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: 1.5 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 111: 12384

  • DOI: 10.1073/pnas.1402850111
  • Primary Citation of Related Structures:  

  • 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 fluoromethylenephosp ...

    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; Structural Biology Group, European Synchrotron Radiation Facility, 38042 Grenoble, Cedex 9, France; European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, Cedex 9, France;,Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom; david.jakeman@dal.ca g.m.blackburn@sheffield.ac.uk j.waltho@sheffield.ac.uk.,Structural Biology Group, European Synchrotron Radiation Facility, 38042 Grenoble, Cedex 9, France; European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, Cedex 9, France; Unit of Virus Host Cell Interactions, University of Grenoble Alpes-European Molecular Biology Laboratory-Centre National de la Recherche Scientifique, 38042 Grenoble, Cedex 9, France.,Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom;,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.,Department of Chemistry, College of Pharmacy, Dalhousie University, Halifax, NS, Canada B3H 4R2;,Department of Chemistry, College of Pharmacy, Dalhousie University, Halifax, NS, Canada B3H 4R2; david.jakeman@dal.ca g.m.blackburn@sheffield.ac.uk j.waltho@sheffield.ac.uk.,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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-PHOSPHOGLUCOMUTASE
A
221Lactococcus lactis subsp. lactis (strain IL1403)Mutation(s): 0 
Gene Names: pgmB
EC: 5.4.2.6
Find proteins for P71447 (Lactococcus lactis subsp. lactis (strain IL1403))
Go to UniProtKB:  P71447
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MGF
Query on MGF

Download SDF File 
Download CCD File 
A
TRIFLUOROMAGNESATE
F3 Mg
GJOMWUHGUQLOAC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GRX
Query on GRX

Download SDF File 
Download CCD File 
A
(S)-1-beta-phosphonofluoromethylene-1-deoxy-D-glucopyranose
C7 H14 F O8 P
BUPRWODHUABASJ-GEGSFZHJSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GRXKd: 660000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.541α = 90.00
b = 54.337β = 90.00
c = 104.346γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-08-20
    Type: Database references
  • Version 1.2: 2014-09-10
    Type: Database references