2PV7 | pdb_00002pv7

Crystal structure of chorismate mutase / prephenate dehydrogenase (tyrA) (1574749) from Haemophilus influenzae RD at 2.00 A resolution

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)
B	d2pv7b1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	TyrA dimerization domain-like	Prephenate dehydrogenase TyrA	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
B	d2pv7b2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	Prephenate dehydrogenase TyrA	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
A	d2pv7a1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	TyrA dimerization domain-like	Prephenate dehydrogenase TyrA	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
A	d2pv7a2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	Prephenate dehydrogenase TyrA	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Prephenate dehydrogenase (TyrA)-like	8058543	4000115	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	6-phosphogluconate dehydrogenase-like	8058544	3000048	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	6-phosphogluconate dehydrogenase-like	8058544	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)
B		e2pv7B2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: FAD_binding_3	F:	ECOD (20:10:01)
B		e2pv7B3	A: DEATH domain	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: PDH_C	F:	ECOD (20:10:01)
A		e2pv7A1	A: 6-phosphogluconate dehydrogenase C-terminal domain-like	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: PDH_C	F:	ECOD (20:10:01)
A		e2pv7A2	A: Rossmann-like	X: Rossmann-related	H: NAD(P)-binding Rossmann-fold domains	T: PDH_N	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
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)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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, B	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, B	T-protein [Includes: Chorismate mutase (EC 5.4.99.5) (CM) and Prephenate dehydrogenase (EC 1.3.1.12) (PDH)]	NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding isomerase activity chorismate mutase activity catalytic activity NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding isomerase activity chorismate mutase activity catalytic activity intramolecular transferase activity 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 prephenate dehydrogenase (NAD+) activity	oxoacid metabolic process L-tyrosine biosynthetic 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 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 L-tyrosine biosynthetic 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 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 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 alpha-amino acid biosynthetic process dicarboxylic acid metabolic process chorismate metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR050812	Prephenate/Arogenate Dehydrogenase	Family
A, B	IPR003099	Prephenate dehydrogenase	Domain
A, B	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR046825	Prephenate dehydrogenase, dimerization domain	Domain
A, B	IPR036979	Chorismate mutase domain superfamily	Homologous Superfamily
A, B	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR008244	Bifunctional chorismate mutase/prephenate dehydrogenase T-protein	Family
A, B	IPR002701	Chorismate mutase II, prokaryotic-type	Domain
A, B	IPR036263	Chorismate mutase type II superfamily	Homologous Superfamily
A, B	IPR046826	Prephenate dehydrogenase, nucleotide-binding domain	Domain
A, B	IPR011277	Chorismate mutase, T-protein	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.