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PDBsum entry 1pdw

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protein Protein-protein interface(s) links
Protein binding PDB id
1pdw
Jmol
Contents
Protein chain
(+ 2 more) 187 a.a. *
Waters ×970
* Residue conservation analysis
PDB id:
1pdw
Name: Protein binding
Title: Crystal structure of human dj-1, p 1 21 1 space group
Structure: Dj-1. Chain: a, b, c, d, e, f, g, h. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.180     R-free:   0.243
Authors: X.Tao,L.Tong
Key ref:
X.Tao and L.Tong (2003). Crystal structure of human DJ-1, a protein associated with early onset Parkinson's disease. J Biol Chem, 278, 31372-31379. PubMed id: 12761214 DOI: 10.1074/jbc.M304221200
Date:
20-May-03     Release date:   24-Jun-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q99497  (PARK7_HUMAN) -  Protein DJ-1
Seq:
Struc:
189 a.a.
187 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   12 terms 
  Biological process     mitochondrion organization   72 terms 
  Biochemical function     protein binding     31 terms  

 

 
DOI no: 10.1074/jbc.M304221200 J Biol Chem 278:31372-31379 (2003)
PubMed id: 12761214  
 
 
Crystal structure of human DJ-1, a protein associated with early onset Parkinson's disease.
X.Tao, L.Tong.
 
  ABSTRACT  
 
We report the crystal structure at 1.8-A resolution of human DJ-1, which has been linked to early onset Parkinson's disease. The monomer of DJ-1 contains the alpha/beta-fold that is conserved among members of the DJ-1/ThiJ/PfpI superfamily. However, the structure also contains an extra helix at the C terminus, which mediates a novel mode of dimerization for the DJ-1 proteins. A putative active site has been identified near the dimer interface, and the residues Cys-106, His-126, and Glu-18 may play important roles in the catalysis by this protein. Studies with the disease-causing L166P mutant suggest that the mutation has disrupted the C-terminal region and the dimerization of the protein. The DJ-1 proteins may function only as dimers. The Lys to Arg mutation at residue 130, the site of sumoylation of DJ-1, has minimal impact on the structure of the protein.
 
  Selected figure(s)  
 
Figure 4.
FIG. 4. The putative active site of DJ-1. A, schematic drawing of the structure near the Cys-106 residue of DJ-1. The two monomers are colored in green and cyan, respectively. B, molecular surface of the DJ-1 dimer near the putative active site. Panel A was produced with Ribbons (39), and panel B was produced with Grasp (40).
Figure 6.
FIG. 6. The environment of the Leu-166 residue. Stereo drawing showing the hydrophobic core among helices A, G, and H. The side chain of Leu-166 is shown in red. Residues Ile-168 and Leu-172 belong to the hydrophobic core with the central -sheet of the structure. This figure was produced with Ribbons (39).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 31372-31379) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21322020 F.Ghazavi, Z.Fazlali, S.S.Banihosseini, S.R.Hosseini, M.H.Kazemi, S.Shojaee, K.Parsa, H.Sadeghi, F.Sina, M.Rohani, G.A.Shahidi, N.Ghaemi, M.Ronaghi, and E.Elahi (2011).
PRKN, DJ-1, and PINK1 screening identifies novel splice site mutation in PRKN and two novel DJ-1 mutations.
  Mov Disord, 26, 80-89.  
21439347 H.M.Gao, and J.S.Hong (2011).
Gene-environment interactions: Key to unraveling the mystery of Parkinson's disease.
  Prog Neurobiol, 94, 1.  
20304780 J.Chen, L.Li, and L.S.Chin (2010).
Parkinson disease protein DJ-1 converts from a zymogen to a protease by carboxyl-terminal cleavage.
  Hum Mol Genet, 19, 2395-2408.  
20172943 M.Natale, D.Bonino, P.Consoli, T.Alberio, R.G.Ravid, M.Fasano, and E.M.Bucci (2010).
A meta-analysis of two-dimensional electrophoresis pattern of the Parkinson's disease-related protein DJ-1.
  Bioinformatics, 26, 946-952.  
18711745 E.Junn, W.H.Jang, X.Zhao, B.S.Jeong, and M.M.Mouradian (2009).
Mitochondrial localization of DJ-1 leads to enhanced neuroprotection.
  J Neurosci Res, 87, 123-129.  
19497122 H.Nural, P.He, T.Beach, L.Sue, W.Xia, and Y.Shen (2009).
Dissembled DJ-1 high molecular weight complex in cortex mitochondria from Parkinson's disease patients.
  Mol Neurodegener, 4, 23.  
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.  
20087465 K.Yamane, Y.Kitamura, T.Yanagida, K.Takata, D.Yanagisawa, T.Taniguchi, T.Taira, and H.Ariga (2009).
Oxidative Neurodegeneration Is Prevented by UCP0045037, an Allosteric Modulator for the Reduced Form of DJ-1, a Wild-Type of Familial Parkinson's Disease-Linked PARK7.
  Int J Mol Sci, 10, 4789-4804.  
18973254 M.G.Macedo, D.Verbaan, Y.Fang, S.M.van Rooden, M.Visser, B.Anar, A.Uras, J.L.Groen, P.Rizzu, J.J.van Hilten, and P.Heutink (2009).
Genotypic and phenotypic characteristics of Dutch patients with early onset Parkinson's disease.
  Mov Disord, 24, 196-203.  
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.  
  20046643 T.Yanagida, J.Tsushima, Y.Kitamura, D.Yanagisawa, K.Takata, T.Shibaike, A.Yamamoto, T.Taniguchi, H.Yasui, T.Taira, S.Morikawa, T.Inubushi, I.Tooyama, and H.Ariga (2009).
Oxidative stress induction of DJ-1 protein in reactive astrocytes scavenges free radicals and reduces cell injury.
  Oxid Med Cell Longev, 2, 36-42.  
18570440 A.C.Witt, M.Lakshminarasimhan, B.C.Remington, S.Hasim, E.Pozharski, and M.A.Wilson (2008).
Cysteine pKa depression by a protonated glutamic acid in human DJ-1.
  Biochemistry, 47, 7430-7440.
PDB codes: 2or3 3cy6 3cyf 3cz9 3cza
18822273 C.P.Ramsey, and B.I.Giasson (2008).
The E163K DJ-1 mutant shows specific antioxidant deficiency.
  Brain Res, 1239, 1.  
17882163 D.Yanagisawa, Y.Kitamura, M.Inden, K.Takata, T.Taniguchi, S.Morikawa, M.Morita, T.Inubushi, I.Tooyama, T.Taira, S.M.Iguchi-Ariga, A.Akaike, and H.Ariga (2008).
DJ-1 protects against neurodegeneration caused by focal cerebral ischemia and reperfusion in rats.
  J Cereb Blood Flow Metab, 28, 563-578.  
18436956 G.Malgieri, and D.Eliezer (2008).
Structural effects of Parkinson's disease linked DJ-1 mutations.
  Protein Sci, 17, 855-868.  
18309325 J.S.Mo, M.Y.Kim, E.J.Ann, J.A.Hong, and H.S.Park (2008).
DJ-1 modulates UV-induced oxidative stress signaling through the suppression of MEKK1 and cell death.
  Cell Death Differ, 15, 1030-1041.  
18181649 M.Lakshminarasimhan, M.T.Maldonado, W.Zhou, A.L.Fink, and M.A.Wilson (2008).
Structural impact of three Parkinsonism-associated missense mutations on human DJ-1.
  Biochemistry, 47, 1381-1392.
PDB codes: 2rk3 2rk4 2rk6 3b36 3b38 3b3a
18707128 P.C.Anderson, and V.Daggett (2008).
Molecular basis for the structural instability of human DJ-1 induced by the L166P mutation associated with Parkinson's disease.
  Biochemistry, 47, 9380-9393.  
18922803 S.S.Cha, H.I.Jung, H.Jeon, Y.J.An, I.K.Kim, S.Yun, H.J.Ahn, K.C.Chung, S.H.Lee, P.G.Suh, and S.O.Kang (2008).
Crystal structure of filamentous aggregates of human DJ-1 formed in an inorganic phosphate-dependent manner.
  J Biol Chem, 283, 34069-34075.
PDB code: 3bwe
17766438 E.Andres-Mateos, C.Perier, L.Zhang, B.Blanchard-Fillion, T.M.Greco, B.Thomas, H.S.Ko, M.Sasaki, H.Ischiropoulos, S.Przedborski, T.M.Dawson, and V.L.Dawson (2007).
DJ-1 gene deletion reveals that DJ-1 is an atypical peroxiredoxin-like peroxidase.
  Proc Natl Acad Sci U S A, 104, 14807-14812.  
17120294 J.A.Olzmann, J.R.Bordelon, E.C.Muly, H.D.Rees, A.I.Levey, L.Li, and L.S.Chin (2007).
Selective enrichment of DJ-1 protein in primate striatal neuronal processes: implications for Parkinson's disease.
  J Comp Neurol, 500, 585-599.  
16390825 A.Sekito, S.Koide-Yoshida, T.Niki, T.Taira, S.M.Iguchi-Ariga, and H.Ariga (2006).
DJ-1 interacts with HIPK1 and affects H2O2-induced cell death.
  Free Radic Res, 40, 155-165.  
16639500 H.L.Melrose, S.J.Lincoln, G.M.Tyndall, and M.J.Farrer (2006).
Parkinson's disease: a rethink of rodent models.
  Exp Brain Res, 173, 196-204.  
16517609 J.Choi, M.C.Sullards, J.A.Olzmann, H.D.Rees, S.T.Weintraub, D.E.Bostwick, M.Gearing, A.I.Levey, L.S.Chin, and L.Li (2006).
Oxidative damage of DJ-1 is linked to sporadic Parkinson and Alzheimer diseases.
  J Biol Chem, 281, 10816-10824.  
16894167 M.C.Meulener, K.Xu, L.Thomson, L.Thompson, H.Ischiropoulos, and N.M.Bonini (2006).
Mutational analysis of DJ-1 in Drosophila implicates functional inactivation by oxidative damage and aging.
  Proc Natl Acad Sci U S A, 103, 12517-12522.  
16543934 M.J.Farrer (2006).
Genetics of Parkinson disease: paradigm shifts and future prospects.
  Nat Rev Genet, 7, 306-318.  
16796689 M.Mujacic, and F.Baneyx (2006).
Regulation of Escherichia coli hchA, a stress-inducible gene encoding molecular chaperone Hsp31.
  Mol Microbiol, 60, 1576-1589.  
16495942 P.M.Abou-Sleiman, M.M.Muqit, and N.W.Wood (2006).
Expanding insights of mitochondrial dysfunction in Parkinson's disease.
  Nat Rev Neurosci, 7, 207-219.  
16615060 S.Kubo, N.Hattori, and Y.Mizuno (2006).
Recessive Parkinson's disease.
  Mov Disord, 21, 885-893.  
15976810 Y.Shinbo, T.Niki, T.Taira, H.Ooe, K.Takahashi-Niki, C.Maita, C.Seino, S.M.Iguchi-Ariga, and H.Ariga (2006).
Proper SUMO-1 conjugation is essential to DJ-1 to exert its full activities.
  Cell Death Differ, 13, 96.  
16022590 D.J.Moore, A.B.West, V.L.Dawson, and T.M.Dawson (2005).
Molecular pathophysiology of Parkinson's disease.
  Annu Rev Neurosci, 28, 57-87.  
16298734 H.M.Li, T.Niki, T.Taira, S.M.Iguchi-Ariga, and H.Ariga (2005).
Association of DJ-1 with chaperones and enhanced association and colocalization with mitochondrial Hsp70 by oxidative stress.
  Free Radic Res, 39, 1091-1099.  
15935068 M.C.Meulener, C.L.Graves, D.M.Sampathu, C.E.Armstrong-Gold, N.M.Bonini, and B.I.Giasson (2005).
DJ-1 is present in a large molecular complex in human brain tissue and interacts with alpha-synuclein.
  J Neurochem, 93, 1524-1532.  
15766664 R.H.Kim, M.Peters, Y.Jang, W.Shi, M.Pintilie, G.C.Fletcher, C.DeLuca, J.Liepa, L.Zhou, B.Snow, R.C.Binari, A.S.Manoukian, M.R.Bray, F.F.Liu, M.S.Tsao, and T.W.Mak (2005).
DJ-1, a novel regulator of the tumor suppressor PTEN.
  Cancer Cell, 7, 263-273.  
15784737 R.H.Kim, P.D.Smith, H.Aleyasin, S.Hayley, M.P.Mount, S.Pownall, A.Wakeham, A.J.You-Ten, S.K.Kalia, P.Horne, D.Westaway, A.M.Lozano, H.Anisman, D.S.Park, and T.W.Mak (2005).
Hypersensitivity of DJ-1-deficient mice to 1-methyl-4-phenyl-1,2,3,6-tetrahydropyrindine (MPTP) and oxidative stress.
  Proc Natl Acad Sci U S A, 102, 5215-5220.  
16155123 Y.Yang, S.Gehrke, M.E.Haque, Y.Imai, J.Kosek, L.Yang, M.F.Beal, I.Nishimura, K.Wakamatsu, S.Ito, R.Takahashi, and B.Lu (2005).
Inactivation of Drosophila DJ-1 leads to impairments of oxidative stress response and phosphatidylinositol 3-kinase/Akt signaling.
  Proc Natl Acad Sci U S A, 102, 13670-13675.  
15112332 A.B.Siva, V.R.Sundareswaran, C.H.Yeung, T.G.Cooper, and S.Shivaji (2004).
Hamster contraception associated protein 1 (CAP1).
  Mol Reprod Dev, 68, 373-383.  
15228534 H.Yamazaki, A.Tomono, Y.Ohnishi, and S.Horinouchi (2004).
DNA-binding specificity of AdpA, a transcriptional activator in the A-factor regulatory cascade in Streptomyces griseus.
  Mol Microbiol, 53, 555-572.  
14745011 M.A.Wilson, C.V.St Amour, J.L.Collins, D.Ringe, and G.A.Petsko (2004).
The 1.8-A resolution crystal structure of YDR533Cp from Saccharomyces cerevisiae: a member of the DJ-1/ThiJ/PfpI superfamily.
  Proc Natl Acad Sci U S A, 101, 1531-1536.
PDB codes: 1rw7 4qyx
15130476 M.Graille, S.Quevillon-Cheruel, N.Leulliot, C.Z.Zhou, I.Li de la Sierra Gallay, L.Jacquamet, J.L.Ferrer, D.Liger, A.Poupon, J.Janin, and H.van Tilbeurgh (2004).
Crystal structure of the YDR533c S. cerevisiae protein, a class II member of the Hsp31 family.
  Structure, 12, 839-847.
PDB codes: 1qvv 1qvw 1qvz
15173574 M.S.Sastry, P.M.Quigley, W.G.Hol, and F.Baneyx (2004).
The linker-loop region of Escherichia coli chaperone Hsp31 functions as a gate that modulates high-affinity substrate binding at elevated temperatures.
  Proc Natl Acad Sci U S A, 101, 8587-8592.  
15503154 P.M.Abou-Sleiman, D.G.Healy, and N.W.Wood (2004).
Causes of Parkinson's disease: genetics of DJ-1.
  Cell Tissue Res, 318, 185-188.  
14691241 P.M.Quigley, K.Korotkov, F.Baneyx, and W.G.Hol (2004).
A new native EcHsp31 structure suggests a key role of structural flexibility for chaperone function.
  Protein Sci, 13, 269-277.
PDB code: 1pv2
15365989 R.Hering, K.M.Strauss, X.Tao, A.Bauer, D.Woitalla, E.M.Mietz, S.Petrovic, P.Bauer, W.Schaible, T.Müller, L.Schöls, C.Klein, D.Berg, P.T.Meyer, J.B.Schulz, B.Wollnik, L.Tong, R.Krüger, and O.Riess (2004).
Novel homozygous p.E64D mutation in DJ1 in early onset Parkinson disease (PARK7).
  Hum Mutat, 24, 321-329.  
15181200 R.M.Canet-Avilés, M.A.Wilson, D.W.Miller, R.Ahmad, C.McLendon, S.Bandyopadhyay, M.J.Baptista, D.Ringe, G.A.Petsko, and M.R.Cookson (2004).
The Parkinson's disease protein DJ-1 is neuroprotective due to cysteine-sulfinic acid-driven mitochondrial localization.
  Proc Natl Acad Sci U S A, 101, 9103-9108.
PDB code: 1soa
15070401 S.Bandyopadhyay, and M.R.Cookson (2004).
Evolutionary and functional relationships within the DJ1 superfamily.
  BMC Evol Biol, 4, 6.  
15502874 S.Shendelman, A.Jonason, C.Martinat, T.Leete, and A.Abeliovich (2004).
DJ-1 is a redox-dependent molecular chaperone that inhibits alpha-synuclein aggregate formation.
  PLoS Biol, 2, e362.  
14749723 T.Taira, Y.Saito, T.Niki, S.M.Iguchi-Ariga, K.Takahashi, and H.Ariga (2004).
DJ-1 has a role in antioxidative stress to prevent cell death.
  EMBO Rep, 5, 213-218.  
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.