Crystal Structure of D,D-heptose 1.7-bisphosphate phosphatase from E. Coli.

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

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Structural and kinetic characterization of the LPS biosynthetic enzyme D-alpha,beta-D-heptose-1,7-bisphosphate phosphatase (GmhB) from Escherichia coli.

Taylor, P.L.Sugiman-Marangos, S.Zhang, K.Valvano, M.A.Wright, G.D.Junop, M.S.

(2010) Biochemistry 49: 1033-1041

  • DOI: https://doi.org/10.1021/bi901780j
  • Primary Citation of Related Structures:  
    2GMW, 3L1U, 3L1V

  • PubMed Abstract: 

    Lipopolysaccharide is a major component of the outer membrane of gram-negative bacteria and provides a permeability barrier to many commonly used antibiotics. ADP-heptose residues are an integral part of the LPS inner core, and mutants deficient in heptose biosynthesis demonstrate increased membrane permeability. The heptose biosynthesis pathway involves phosphorylation and dephosphorylation steps not found in other pathways for the synthesis of nucleotide sugar precursors. Consequently, the heptose biosynthetic pathway has been marked as a novel target for antibiotic adjuvants, which are compounds that facilitate and potentiate antibiotic activity. D-alpha,beta-D-heptose-1,7-bisphosphate phosphatase (GmhB) catalyzes the third essential step of LPS heptose biosynthesis. This study describes the first crystal structure of GmhB and enzymatic analysis of the protein. Structure-guided mutations followed by steady state kinetic analysis, together with established precedent for HAD phosphatases, suggest that GmhB functions through a phosphoaspartate intermediate. This study provides insight into the structure-function relationship of GmhB, a new target for combatting gram-negative bacterial infection.

  • Organizational Affiliation

    Department of Biochemistry and Biomedical Sciences and M. G. DeGroote Institute for Infectious Disease Research, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D,D-heptose 1,7-bisphosphate phosphatase
A, B
211Escherichia coliMutation(s): 0 
Gene Names: gmhB
EC: 3.1.3
Find proteins for P63228 (Escherichia coli (strain K12))
Explore P63228 
Go to UniProtKB:  P63228
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63228
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.904α = 90
b = 63.977β = 90
c = 103.324γ = 90
Software Package:
Software NamePurpose
CrystalCleardata reduction
d*TREKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2017-10-25
    Changes: Author supporting evidence
  • Version 1.5: 2024-02-14
    Changes: Data collection, Database references, Derived calculations