD_EDD_2nd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	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

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	Dihydroxy-acid dehydratase	hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity L-arabinonate dehydratase activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding D-fuconate dehydratase activity galactonate dehydratase activity cation binding ion binding hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity L-arabinonate dehydratase activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding D-fuconate dehydratase activity galactonate dehydratase activity cation binding ion binding metal ion binding	monosaccharide metabolic process arabinose metabolic process carbohydrate metabolic process catabolic process arabinose catabolic process carbohydrate catabolic process primary metabolic process small molecule metabolic process metabolic process cellular process pentose metabolic process monosaccharide catabolic process small molecule catabolic process pentose catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000581	Dihydroxy-acid/6-phosphogluconate dehydratase, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR037237	IlvD/EDD, N-terminal domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR042096	Dihydroxy-acid dehydratase, C-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR056740	Dihydroxy-acid/6-phosphogluconate dehydratase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	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.