2I22

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 

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Ligand Structure Quality Assessment 


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, 2I22, 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-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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphoheptose isomeraseA, B, C, D212Escherichia coliMutation(s): 0 
Gene Names: gmhAlpcAtfrAb0222
EC: 5.3.1 (PDB Primary Data), 5.3.1.28 (UniProt)
UniProt
Find proteins for P63224 (Escherichia coli (strain K12))
Explore P63224 
Go to UniProtKB:  P63224
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63224
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I22
Query on I22

Download Ideal Coordinates CCD File 
E [auth B]D-ALTRO-HEPT-2-ULOSE 7-PHOSPHATE
C7 H15 O10 P
JDTUMPKOJBQPKX-GBNDHIKLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.045α = 90
b = 76.54β = 106.13
c = 78.316γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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