PDBsum entry 1kfl

Lyase

PDB id: 1kfl

Contents

Protein chains

(+ 2 more) 350 a.a. *

Ligands

SO4 ×16

PHE ×8

PEP ×8

Metals

_MN ×8

* Residue conservation analysis

PDB id:

1kfl

Name:

Lyase

Title:

Crystal structure of phenylalanine-regulated 3-deoxy-d-arabino- heptulosonate-7-phosphate synthase (dahp synthase) from e.Coli complexed with mn2+, pep, and phe

Structure:

3-deoxy-d-arabino-heptulosonate-7-phosphate synthase. Chain: a, b, c, d, e, f, g, h. Synonym: phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive. Dahp synthetase, phenylalanine repressible. Phospho-2-keto-3- deoxyheptonate aldolase. Engineered: yes

Source:

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

Biol. unit:

Tetramer (from PQS)

Resolution:

2.80Å R-factor: 0.218 R-free: 0.246

Authors:

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

Key ref:

I.A.Shumilin et al. (2002). Allosteric inhibition of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase alters the coordination of both substrates. J Mol Biol, 320, 1147-1156. PubMed id: 12126632 DOI: 10.1016/S0022-2836(02)00545-4

Date:

21-Nov-01 Release date: 23-Aug-02

Protein chains

P0AB91  (AROG_ECOLI) -  Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive from Escherichia coli (strain K12)

Seq: 350 a.a.

Struc: 350 a.a.

Enzyme reactions

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

D-erythrose 4-phosphate + phosphoenolpyruvate + H2O (Bound ligand (Het Group name = PEP) corresponds exactly) = 7-phospho-2- dehydro-3-deoxy-D-arabino-heptonate + phosphate

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

reference

DOI no: 10.1016/S0022-2836(02)00545-4

J Mol Biol 320:1147-1156 (2002)

PubMed id: 12126632

Allosteric inhibition of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase alters the coordination of both substrates.

I.A.Shumilin, C.Zhao, 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 and D-erythrose-4-phosphate with the formation of 3-deoxy-D-arabino-heptulosonate-7-phosphate. In Escherichia coli, there are three isoforms of DAHPS, each specifically feedback-regulated by one of the three aromatic amino acid end products. The crystal structure of the phenylalanine-regulated DAHPS from E.coli in complex with its inhibitor, L-phenylalanine, phosphoenolpyruvate, and metal cofactor, Mn(2+), has been determined to 2.8A resolution. Phe binds in a cavity formed by residues of two adjacent subunits and is located about 20A from the closest active site. A model for the mechanism of allosteric inhibition has been derived from conformational differences between the Phe-bound and previously determined Phe-free structures. Two interrelated paths of conformational changes transmit the inhibitory signal from the Phe-binding site to the active site of DAHPS. The first path involves transmission within a single subunit due to the movement of adjacent segments of the protein. The second involves alterations in the contacts between subunits. The combination of these two paths changes the conformation of one of the active site loops significantly and shifts the other slightly. This alters the interaction of DAHPS with both of its substrates. Upon binding of Phe, the enzyme loses the ability to bind D-erythrose-4-phosphate and binds phosphoenolpyruvate in a flipped orientation.

Selected figure(s)

Figure 1.
Figure 1. The DAHPS*Mn*PEP*Phe tetramer. (a) One of two nearly identical +Phe tetramers in the asymmetric unit. Each of the tight dimers forming the tetramer (AB and CD) consists of a green and a purple subunit. The eight strands of the (b/a)[8] barrel are blue in all subunits. Mn2+ (cyan) and PEP (gold) are at the C-end of the barrel. Bound Phe (gold) is near the inter-subunit b6a/b6b/b0^* sheets. The orange square outlines the area represented in (b), which shows the superposition of Leu16 and the Trp215-Gly216-His217 segments of four subunits of -Phe (gray) and +Phe (same color as in (a)). The 222 symmetry of the -Phe enzyme is reduced to 2-fold symmetry in the +Phe enzyme. H-bonds formed in +Phe DAHPS are shown as light blue dotted lines. All figures were drawn with RIBBONS.[15]

Figure 6.
Figure 6. Flipping of PEP in the active site of DAHPS upon Phe binding. The PEP coordinating sphere shown in the same orientation in (a) -Phe and (b) +Phe DAHPS. H-bonds, shown as dotted lines, are in the range of 2.8-3.3 Å. In both forms, PEP also has p,p interaction with the imidazole ring of His268. The thin gray trace in (b) represents superimposed PEP from (a). Non-coordinating Lys97 and Arg165 (two conformers) are shown in (b).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 320, 1147-1156) copyright 2002.

Figures were selected by an automated process.