3JS3 | pdb_00003js3

Crystal structure of type I 3-dehydroquinate dehydratase (aroD) from Clostridium difficile with covalent reaction intermediate

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	d3js3d_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Clostridioides difficile 630 ) [TaxId: 272563 ],	SCOPe (2.08)
C	d3js3c_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Clostridioides difficile 630 ) [TaxId: 272563 ],	SCOPe (2.08)
B	d3js3b_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Clostridioides difficile 630 ) [TaxId: 272563 ],	SCOPe (2.08)
A	d3js3a_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Clostridioides difficile 630 ) [TaxId: 272563 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Aldolase	8079121	3000445	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Aldolase	8079121	3000445	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Aldolase	8079121	3000445	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Aldolase	8079121	3000445	SCOP2B (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	PDEase_I	e3js3D1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (develop294)
C	PDEase_I	e3js3C1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (develop294)
B	PDEase_I	e3js3B1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (develop294)
A	EcoRII-N	e3js3A1	A: alpha bundles	X: Spectrin repeat-like	H: SH3	T: SH3	F: EcoRII-N	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01487	Type I 3-dehydroquinase (DHquinase_I)	Type I 3-dehydroquinase	Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase.) Catalyses the cis-dehydration of 3-dehydroquinate via a covalent imine intermediate giving dehydroshikimate. Dehydroquinase functions in the shikimate pathway which is involved in the ...	Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase.) Catalyses the cis-dehydration of 3-dehydroquinate via a covalent imine intermediate giving dehydroshikimate. Dehydroquinase functions in the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. Type II 3-dehydroquinase catalyses the trans-dehydration of 3-dehydroshikimate see Pfam:PF01220.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	3-dehydroquinate dehydratase	hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity 3-dehydroquinate dehydratase activity	amino acid biosynthetic process biosynthetic process amino acid metabolic process primary metabolic process metabolic process cellular process monocarboxylic acid biosynthetic process 3,4-dihydroxybenzoate metabolic process benzene-containing compound metabolic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process organic acid biosynthetic process organic acid metabolic process amino acid biosynthetic process biosynthetic process amino acid metabolic process primary metabolic process metabolic process cellular process monocarboxylic acid biosynthetic process 3,4-dihydroxybenzoate metabolic process benzene-containing compound metabolic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process organic acid biosynthetic process organic acid metabolic process catechol-containing compound metabolic process carboxylic acid biosynthetic process phenol-containing compound metabolic process 3,4-dihydroxybenzoate biosynthetic process phenol-containing compound biosynthetic process small molecule metabolic process catechol-containing compound biosynthetic process monocarboxylic acid metabolic process dicarboxylic acid metabolic process chorismate metabolic process chorismate biosynthetic process dicarboxylic acid biosynthetic process aromatic amino acid family biosynthetic process aromatic amino acid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR018508	3-dehydroquinate dehydratase, active site	Active Site
A, B, C, D	IPR001381	3-dehydroquinate dehydratase type I	Family
A, B, C, D	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D	IPR050146	Type-I 3-dehydroquinase	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.