3MXO

Crystal structure oh human phosphoglycerate mutase family member 5 (PGAM5)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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 

  • DOI: 10.1016/j.str.2017.05.020
  • Structures With Same Primary Citation

  • 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-te ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein phosphatase PGAM5, mitochondrial
A, B
202Homo sapiensMutation(s): 0 
Gene Names: PGAM5
EC: 3.1.3.16
Find proteins for Q96HS1 (Homo sapiens)
Go to UniProtKB:  Q96HS1
NIH Common Fund Data Resources
PHAROS  Q96HS1
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download CCD File 
B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.602α = 90
b = 70.946β = 90
c = 81.476γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
SHARPphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-07-12
    Changes: Database references