2QMX

The crystal structure of L-Phe inhibited prephenate dehydratase from Chlorobium tepidum TLS

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	ACT_1	e2qmxA3	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: ACT_1	ECOD (1.6)
A	PDT_N	e2qmxA2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: PDT_N	ECOD (1.6)
A	PDT_C	e2qmxA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: PDT_C	ECOD (1.6)
B	ACT_1	e2qmxB4	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: ACT_1	ECOD (1.6)
B	PDT_N	e2qmxB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: PDT_N	ECOD (1.6)
B	PDT_C	e2qmxB2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: PDT_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
A	3.30.70.260	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT domain	CATH (4.3.0)
B	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
B	3.30.70.260	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00800	Prephenate dehydratase (PDT)	Prephenate dehydratase	-	Family
A, B	PF01842	ACT domain (ACT)	ACT domain	This family of domains generally have a regulatory role. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulati ...	This family of domains generally have a regulatory role. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. The ACT domain is found in: D-3-phosphoglycerate dehydrogenase EC:1.1.1.95 Swiss:P08328, which is inhibited by serine [1]. Aspartokinase EC:2.7.2.4 Swiss:P53553, which is regulated by lysine. Acetolactate synthase small regulatory subunit Swiss:P00894, which is inhibited by valine. Phenylalanine-4-hydroxylase EC:1.14.16.1 Swiss:P00439, which is regulated by phenylalanine. Prephenate dehydrogenase EC:4.2.1.51 Swiss:P21203. formyltetrahydrofolate deformylase EC:3.5.1.10, Swiss:P37051, which is activated by methionine and inhibited by glycine. GTP pyrophosphokinase EC:2.7.6.5 Swiss:P11585	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Prephenate dehydratase	isomerase activity chorismate mutase activity catalytic activity intramolecular transferase activity prephenate dehydratase activity hydro-lyase activity lyase activity carbon-oxygen lyase activity	oxoacid metabolic process cellular 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 erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process L-phenylalanine biosynthetic process aromatic amino acid family biosynthetic process aromatic amino acid metabolic process small molecule biosynthetic process cellular metabolic process oxoacid metabolic process cellular 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 erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process L-phenylalanine biosynthetic process aromatic amino acid family biosynthetic process aromatic amino acid metabolic process small molecule biosynthetic process cellular metabolic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process L-amino acid metabolic process L-phenylalanine 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 alpha-amino acid biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR018528	Prephenate dehydratase, conserved site	Conserved Site
A, B	IPR008242	Bifunctional P-protein, chorismate mutase/prephenate dehydratase	Family
A, B	IPR045865	ACT-like domain	Homologous Superfamily
A, B	IPR002912	ACT domain	Domain
A, B	IPR001086	Prephenate dehydratase	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	prephenate dehydratase M-CSA #485	Prephenate dehydratase (EC:4.2.1.51, PDT) catalyses the decarboxylation of prephenate to phenylpyruvate. In microorganisms it is part of the terminal pathway of phenylalanine biosynthesis. In some bacteria, e.g. E. coli PDT is part of the multi-functional P-protein that also catalyses the transformation of chorismate into prephenate (chorismate mutase), while in other bacteria it is a monofunctional enzyme.	Defined by 2 residues: THR:A-174 [auth A-171]PHE:A-176 [auth A-173] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.2.1.51 (PDB Primary Data) Search M-CSA Motif + EC 4.2.1.51

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.