Crystal structure of human phosphoglycerate mutase family member 5 (PGAM5) in its enzymatically active dodecameric form induced by the presence of the N-terminal WDPNWD motif

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

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Structures of PGAM5 Provide Insight into Active Site Plasticity and Multimeric Assembly.

Chaikuad, A.Filippakopoulos, P.Marcsisin, S.R.Picaud, S.Schroder, M.Sekine, S.Ichijo, H.Engen, J.R.Takeda, K.Knapp, S.

(2017) Structure 25: 1089-1099.e3

  • DOI: https://doi.org/10.1016/j.str.2017.05.020
  • Primary Citation of Related Structures:  
    3MXO, 3O0T, 5MUF

  • PubMed Abstract: 

    PGAM5 is a mitochondrial membrane protein that functions as an atypical Ser/Thr phosphatase and is a regulator of oxidative stress response, necroptosis, and autophagy. Here we present several crystal structures of PGAM5 including the activating N-terminal regulatory sequences, providing a model for structural plasticity, dimerization of the catalytic domain, and the assembly into an enzymatically active dodecameric form. Oligomeric states observed in structures were supported by hydrogen exchange mass spectrometry, size-exclusion chromatography, and analytical ultracentrifugation experiments in solution. We report that the catalytically important N-terminal WDPNWD motif acts as a structural integrator assembling PGAM5 into a dodecamer, allosterically activating the phosphatase by promoting an ordering of the catalytic loop. Additionally the observed active site plasticity enabled visualization of essential conformational rearrangements of catalytic elements. The comprehensive biophysical characterization offers detailed structural models of this key mitochondrial phosphatase that has been associated with the development of diverse diseases.

  • Organizational Affiliation

    Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University and Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany; Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK. Electronic address: chaikuad@pharmchem.uni-frankfurt.de.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase PGAM5, mitochondrial
A, B, C
238Homo sapiensMutation(s): 0 
Gene Names: PGAM5
UniProt & NIH Common Fund Data Resources
Find proteins for Q96HS1 (Homo sapiens)
Explore Q96HS1 
Go to UniProtKB:  Q96HS1
GTEx:  ENSG00000247077 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96HS1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.215α = 90
b = 141.403β = 90
c = 183.12γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2017-07-19
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description