9CMY

Human DJ-1, 6.5-18.5 min mixing with methylglyoxal, fixed target serial crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 
    0.175 (Depositor), 0.175 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
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Literature

Resolving DJ-1 Glyoxalase Catalysis Using Mix-and-Inject Serial Crystallography at a Synchrotron.

Zielinski, K.A.Dolamore, C.Dalton, K.M.Smith, N.Termini, J.Henning, R.Srajer, V.Hekstra, D.R.Pollack, L.Wilson, M.A.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.07.19.604369
  • Primary Citation of Related Structures:  
    9CEI, 9CFI, 9CFM, 9CFO, 9CFQ, 9CFY, 9CFZ, 9CG0, 9CGA, 9CGB, 9CGD, 9CGE, 9CGF, 9CGG, 9CMX, 9CMY

  • PubMed Abstract: 

    DJ-1 (PARK7) is an intensively studied protein whose cytoprotective activities are dysregulated in multiple diseases. DJ-1 has been reported as having two distinct enzymatic activities in defense against reactive carbonyl species that are difficult to distinguish in conventional biochemical experiments. Here, we establish the mechanism of DJ-1 using a synchrotron-compatible version of mix-and-inject-serial crystallography (MISC), which was previously performed only at XFELs, to directly observe DJ-1 catalysis. We designed and used new diffusive mixers to collect time-resolved Laue diffraction data of DJ-1 catalysis at a pink beam synchrotron beamline. Analysis of structurally similar methylglyoxal-derived intermediates formed through the DJ-1 catalytic cycle shows that the enzyme catalyzes nearly two turnovers in the crystal and defines key aspects of its glyoxalase mechanism. In addition, DJ-1 shows allosteric communication between a distal site at the dimer interface and the active site that changes during catalysis. Our results rule out the widely cited deglycase mechanism for DJ-1 action and provide an explanation for how DJ-1 produces L-lactate with high chiral purity.


  • Organizational Affiliation

    School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein deglycase DJ-1192Homo sapiensMutation(s): 0 
Gene Names: PARK7
EC: 3.1.2 (PDB Primary Data), 3.5.1 (PDB Primary Data), 3.5.1.124 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q99497 (Homo sapiens)
Explore Q99497 
Go to UniProtKB:  Q99497
PHAROS:  Q99497
GTEx:  ENSG00000116288 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99497
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free:  0.175 (Depositor), 0.175 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.234α = 90
b = 76.234β = 90
c = 76.392γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM153337

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release