PDBsum entry: 2jfu

Isomerase

PDB id: 2jfu

Contents

Protein chain

272 a.a. *

Ligands

PO4 ×2

Waters ×249

* Residue conservation analysis

PDB id:

2jfu

Name:

Isomerase

Title:

Crystal structure of enterococcus faecium glutamate racemase in complex with phosphate

Structure:

Glutamate racemase. Chain: a. Fragment: residues 4-277. Engineered: yes

Source:

Enterococcus faecium. Organism_taxid: 1352. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.80Å R-factor: 0.192 R-free: 0.209

Authors:

T.Lundqvist

Key ref:

T.Lundqvist et al. (2007). Exploitation of structural and regulatory diversity in glutamate racemases. Nature, 447, 817-822. PubMed id: 17568739 DOI: 10.1038/nature05689

Date:

04-Feb-07 Release date: 03-Jul-07

Protein chain

Q3XZW8  (Q3XZW8_ENTFC) -  Glutamate racemase

Seq: 277 a.a.

Struc: 272 a.a.

Enzyme reactions

• Enzyme class: E.C.5.1.1.3 - Glutamate racemase.
• Reaction: L-glutamate = D-glutamate
• Cofactor: Pyridoxal 5'-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: isomerase activity (3 terms)

reference

DOI no: 10.1038/nature05689

Nature 447:817-822 (2007)

PubMed id: 17568739

Exploitation of structural and regulatory diversity in glutamate racemases.

T.Lundqvist, S.L.Fisher, G.Kern, R.H.Folmer, Y.Xue, D.T.Newton, T.A.Keating, R.A.Alm, B.L.de Jonge.

ABSTRACT

Glutamate racemase is an enzyme essential to the bacterial cell wall biosynthesis pathway, and has therefore been considered as a target for antibacterial drug discovery. We characterized the glutamate racemases of several pathogenic bacteria using structural and biochemical approaches. Here we describe three distinct mechanisms of regulation for the family of glutamate racemases: allosteric activation by metabolic precursors, kinetic regulation through substrate inhibition, and D-glutamate recycling using a d-amino acid transaminase. In a search for selective inhibitors, we identified a series of uncompetitive inhibitors specifically targeting Helicobacter pylori glutamate racemase that bind to a cryptic allosteric site, and used these inhibitors to probe the mechanistic and dynamic features of the enzyme. These structural, kinetic and mutational studies provide insight into the physiological regulation of these essential enzymes and provide a basis for designing narrow-spectrum antimicrobial agents.

Selected figure(s)

Figure 1.
Figure 1: Crystal structures of MurI proteins. a, Crystal structure of H. pylori MurI dimer containing d-glutamate (green) with monomer domains A (N-terminal domain; yellow/orange) and B (C-terminal domain; blue) and the C-terminal helix (red) in the left monomer highlighted. Resistance mutation sites A75T/V (cyan), E151K (red), A35T, C162Y, I178T, G180S, L186F, L206P, Q248R (all in green) and a putative intermonomer salt bridge contact between E151 & K117' (arrow) are shown. b, Overlay of MurI monomers (based on domain A) from E. faecalis/l-glutamate (blue) and E. faecalis/d-glutamate (green). Domain A is indicated in light colours. Glutamate substrates are shown. The hinge axis is shown as a line of red spheres. c, Crystal structure of E. coli MurI containing l-glutamate (green) and the activator UDP-MurNAc-Ala (pink, 2F[O]–F[C] electron density map contoured at 1 ) with monomer domains A (yellow) and B (blue). The C-terminal helix and the 12-amino-acid C-terminal extension (relative to H. pylori sequence) are in red. The orientation is equivalent to the left monomer of H. pylori MurI in a. d, Crystal structure of E. faecalis MurI containing l- (right monomer) and d-glutamate (left monomer), showing monomer domains A (yellow/orange) and B (blue); the C-terminal helix and extension (relative to H. pylori sequence) are highlighted in red. The orientation of the right monomer is equivalent to the left monomer in H. pylori MurI in a.

Figure 3.
Figure 3: Inhibitor-binding site in H. pylori MurI. a, Detailed view of compound binding site of the enzyme–substrate–inhibitor complex of H. pylori MurI and compound A. On compound binding, the C-terminal helix movement induces W252 side-chain displacement and rotation to form a surface for -stacking with the pyrazolopyrimidinedione core of the inhibitor. The pocket vacated by the indole ring movement is filled with the naphthyl moiety of compound A and further stabilized by interactions with V10, G11 (not shown), H183, L186, and W244 (not shown). Additional interactions are formed between the isobutyl substituent of compound A and the F13, S14 (not shown), K17, L253 (not shown) residues, while the pyridyl ring substituent makes contacts with the main-chain atoms of residues E150 and S152. The N-methyl substituent resides in a large cleft that is accessible to solvent. Electron density map for compound A, the substrate and W244 are shown (2F[O]–F[C] electron density map contoured at 1 ) b, Detailed view of compound binding site in the native H. pylori MurI structure. Colour scheme and key residues annotated as described for Fig. 1a.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 447, 817-822) copyright 2007.

Figures were selected by an automated process.