6MNV

Crystal structure of X. citri phosphoglucomutase in complex with CH2FG1P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report

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This is version 2.1 of the entry. See complete history


Literature

Inhibitory Evaluation of alpha PMM/PGM fromPseudomonas aeruginosa: Chemical Synthesis, Enzyme Kinetics, and Protein Crystallographic Study.

Zhu, J.S.Stiers, K.M.Soleimani, E.Groves, B.R.Beamer, L.J.Jakeman, D.L.

(2019) J Org Chem 84: 9627-9636

  • DOI: https://doi.org/10.1021/acs.joc.9b01305
  • Primary Citation of Related Structures:  
    6MLF, 6MLH, 6MLW, 6MNV

  • PubMed Abstract: 

    α-Phosphomannomutase/phosphoglucomutase (αPMM/PGM) from P. aeruginosa is involved in bacterial cell wall assembly and is implicated in P. aeruginosa virulence, yet few studies have addressed αPMM/PGM inhibition from this important Gram-negative bacterial human pathogen. Four structurally different α-d-glucopyranose 1-phosphate (αG1P) derivatives including 1- C -fluoromethylated analogues ( 1 - 3 ), 1,2-cyclic phosph(on)ate analogues ( 4 - 6 ), isosteric methylene phosphono analogues ( 7 and 8 ), and 6-fluoro-αG1P ( 9 ), were synthesized and assessed as potential time-dependent or reversible αPMM/PGM inhibitors. The resulting kinetic data were consistent with the crystallographic structures of the highly homologous Xanthomonas citri αPGM with inhibitors 3 and 7 - 9 binding to the enzyme active site (1.65-1.9 Å). These structural and kinetic insights will enhance the design of future αPMM/PGM inhibitors.


  • Organizational Affiliation

    Department of Chemistry , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphomannomutase/phosphoglucomutase468Xanthomonas citriMutation(s): 0 
Gene Names: xavtCFBP7764_14885
EC: 5.4.2.2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JVS
Query on JVS

Download Ideal Coordinates CCD File 
B [auth A]1-deoxy-1-fluoro-2-O-phosphono-alpha-D-gluco-hept-2-ulopyranose
C7 H14 F O9 P
QZQSCDCQGPJKOV-XUUWZHRGSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
D [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
JVS Binding MOAD:  6MNV Ki: 4.28e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.65α = 90
b = 54.46β = 90
c = 171.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB 1409898

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary