9CFY | pdb_00009cfy

Human DJ-1, 15 sec mixing with methylglyoxal, pink beam time-resolved serial crystallography

• PDB DOI: https://doi.org/10.2210/pdb9CFY/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-27 Released: 2025-03-12 
• Deposition Author(s): Zielinski, K.A., Dolamore, C., Dalton, K., Meisburger, S.P., Smith, N., Termini, T., Henning, R., Srajer, V., Hekstra, D., Pollack, L., Wilson, M.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.230 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

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 

• PubMed: 39071394 
• DOI: https://doi.org/10.1101/2024.07.19.604369
• Primary Citation 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.

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Organizational Affiliation: 
• School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853.
Department of Biochemistry, University of Nebraska, Lincoln, NE 68588.
Department of Biology, New York University, New York, NY 10003.
Linac Coherent Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025.
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138.
Department of Molecular Medicine, Beckman Research Institute at City of Hope, Duarte, CA 91010.
BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Lemont, IL 60439.
John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 20.27 kDa 
• Atom Count: 1,557 
• Modeled Residue Count: 188 
• Deposited Residue Count: 192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Parkinson disease protein 7	A	192	Homo sapiens	Mutation(s): 0  Gene Names: PARK7 EC: 3.1.2 (PDB Primary Data), 3.5.1 (PDB Primary Data), 3.5.1.124 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q99497 (Homo sapiens) Explore Q99497  Go to UniProtKB:  Q99497
PHAROS:  Q99497 GTEx:  ENSG00000116288

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1A7V	A	L-PEPTIDE LINKING	C6 H11 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.230 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.03	α = 90
b = 76.03	β = 90
c = 76.14	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Precognition	data reduction
careless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Zielinski, K.A., Dolamore, C., Dalton, K., Meisburger, S.P., Smith, N., Termini, T., Henning, R., Srajer, V., Hekstra, D., Pollack, L., Wilson, M.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM153337

Revision History  

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