3GGG

The crystal structure of A. aeolicus prephenate dehydrogenase in complex with tyrosine and NAD+

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 [auth D]	SCOP2B Superfamily	6-phosphogluconate dehydrogenase-like	8001196	3000048	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	6-phosphogluconate dehydrogenase-like	8001196	3000048	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	6-phosphogluconate dehydrogenase-like	8001196	3000048	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	6-phosphogluconate dehydrogenase-like	8001196	3000048	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 [auth D]	PDH	e3gggD2	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: PDH	ECOD (1.6)
A [auth D]	NAD_binding_2	e3gggD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_2	ECOD (1.6)
B [auth A]	PDH	e3gggA1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: PDH	ECOD (1.6)
B [auth A]	NAD_binding_2	e3gggA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_2	ECOD (1.6)
D [auth C]	PDH	e3gggC1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: PDH	ECOD (1.6)
D [auth C]	NAD_binding_2	e3gggC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_2	ECOD (1.6)
C [auth B]	PDH	e3gggB1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: PDH	ECOD (1.6)
C [auth B]	NAD_binding_2	e3gggB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth D]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A [auth D]	1.10.3660.10	Mainly Alpha	Orthogonal Bundle	6-phosphogluconate dehydrogenase C-terminal fold	6-phosphogluconate dehydrogenase C-terminal like domain	CATH (4.3.0)
B [auth A]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B [auth A]	1.10.3660.10	Mainly Alpha	Orthogonal Bundle	6-phosphogluconate dehydrogenase C-terminal fold	6-phosphogluconate dehydrogenase C-terminal like domain	CATH (4.3.0)
D [auth C]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D [auth C]	1.10.3660.10	Mainly Alpha	Orthogonal Bundle	6-phosphogluconate dehydrogenase C-terminal fold	6-phosphogluconate dehydrogenase C-terminal like domain	CATH (4.3.0)
C [auth B]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C [auth B]	1.10.3660.10	Mainly Alpha	Orthogonal Bundle	6-phosphogluconate dehydrogenase C-terminal fold	6-phosphogluconate dehydrogenase C-terminal like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D], B [auth A], C [auth B], D [auth C]	PF20463	Prephenate dehydrogenase, dimerization domain (PDH_C)	Prephenate dehydrogenase, dimerization domain	Members of this family are prephenate dehydrogenases EC:1.3.1.12 (PDHs) involved in tyrosine biosynthesis [1]. This is the C-terminal, helical dimerization domain of PDHs [1].	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	PF02153	Prephenate dehydrogenase, nucleotide-binding domain (PDH_N)	Prephenate dehydrogenase, nucleotide-binding domain	Members of this family are prephenate dehydrogenases (PDHs) EC:1.3.1.12 involved in tyrosine biosynthesis. This is the N-terminal nucleotide-binding domain of PDHs, which has a modified Rossmann nucleotide-binding fold with an extended beta-sheet san ...	Members of this family are prephenate dehydrogenases (PDHs) EC:1.3.1.12 involved in tyrosine biosynthesis. This is the N-terminal nucleotide-binding domain of PDHs, which has a modified Rossmann nucleotide-binding fold with an extended beta-sheet sandwiched by three helices on each face [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D], B [auth A], C [auth B], D [auth C]	Prephenate dehydrogenase	NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor prephenate dehydrogenase (NADP+) activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity prephenate dehydrogenase (NAD+) activity	oxoacid metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process tyrosine metabolic process erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process aromatic amino acid family biosynthetic process aromatic amino acid metabolic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process oxoacid metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process tyrosine metabolic process erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process aromatic amino acid family biosynthetic process aromatic amino acid metabolic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process L-amino acid metabolic process aromatic amino acid family biosynthetic process, prephenate pathway proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process erythrose 4-phosphate/phosphoenolpyruvate family amino acid biosynthetic process tyrosine biosynthetic process alpha-amino acid biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D], B [auth A], C [auth B], D [auth C]	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A [auth D], B [auth A], C [auth B], D [auth C]	IPR050812	Prephenate/Arogenate Dehydrogenase	Family
A [auth D], B [auth A], C [auth B], D [auth C]	IPR046826	Prephenate dehydrogenase, nucleotide-binding domain	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR003099	Prephenate dehydrogenase	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily
A [auth D], B [auth A], C [auth B], D [auth C]	IPR046825	Prephenate dehydrogenase, dimerization domain	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.