3SEF

2.4 Angstrom resolution crystal structure of shikimate 5-dehydrogenase (aroE) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with shikimate and NADPH

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	MtdA-like	8074738	3000046	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MtdA-like	8074738	3000046	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MtdA-like	8074738	3000046	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	MtdA-like	8074738	3000046	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)
A	Shikimate_DH	e3sefA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Shikimate_DH	ECOD (1.6)
A	Shikimate_dh_N	e3sefA2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Aminoacid dehydrogenase-like, N-terminal domain	F: Shikimate_dh_N	ECOD (1.6)
B	Shikimate_DH	e3sefB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Shikimate_DH	ECOD (1.6)
B	Shikimate_dh_N	e3sefB2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Aminoacid dehydrogenase-like, N-terminal domain	F: Shikimate_dh_N	ECOD (1.6)
C	Shikimate_DH	e3sefC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Shikimate_DH	ECOD (1.6)
C	Shikimate_dh_N	e3sefC2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Aminoacid dehydrogenase-like, N-terminal domain	F: Shikimate_dh_N	ECOD (1.6)
D	Shikimate_DH	e3sefD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Shikimate_DH	ECOD (1.6)
D	Shikimate_dh_N	e3sefD2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Aminoacid dehydrogenase-like, N-terminal domain	F: Shikimate_dh_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01488	Shikimate / quinate 5-dehydrogenase (Shikimate_DH)	Shikimate / quinate 5-dehydrogenase	-	Family
A, B, C, D	PF08501	Shikimate dehydrogenase substrate binding domain (Shikimate_dh_N)	Shikimate dehydrogenase substrate binding domain	This domain is the substrate binding domain of shikimate dehydrogenase [1].	Domain
A, B, C, D	PF18317	Shikimate 5'-dehydrogenase C-terminal domain (SDH_C)	Shikimate 5'-dehydrogenase C-terminal domain	This domain is found in the C-terminal region of Shikimate 5'-dehydrogenase (SDH) present in Methanocaldococcus jannaschii. SDH catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway. The domain is found j ...	This domain is found in the C-terminal region of Shikimate 5'-dehydrogenase (SDH) present in Methanocaldococcus jannaschii. SDH catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway. The domain is found just after the C-terminal domain (Pfam:PF01488) which is responsible for NADP binding [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Shikimate 5-dehydrogenase	binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors shikimate 3-dehydrogenase (NADP+) activity catalytic activity	amino acid biosynthetic process organic substance metabolic process biosynthetic process organic substance biosynthetic process metabolic process amino acid metabolic process primary metabolic process organonitrogen compound metabolic process aromatic amino acid family biosynthetic process aromatic amino acid metabolic process small molecule biosynthetic process oxoacid metabolic process cellular biosynthetic process cellular metabolic process amino acid biosynthetic process organic substance metabolic process biosynthetic process organic substance biosynthetic process metabolic process amino acid metabolic process primary metabolic process organonitrogen compound metabolic process aromatic amino acid family biosynthetic process aromatic amino acid metabolic process small molecule biosynthetic process oxoacid metabolic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process carboxylic acid metabolic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process organic cyclic compound metabolic process organic cyclic compound biosynthetic process small molecule metabolic process cellular process organic hydroxy compound metabolic process shikimate metabolic process monocarboxylic acid metabolic process dicarboxylic acid metabolic process chorismate metabolic process chorismate biosynthetic process dicarboxylic acid biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR046346	Aminoacid dehydrogenase-like, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR006151	Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase	Domain
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR022893	Shikimate dehydrogenase family	Family
A, B, C, D	IPR011342	Shikimate dehydrogenase	Family
A, B, C, D	IPR041121	SDH, C-terminal	Domain
A, B, C, D	IPR013708	Shikimate dehydrogenase substrate binding, N-terminal	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.