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 9CSJ | pdb_00009csj

Crystal structure of human glyoxalase domain-containing protein 4 (GLOD4) at 2.33 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 
    0.269 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9CSJ

This is version 1.1 of the entry. See complete history. 

Literature

Selective peroxynitrite-mediated protein nitration catalyzed by glyoxalase domain containing protein 4.

Wright, S., Dang, V.C., Hussain, S., Kandel, P., Brendza, R.P., Mazhar, S., Whitmore, M., Boudoukha, S., Kaur Banwait, J., Van Der Linden, R., Vertudes, E., Markham, K., Trzeciak, M., Pohan, G., Jennings, A., Shahidi-Latham, S., Kayser, F., Beckstead, M., Lucius, A.L., Kashyap, A., Ischiropoulos, H., Griswold-Prenner, I.

(2026) Proc Natl Acad Sci U S A 123: e2515002123-e2515002123

  • DOI: https://doi.org/10.1073/pnas.2515002123
  • Primary Citation Related Structures: 
    9CSJ

  • PubMed Abstract: 

    Tyrosine nitration alters the structure, function, and cellular localization of proteins and is implicated in the pathology of multiple diseases [G. Ferrer-Sueta et al. , Chem. Rev. 118 , 1338-1408 (2018), H. Ischiropoulos, Arch. Biochem. Biophys. 356 , 1-11 (1998), I. Griswold-Prenner et al. , J. Biol. Chem. 299 , 105038-10554 (2023)]. Although protein nitration is assumed to proceed via nonspecific chemical mechanisms, it is highly selective, suggesting the possibility of enzymatic catalysis. Here, we showed that glyoxalase domain-containing protein 4 (GLOD4), a previously uncharacterized protein, is an enzyme that catalyzes selective protein nitration. A primary in vivo target for GLOD4-mediated nitration is alpha-synuclein (α-syn), which is central to the pathogenesis of Parkinson's disease (PD) and related disorders. We document tyrosine nitration of α-syn by GLOD4 in vitro, in cells, and in a murine model of synuclein pathology. The data identified a function of GLOD4 and other structurally related proteins that catalyze the peroxynitrite-mediated selective protein tyrosine nitration. This enzymatic catalysis of nitration may unearth pathophysiological mechanisms and potential interventions in diseases such as PD, cancer, and autoimmunity.


  • Organizational Affiliation: 
    • Nitrase Therapeutics, Brisbane, CA 94005.

Macromolecule Content 

  • Total Structure Weight: 101.6 kDa 
  • Atom Count: 7,425 
  • Modeled Residue Count: 868 
  • Deposited Residue Count: 897 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 2 of Glyoxalase domain-containing protein 4
A, B, C
299Homo sapiensMutation(s): 0 
Gene Names: GLOD4, C17orf25, CGI-150, My027
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HC38 (Homo sapiens)
Explore Q9HC38 
Go to UniProtKB:  Q9HC38
PHAROS:  Q9HC38
GTEx:  ENSG00000167699 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HC38
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE

Query on EPE



Download:Ideal Coordinates CCD File
R [auth B],
Y [auth C]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
O [auth A],
X [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
S [auth B],
Z [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
AA [auth C]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
AA [auth C],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
T [auth B],
U [auth B],
V [auth B],
W [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A],
P [auth B],
Q [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free:  0.269 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.96α = 90
b = 85.96β = 90
c = 135.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
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: 2025-08-13
    Type: Initial release
  • Version 1.1: 2026-02-25
    Changes: Database references