PDBsum entry: 1n8f

Metal binding protein

PDB id: 1n8f

Contents

Protein chains

343 a.a. *

Ligands

SO4 ×8

PEP ×4

Metals

_MN ×4

Waters ×1395

* Residue conservation analysis

PDB id:

1n8f

Name:

Metal binding protein

Title:

Crystal structure of e24q mutant of phenylalanine-regulated 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase (dahp synthase) from escherichia coli in complex with mn2+ and pep

Structure:

Dahp synthetase. Chain: a, b, c, d. Synonym: 2-dehydro-3-deoxyphosphoheptonate aldolase. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: arog. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.75Å R-factor: 0.209 R-free: 0.237

Authors:

I.A.Shumilin,R.Bauerle,R.H.Kretsinger

Key ref:

I.A.Shumilin et al. (2003). The high-resolution structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase reveals a twist in the plane of bound phosphoenolpyruvate. Biochemistry, 42, 3766-3776. PubMed id: 12667068 DOI: 10.1021/bi027257p

Date:

20-Nov-02 Release date: 22-Apr-03

Protein chains

P0AB91  (AROG_ECOLI) -  Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive

Seq: 350 a.a.

Struc: 343 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.5.1.54 - 3-deoxy-7-phosphoheptulonate synthase.
• Pathway: Shikimate and Chorismate Biosynthesis
• Reaction: Phosphoenolpyruvate + D-erythrose 4-phosphate + H₂O = 3-deoxy-D- arabino-hept-2-ulosonate 7-phosphate + phosphate

Phosphoenolpyruvate (Bound ligand (Het Group name = PEP) corresponds exactly) + D-erythrose 4-phosphate + H(2)O = 3-deoxy-D- arabino-hept-2-ulosonate 7-phosphate + phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (4 terms)
• Biochemical function: catalytic activity (3 terms)

reference

DOI no: 10.1021/bi027257p

Biochemistry 42:3766-3776 (2003)

PubMed id: 12667068

The high-resolution structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase reveals a twist in the plane of bound phosphoenolpyruvate.

I.A.Shumilin, R.Bauerle, R.H.Kretsinger.

ABSTRACT

3-Deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS), the first enzyme of the aromatic biosynthetic pathway in microorganisms and plants, catalyzes the aldol-like condensation of phosphoenolpyruvate (PEP) and D-erythrose 4-phosphate (E4P) with the formation of DAHP. The native and the selenomethionine-substituted forms of the phenylalanine-regulated isozyme from Escherichia coli were crystallized in complex with PEP and a metal cofactor, Mn(2+), but the crystals displayed disorder in their unit cells, preventing satisfactory refinement. However, the crystal structure of the E24Q mutant form of DAHPS(Phe) in complex with PEP and Mn(2+) has been determined at 1.75 A resolution. Unlike the tetrameric wild-type enzyme, the E24Q enzyme is dimeric in solution, as a result of the mutational perturbation of four intersubunit salt bridges that are critical for tetramer formation. The protein chain conformation and subunit arrangement in the crystals of E24Q and wild-type DAHPS are very similar. However, the interaction of Mn(2+) and PEP in the enzymatically active E24Q mutant complex differs from the Pb(2+)-PEP and Mn(2+)-phosphoglycolate interactions in two enzymatically inactive wild-type complexes whose structures have been determined previously. The geometry of PEP bound in the active site of the E24Q enzyme deviates from planarity due to a 30 degrees twist of the carboxylate plane relative to the enol plane. In addition, seven water molecules are within contact distance of PEP, two of which are close enough to its C2 atom to serve as the nucleophile required in the reaction.