1VR6 | pdb_00001vr6

Crystal structure of Phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthase) (TM0343) from Thermotoga Maritima at 1.92 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)
D	d1vr6d2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I DAHP synthetase	automated matches	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
D	d1vr6d3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
C	d1vr6c2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I DAHP synthetase	automated matches	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
C	d1vr6c3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d1vr6b2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I DAHP synthetase	automated matches	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d1vr6b3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d1vr6a2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I DAHP synthetase	automated matches	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d1vr6a3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima ) [TaxId: 2336 ],	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	8032694	3000445	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Aldolase	8032694	3000445	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Aldolase	8032694	3000445	SCOP2B (2022-06-29)
A	SCOP2 Family	Class I DAHP synthetase	8020314	4003245	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Aldolase	8032694	3000445	SCOP2 (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	Sigma_1_2	e1vr6D1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
C	Sigma_1_2	e1vr6C1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
B	Sigma_1_2	e1vr6B1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
A	Gln-synt_C	e1vr6A2	A: a/b three-layered sandwiches	X: Hormone receptor domain (HRM, Pfam 02793)	H: dsRNA-binding domain-like	T: dsRNA-binding domain-like	F: Gln-synt_C	ECOD (v294.1)
A	DAHP_synth_1	e1vr6A3	A: a/b three-layered sandwiches	X: Metallothionein	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DAHP_synth_1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.70.1140	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Phospho-2-dehydro-3-deoxyheptonate aldolase	CATH (4.3.0)
D	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	3.30.70.1140	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Phospho-2-dehydro-3-deoxyheptonate aldolase	CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	3.30.70.1140	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Phospho-2-dehydro-3-deoxyheptonate aldolase	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	3.30.70.1140	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Phospho-2-dehydro-3-deoxyheptonate aldolase	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	PF18152	DAHP synthase ferredoxin-like domain (DAHP_snth_FXD)	DAHP synthase ferredoxin-like domain	This domain is found in 3-Deoxy-d-arabino-heptulosonate-7-phosphate synthase (DAHPS) present in Thermotoga maritime. DAHPS catalyzes the first reaction of the aromatic biosynthetic pathway in bacteria, fungi, and plants, the condensation of PEP and E ...	This domain is found in 3-Deoxy-d-arabino-heptulosonate-7-phosphate synthase (DAHPS) present in Thermotoga maritime. DAHPS catalyzes the first reaction of the aromatic biosynthetic pathway in bacteria, fungi, and plants, the condensation of PEP and E4P with the formation of DAHP. The domain is ferredoxin-like and is thought to play a critical role in feedback regulation of the enzyme [1].	Domain
A, B, C, D	PF00793	DAHP synthetase I family (DAHP_synth_1)	DAHP synthetase I family	Members of this family catalyse the first step in aromatic amino acid biosynthesis from chorismate. E-coli has three related synthetases, which are inhibited by different aromatic amino acids. This family also includes KDSA which has very similar cat ...	Members of this family catalyse the first step in aromatic amino acid biosynthesis from chorismate. E-coli has three related synthetases, which are inhibited by different aromatic amino acids. This family also includes KDSA which has very similar catalytic activity but is involved in the first step of liposaccharide biosynthesis. The enzyme is also part of the shikimate pathway, EC:2.5.1.54.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Phospho-2-dehydro-3-deoxyheptonate aldolase	lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity transferase activity 3-deoxy-7-phosphoheptulonate synthase activity transferase activity, transferring alkyl or aryl (other than methyl) groups	amino acid biosynthetic process biosynthetic process amino acid metabolic process primary metabolic process metabolic process cellular process oxoacid metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process chorismate metabolic process amino acid biosynthetic process biosynthetic process amino acid metabolic process primary metabolic process metabolic process cellular process oxoacid metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process chorismate metabolic process chorismate biosynthetic process small molecule metabolic 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	IPR041071	DAHP synthase ferredoxin-like domain	Domain
A, B, C, D	IPR052899	Class-I DAHP synthase	Family
A, B, C, D	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D	IPR006218	DAHP synthetase I/KDSA	Domain
A, B, C, D	IPR006268	Phospho-2-dehydro-3-deoxyheptonate aldolase, subtype 2	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.