7PO7

Phosphoglycolate phosphatase from Mus musculus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Glycolytic flux control by drugging phosphoglycolate phosphatase.

Jeanclos, E.Schlotzer, J.Hadamek, K.Yuan-Chen, N.Alwahsh, M.Hollmann, R.Fratz, S.Yesilyurt-Gerhards, D.Frankenbach, T.Engelmann, D.Keller, A.Kaestner, A.Schmitz, W.Neuenschwander, M.Hergenroder, R.Sotriffer, C.von Kries, J.P.Schindelin, H.Gohla, A.

(2022) Nat Commun 13: 6845-6845

  • DOI: https://doi.org/10.1038/s41467-022-34228-2
  • Primary Citation of Related Structures:  
    7PO7, 7POE

  • PubMed Abstract: 

    Targeting the intrinsic metabolism of immune or tumor cells is a therapeutic strategy in autoimmunity, chronic inflammation or cancer. Metabolite repair enzymes may represent an alternative target class for selective metabolic inhibition, but pharmacological tools to test this concept are needed. Here, we demonstrate that phosphoglycolate phosphatase (PGP), a prototypical metabolite repair enzyme in glycolysis, is a pharmacologically actionable target. Using a combination of small molecule screening, protein crystallography, molecular dynamics simulations and NMR metabolomics, we discover and analyze a compound (CP1) that inhibits PGP with high selectivity and submicromolar potency. CP1 locks the phosphatase in a catalytically inactive conformation, dampens glycolytic flux, and phenocopies effects of cellular PGP-deficiency. This study provides key insights into effective and precise PGP targeting, at the same time validating an allosteric approach to control glycolysis that could advance discoveries of innovative therapeutic candidates.


  • Organizational Affiliation

    Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycerol-3-phosphate phosphatase
A, B, C, D, E
A, B, C, D, E, F, G, H
321Mus musculusMutation(s): 2 
Gene Names: Pgp
EC: 3.1.3.21 (PDB Primary Data), 3.1.3.48 (PDB Primary Data)
UniProt
Find proteins for Q8CHP8 (Mus musculus)
Explore Q8CHP8 
Go to UniProtKB:  Q8CHP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8CHP8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth F]
EA [auth F]
J [auth A]
N [auth B]
NA [auth H]
DA [auth F],
EA [auth F],
J [auth A],
N [auth B],
NA [auth H],
S [auth C],
W [auth D],
Z [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth F]
CA [auth F]
GA [auth G]
IA [auth H]
JA [auth H]
AA [auth F],
CA [auth F],
GA [auth G],
IA [auth H],
JA [auth H],
K [auth B],
KA [auth H],
LA [auth H],
M [auth B],
O [auth C],
Q [auth C],
R [auth C],
T [auth D],
V [auth D],
Y [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
BA [auth F]
FA [auth G]
HA [auth H]
I [auth A]
L [auth B]
BA [auth F],
FA [auth G],
HA [auth H],
I [auth A],
L [auth B],
P [auth C],
U [auth D],
X [auth E]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
MA [auth H]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.262α = 103.457
b = 91.197β = 89.98
c = 101.317γ = 104.632
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-07-03
    Changes: Database references