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PDBsum entry 3f71

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protein links
Chaperone PDB id
3f71
Jmol
Contents
Protein chain
187 a.a. *
Waters ×261
* Residue conservation analysis
PDB id:
3f71
Name: Chaperone
Title: Crystal structure of e18d dj-1 with oxidized c106
Structure: Protein dj-1. Chain: a. Synonym: oncogene dj1, parkinson disease protein 7. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: park 7, park7. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.20Å     R-factor:   0.124     R-free:   0.155
Authors: M.Lakshminarasimhan,M.A.Wilson
Key ref:
J.Blackinton et al. (2009). Formation of a stabilized cysteine sulfinic acid is critical for the mitochondrial function of the parkinsonism protein DJ-1. J Biol Chem, 284, 6476-6485. PubMed id: 19124468 DOI: 10.1074/jbc.M806599200
Date:
07-Nov-08     Release date:   30-Dec-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q99497  (PARK7_HUMAN) -  Protein DJ-1
Seq:
Struc:
189 a.a.
187 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   11 terms 
  Biological process     response to stress   65 terms 
  Biochemical function     protein binding     31 terms  

 

 
DOI no: 10.1074/jbc.M806599200 J Biol Chem 284:6476-6485 (2009)
PubMed id: 19124468  
 
 
Formation of a stabilized cysteine sulfinic acid is critical for the mitochondrial function of the parkinsonism protein DJ-1.
J.Blackinton, M.Lakshminarasimhan, K.J.Thomas, R.Ahmad, E.Greggio, A.S.Raza, M.R.Cookson, M.A.Wilson.
 
  ABSTRACT  
 
The formation of cysteine-sulfinic acid has recently become appreciated as a modification that links protein function to cellular oxidative status. Human DJ-1, a protein associated with inherited parkinsonism, readily forms cysteine-sulfinic acid at a conserved cysteine residue (Cys106 in human DJ-1). Mutation of Cys106 causes the protein to lose its normal protective function in cell culture and model organisms. However, it is unknown whether the loss of DJ-1 protective function in these mutants is due to the absence of Cys106 oxidation or the absence of the cysteine residue itself. To address this question, we designed a series of substitutions at a proximal glutamic acid residue (Glu18) in human DJ-1 that alter the oxidative propensity of Cys106 through changes in hydrogen bonding. We show that two mutations, E18N and E18Q, allow Cys106 to be oxidized to Cys106-sulfinic acid under mild conditions. In contrast, the E18D mutation stabilizes a cysteine-sulfenic acid that is readily reduced to the thiol in solution and in vivo. We show that E18N and E18Q can both partially substitute for wild-type DJ-1 using mitochondrial fission and cell viability assays. In contrast, the oxidatively impaired E18D mutant behaves as an inactive C106A mutant and fails to protect cells. We therefore conclude that formation of Cys106-sulfinic acid is a key modification that regulates the protective function of DJ-1.
 
  Selected figure(s)  
 
Figure 1.
Structural effects of mutations designed to test the hypothesis that Cys^106-sulfinic acid formation is critical to DJ-1 function. A, a ribbon representation of the DJ-1 dimer, with one monomer in brown and the other in green. The dimer 2-fold axis is perpendicular to the page and indicated by an ellipse. The oxidationprone cysteine (C106) and the interacting glutamic acid (E18) are represented in each monomer. B, electron density for the 1.15 Å resolution structure of E18Q DJ-1 around Cys^106 is shown at the 1σ contour level and calculated with σ[A] weighted coefficients 2mF[o] - DF[c]. In E18Q DJ-1, Cys^106 is oxidized to the cysteine-sulfinic acid, where stabilizing hydrogen bonds are shown as dotted lines with distances given in Å. C, a superposition of oxidized E18Q (darker model) and wild-type DJ-1 (lighter model) shows that the key stabilizing hydrogen bond between residue 18 and Cys^106- is lengthened in E18Q DJ-1, weakening this interaction. D, 2mF[o] - DF[c] electron density contoured at 1σ is shown in blue for the 1.20 Å resolution crystal structure of E18D DJ-1. Cys^106 is oxidized to the easily reduced Cys^106-SO^- oxidation product in this variant. In addition, there is minor electron density that is consistent with either Cys^106- or an alternate conformation for Cys^106-SO^-. E, a superposition of residues in the vicinity of Cys^106 in E18D DJ-1 (darker model) and the corresponding region in oxidized wild-type DJ-1 (lighter model). The E18D substitution results in structural perturbations at Cys^106 that stabilize the Cys^106-SO^- oxidation product and hinder further oxidation. All figures were created using POVscript+ (40).
Figure 2.
Substitutions at position 18 of DJ-1 impact Cys^106- formation. A, oxidation of Cys^106 in vitro to Cys^106- . Mass spectrometry was used to monitor the oxidation of DJ-1 as a function of hydrogen peroxide concentration in solution. The fraction of protein oxidized was calculated as a ratio of the integrated area of the oxidized protein peak to the total area of both the oxidized and reduced peaks. A comparison of the oxidation curves of these proteins shows that every substitution at position 18 results in diminished oxidation compared with the wild-type protein, although the extent of this diminution varies among the three substitutions. E18D abolishes the ability of Cys^106 to be oxidized to cysteine-sulfinic acid, and E18N oxidizes very easily at low H[2]O[2] levels. B, oxidation of DJ-1 in vivo. Human M17 neuroblastoma cells were transfected with V5-tagged versions of the indicated DJ-1 constructs (wild type (WT), E18N, E18Q, E18D, and C106A, from top to bottom) and exposed to 300 μm paraquat for 24 h. Protein extracts were separated on two-dimensional gels and blotted for DJ-1. Estimated pI values for each isoform are indicated above the blots. Images are representative of duplicate experiments for each construct.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 6476-6485) copyright 2009.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21413989 D.N.Hauser, and M.R.Cookson (2011).
Astrocytes in Parkinson's disease and DJ-1.
  J Neurochem, 117, 357-358.  
21455296 H.Tabunoki, H.Ode, Y.Banno, S.Katsuma, T.Shimada, K.Mita, K.Yamamoto, R.Sato, R.Ishii-Nozawa, and J.Satoh (2011).
BmDJ-1 is a key regulator of oxidative modification in the development of the silkworm, Bombyx mori.
  PLoS One, 6, e17683.  
20940149 K.J.Thomas, M.K.McCoy, J.Blackinton, A.Beilina, M.van der Brug, A.Sandebring, D.Miller, D.Maric, A.Cedazo-Minguez, and M.R.Cookson (2011).
DJ-1 acts in parallel to the PINK1/parkin pathway to control mitochondrial function and autophagy.
  Hum Mol Genet, 20, 40-50.  
  21219333 S.J.Mullett, and D.A.Hinkle (2011).
DJ-1 deficiency in astrocytes selectively enhances mitochondrial Complex I inhibitor-induced neurotoxicity.
  J Neurochem, 117, 375-387.  
  21401899 X.Y.He, B.Y.Liu, W.Y.Yao, X.J.Zhao, Z.Zheng, J.F.Li, B.Q.Yu, and Y.Z.Yuan (2011).
Serum DJ-1 as a diagnostic marker and prognostic factor for pancreatic cancer.
  J Dig Dis, 12, 131-137.  
20025614 A.G.Cox, C.C.Winterbourn, and M.B.Hampton (2010).
Mitochondrial peroxiredoxin involvement in antioxidant defence and redox signalling.
  Biochem J, 425, 313-325.  
19799998 B.Su, X.Wang, L.Zheng, G.Perry, M.A.Smith, and X.Zhu (2010).
Abnormal mitochondrial dynamics and neurodegenerative diseases.
  Biochim Biophys Acta, 1802, 135-142.  
20735469 L.F.Burbulla, G.Krebiehl, and R.Krüger (2010).
Balance is the challenge--the impact of mitochondrial dynamics in Parkinson's disease.
  Eur J Clin Invest, 40, 1048-1060.  
20421364 M.R.Cookson, and O.Bandmann (2010).
Parkinson's disease: insights from pathways.
  Hum Mol Genet, 19, R21-R27.  
20696314 M.R.Cookson (2010).
Unravelling the role of defective genes.
  Prog Brain Res, 183, 43-57.  
19719386 M.Trebak, R.Ginnan, H.A.Singer, and D.Jourd'heuil (2010).
Interplay between calcium and reactive oxygen/nitrogen species: an essential paradigm for vascular smooth muscle signaling.
  Antioxid Redox Signal, 12, 657-674.  
20653510 P.A.Robinson (2010).
Understanding the molecular basis of Parkinson's disease, identification of biomarkers and routes to therapy.
  Expert Rev Proteomics, 7, 565-578.  
20014998 U.Saeed, A.Ray, R.K.Valli, A.M.Kumar, and V.Ravindranath (2010).
DJ-1 loss by glutaredoxin but not glutathione depletion triggers Daxx translocation and cell death.
  Antioxid Redox Signal, 13, 127-144.  
19293155 J.Waak, S.S.Weber, K.Görner, C.Schall, H.Ichijo, T.Stehle, and P.J.Kahle (2009).
Oxidizable residues mediating protein stability and cytoprotective interaction of DJ-1 with apoptosis signal-regulating kinase 1.
  J Biol Chem, 284, 14245-14257.  
19686841 P.J.Kahle, J.Waak, and T.Gasser (2009).
DJ-1 and prevention of oxidative stress in Parkinson's disease and other age-related disorders.
  Free Radic Biol Med, 47, 1354-1361.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.