4C4S

Structure of beta-phosphoglucomutase in complex with an alpha- fluorophosphonate analogue of beta-glucose-1-phosphate and magnesium trifluoride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Alpha-Fluorophosphonates Reveal How a Phosphomutase Conserves Transition State Conformation Over Hexose Recognition in its Two-Step Reaction.

Jin, Y.Bhattasali, D.Pellegrini, E.Forget, S.M.Baxter, N.J.Cliff, M.J.Bowler, M.W.Jakeman, D.L.Blackburn, G.M.Waltho, J.P.

(2014) Proc Natl Acad Sci U S A 111: 12384

  • DOI: https://doi.org/10.1073/pnas.1402850111
  • Primary Citation of Related Structures:  
    2WF7, 4C4R, 4C4S, 4C4T

  • PubMed Abstract: 

    β-Phosphoglucomutase (βPGM) catalyzes isomerization of β-D-glucose 1-phosphate (βG1P) into D-glucose 6-phosphate (G6P) via sequential phosphoryl transfer steps using a β-D-glucose 1,6-bisphosphate (βG16BP) intermediate. Synthetic fluoromethylenephosphonate and methylenephosphonate analogs of βG1P deliver novel step 1 transition state analog (TSA) complexes for βPGM, incorporating trifluoromagnesate and tetrafluoroaluminate surrogates of the phosphoryl group. Within an invariant protein conformation, the β-D-glucopyranose ring in the βG1P TSA complexes (step 1) is flipped over and shifted relative to the G6P TSA complexes (step 2). Its equatorial hydroxyl groups are hydrogen-bonded directly to the enzyme rather than indirectly via water molecules as in step 2. The (C)O-P bond orientation for binding the phosphate in the inert phosphate site differs by ∼ 30° between steps 1 and 2. By contrast, the orientations for the axial O-Mg-O alignment for the TSA of the phosphoryl group in the catalytic site differ by only ∼ 5°, and the atoms representing the five phosphorus-bonded oxygens in the two transition states (TSs) are virtually superimposable. The conformation of βG16BP in step 1 does not fit into the same invariant active site for step 2 by simple positional interchange of the phosphates: the TS alignment is achieved by conformational change of the hexose rather than the protein.


  • Organizational Affiliation

    Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom;


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-PHOSPHOGLUCOMUTASE221Lactococcus lactisMutation(s): 0 
EC: 5.4.2.6
UniProt
Find proteins for P71447 (Lactococcus lactis subsp. lactis (strain IL1403))
Explore P71447 
Go to UniProtKB:  P71447
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP71447
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.541α = 90
b = 54.337β = 90
c = 104.346γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-08-20
    Changes: Database references
  • Version 1.2: 2014-09-10
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Other, Structure summary
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary