2I22

Crystal structure of Escherichia coli phosphoheptose isomerase in complex with reaction substrate sedoheptulose 7-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and Function of Sedoheptulose-7-phosphate Isomerase, a Critical Enzyme for Lipopolysaccharide Biosynthesis and a Target for Antibiotic Adjuvants

Taylor, P.L.Blakely, K.M.de Leon, G.P.Walker, J.R.McArthur, F.Evdokimova, E.Zhang, K.Valvano, M.A.Wright, G.D.Junop, M.S.

(2008) J.Biol.Chem. 283: 2835-2845

  • DOI: 10.1074/jbc.M706163200
  • Primary Citation of Related Structures:  1X92, 2I2W, 3BJZ

  • PubMed Abstract: 
  • The barrier imposed by lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria presents a significant challenge in treatment of these organisms with otherwise effective hydrophobic antibiotics. The absence of L-glycero-D-manno-heptos ...

    The barrier imposed by lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria presents a significant challenge in treatment of these organisms with otherwise effective hydrophobic antibiotics. The absence of L-glycero-D-manno-heptose in the LPS molecule is associated with a dramatically increased bacterial susceptibility to hydrophobic antibiotics and thus enzymes in the ADP-heptose biosynthesis pathway are of significant interest. GmhA catalyzes the isomerization of D-sedoheptulose 7-phosphate into D-glycero-D-manno-heptose 7-phosphate, the first committed step in the formation of ADP-heptose. Here we report structures of GmhA from Escherichia coli and Pseudomonas aeruginosa in apo, substrate, and product-bound forms, which together suggest that GmhA adopts two distinct conformations during isomerization through reorganization of quaternary structure. Biochemical characterization of GmhA mutants, combined with in vivo analysis of LPS biosynthesis and novobiocin susceptibility, identifies key catalytic residues. We postulate GmhA acts through an enediol-intermediate isomerase mechanism.


    Organizational Affiliation

    Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1200 Main Street West, Hamilton, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoheptose isomerase
A, B, C, D
212Escherichia coli (strain K12)Gene Names: gmhA (lpcA, tfrA, yafI)
EC: 5.3.1.28
Find proteins for P63224 (Escherichia coli (strain K12))
Go to UniProtKB:  P63224
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I22
Query on I22

Download SDF File 
Download CCD File 
B
D-ALTRO-HEPT-2-ULOSE 7-PHOSPHATE
7-O-PHOSPHONO-D-ALTRO-HEPT-2-ULOSE; SEDOHEPTULOSE 7-PHOSPHATE
C7 H15 O10 P
JDTUMPKOJBQPKX-GBNDHIKLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 73.045α = 90.00
b = 76.540β = 106.13
c = 78.316γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata scaling
CrystalCleardata reduction
CrystalCleardata collection
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance