2XBL

Crystal structure of GmhA from Burkholderia pseudomallei in complex with product


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 

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This is version 1.6 of the entry. See complete history


Literature

The Structure of Sedoheptulose-7-Phosphate Isomerase from Burkholderia Pseudomallei Reveals a Zinc Binding Site at the Heart of the Active Site.

Harmer, N.J.

(2010) J Mol Biol 400: 379

  • DOI: https://doi.org/10.1016/j.jmb.2010.04.058
  • Primary Citation of Related Structures:  
    2X3Y, 2XBL

  • PubMed Abstract: 

    Heptoses are found in the surface polysaccharides of most bacteria, contributing to structures that are essential for virulence and antibiotic resistance. Consequently, the biosynthetic enzymes for these sugars are attractive targets for novel antibiotics. The best characterized biosynthetic enzyme is GmhA, which catalyzes the conversion of sedoheptulose-7-phosphate into D-glycero-D-manno-heptopyranose-7-phosphate, the first step in the biosynthesis of heptose. Here, the structure of GmhA from Burkholderia pseudomallei is reported. This enzyme contains a zinc ion at the heart of its active site: this ion stabilizes the active, closed form of the enzyme and presents coordinating side chains as a potential acid and base to drive catalysis. A complex with the product demonstrates that the enzyme retains activity in the crystal and thus suggests that the closed conformation is catalytically relevant and is an excellent target for the development of therapeutics. A revised mechanism for the action of GmhA is postulated on the basis of this structure and the activity of B. pseudomallei GmhA mutants.


  • Organizational Affiliation

    School of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK. [email protected]


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHOHEPTOSE ISOMERASE
A, B, C, D
198Burkholderia pseudomallei K96243Mutation(s): 0 
EC: 5.3.1 (PDB Primary Data), 5.3.1.28 (UniProt)
UniProt
Find proteins for Q93UJ2 (Burkholderia pseudomallei (strain K96243))
Explore Q93UJ2 
Go to UniProtKB:  Q93UJ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93UJ2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M7P
Query on M7P

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
K [auth C],
N [auth D]
7-O-phosphono-D-glycero-alpha-D-manno-heptopyranose
C7 H15 O10 P
SDADNVAZGVDAIM-QTNLNCNHSA-N
PG4
Query on PG4

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G [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

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L [auth C]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

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O [auth D]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
Query on ZN

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E [auth A],
H [auth B],
J [auth C],
M [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.2α = 90
b = 83.68β = 90
c = 126.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXCDEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2010-05-19 
  • Deposition Author(s): Harmer, N.J.

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Data collection
  • Version 1.4: 2018-03-07
    Changes: Source and taxonomy
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Other, Structure summary
  • Version 1.6: 2024-05-08
    Changes: Data collection, Database references, Structure summary