2WF7

Structure of Beta-Phosphoglucomutase inhibited with Glucose-6- phosphonate and Aluminium tetrafluoride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

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This is version 1.3 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: 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 ...

    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; Manchester Institute of Biotechnology, Manchester M1 7DN, United Kingdom; and david.jakeman@dal.ca g.m.blackburn@sheffield.ac.uk j.waltho@sheffield.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-PHOSPHOGLUCOMUTASEA221Lactococcus 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G7P (Subject of Investigation/LOI)
Query on G7P

Download Ideal Coordinates CCD File 
D [auth A]6,7-dideoxy-7-phosphono-beta-D-gluco-heptopyranose
C7 H15 O8 P
POGBMBNNYPHAGN-XUUWZHRGSA-N
 Ligand Interaction
ALF
Query on ALF

Download Ideal Coordinates CCD File 
B [auth A]TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A], E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.5α = 90
b = 54.3β = 90
c = 104.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata 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: 2010-05-19
    Type: Initial release
  • Version 1.1: 2014-08-20
    Changes: Advisory, Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2014-09-10
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Derived calculations, Other, Structure summary