4n0m: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4n0m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4N0M FirstGlance]. <br>
<table><tr><td colspan='2'>[[4n0m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4N0M FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4n0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n0m OCA], [https://pdbe.org/4n0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4n0m RCSB], [https://www.ebi.ac.uk/pdbsum/4n0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4n0m ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4n0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n0m OCA], [https://pdbe.org/4n0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4n0m RCSB], [https://www.ebi.ac.uk/pdbsum/4n0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4n0m ProSAT]</span></td></tr>
</table>
</table>
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== Function ==
== Function ==
[https://www.uniprot.org/uniprot/PARK7_HUMAN PARK7_HUMAN] Protects cells against oxidative stress and cell death. Plays a role in regulating expression or stability of the mitochondrial uncoupling proteins SLC25A14 and SLC25A27 in dopaminergic neurons of the substantia nigra pars compacta and attenuates the oxidative stress induced by calcium entry into the neurons via L-type channels during pacemaking. Eliminates hydrogen peroxide and protects cells against hydrogen peroxide-induced cell death. May act as an atypical peroxiredoxin-like peroxidase that scavenges hydrogen peroxide. Following removal of a C-terminal peptide, displays protease activity and enhanced cytoprotective action against oxidative stress-induced apoptosis. Stabilizes NFE2L2 by preventing its association with KEAP1 and its subsequent ubiquitination. Binds to OTUD7B and inhibits its deubiquitinating activity. Enhances RELA nuclear translocation. Binds to a number of mRNAs containing multiple copies of GG or CC motifs and partially inhibits their translation but dissociates following oxidative stress. Required for correct mitochondrial morphology and function and for autophagy of dysfunctional mitochondria. Regulates astrocyte inflammatory responses. Acts as a positive regulator of androgen receptor-dependent transcription. Prevents aggregation of SNCA. Plays a role in fertilization. Has no proteolytic activity. Has cell-growth promoting activity and transforming activity. May function as a redox-sensitive chaperone.<ref>PMID:9070310</ref> <ref>PMID:11477070</ref> <ref>PMID:12612053</ref> <ref>PMID:14749723</ref> <ref>PMID:15502874</ref> <ref>PMID:15976810</ref> <ref>PMID:16390825</ref> <ref>PMID:17015834</ref> <ref>PMID:18626009</ref> <ref>PMID:18711745</ref> <ref>PMID:20304780</ref> <ref>PMID:21097510</ref> <ref>PMID:12939276</ref> <ref>PMID:15181200</ref>  
[https://www.uniprot.org/uniprot/PARK7_HUMAN PARK7_HUMAN] Protects cells against oxidative stress and cell death. Plays a role in regulating expression or stability of the mitochondrial uncoupling proteins SLC25A14 and SLC25A27 in dopaminergic neurons of the substantia nigra pars compacta and attenuates the oxidative stress induced by calcium entry into the neurons via L-type channels during pacemaking. Eliminates hydrogen peroxide and protects cells against hydrogen peroxide-induced cell death. May act as an atypical peroxiredoxin-like peroxidase that scavenges hydrogen peroxide. Following removal of a C-terminal peptide, displays protease activity and enhanced cytoprotective action against oxidative stress-induced apoptosis. Stabilizes NFE2L2 by preventing its association with KEAP1 and its subsequent ubiquitination. Binds to OTUD7B and inhibits its deubiquitinating activity. Enhances RELA nuclear translocation. Binds to a number of mRNAs containing multiple copies of GG or CC motifs and partially inhibits their translation but dissociates following oxidative stress. Required for correct mitochondrial morphology and function and for autophagy of dysfunctional mitochondria. Regulates astrocyte inflammatory responses. Acts as a positive regulator of androgen receptor-dependent transcription. Prevents aggregation of SNCA. Plays a role in fertilization. Has no proteolytic activity. Has cell-growth promoting activity and transforming activity. May function as a redox-sensitive chaperone.<ref>PMID:9070310</ref> <ref>PMID:11477070</ref> <ref>PMID:12612053</ref> <ref>PMID:14749723</ref> <ref>PMID:15502874</ref> <ref>PMID:15976810</ref> <ref>PMID:16390825</ref> <ref>PMID:17015834</ref> <ref>PMID:18626009</ref> <ref>PMID:18711745</ref> <ref>PMID:20304780</ref> <ref>PMID:21097510</ref> <ref>PMID:12939276</ref> <ref>PMID:15181200</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Lack of oxidative stress control is a common and often prime feature observed in many neurodegenerative diseases. Both DJ-1 and SOD1, proteins involved in familial Parkinson disease and amyotrophic lateral sclerosis, respectively, play a protective role against oxidative stress. Impaired activity and modified expression of both proteins have been observed in different neurodegenerative diseases. A potential cooperative action of DJ-1 and SOD1 in the same oxidative stress response pathway may be suggested based on a copper-mediated interaction between the two proteins reported here. To investigate the mechanisms underlying the antioxidative function of DJ-1 in relation to SOD1 activity, we investigated the ability of DJ-1 to bind copper ions. We structurally characterized a novel copper binding site involving Cys-106, and we investigated, using different techniques, the kinetics of DJ-1 binding to copper ions. The copper transfer between the two proteins was also examined using both fluorescence spectroscopy and specific biochemical assays for SOD1 activity. The structural and functional analysis of the novel DJ-1 copper binding site led us to identify a putative role for DJ-1 as a copper chaperone. Alteration of the coordination geometry of the copper ion in DJ-1 may be correlated to the physiological role of the protein, to a potential failure in metal transfer to SOD1, and to successive implications in neurodegenerative etiopathogenesis.
DJ-1 Is a Copper Chaperone Acting on SOD1 Activation.,Girotto S, Cendron L, Bisaglia M, Tessari I, Mammi S, Zanotti G, Bubacco L J Biol Chem. 2014 Apr 11;289(15):10887-99. doi: 10.1074/jbc.M113.535112. Epub, 2014 Feb 24. PMID:24567322<ref>PMID:24567322</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4n0m" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==

Latest revision as of 15:30, 1 March 2024

Crystal structure of human C53A DJ-1 in complex with CuCrystal structure of human C53A DJ-1 in complex with Cu

Structural highlights

4n0m is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.95Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

PARK7_HUMAN Defects in PARK7 are the cause of Parkinson disease type 7 (PARK7) [MIM:606324. A neurodegenerative disorder characterized by resting tremor, postural tremor, bradykinesia, muscular rigidity, anxiety and psychotic episodes. PARK7 has onset before 40 years, slow progression and initial good response to levodopa. Some patients may show traits reminiscent of amyotrophic lateral sclerosis-parkinsonism/dementia complex (Guam disease).[1] [2] [3] [4] [5] [6] [7] [8]

Function

PARK7_HUMAN Protects cells against oxidative stress and cell death. Plays a role in regulating expression or stability of the mitochondrial uncoupling proteins SLC25A14 and SLC25A27 in dopaminergic neurons of the substantia nigra pars compacta and attenuates the oxidative stress induced by calcium entry into the neurons via L-type channels during pacemaking. Eliminates hydrogen peroxide and protects cells against hydrogen peroxide-induced cell death. May act as an atypical peroxiredoxin-like peroxidase that scavenges hydrogen peroxide. Following removal of a C-terminal peptide, displays protease activity and enhanced cytoprotective action against oxidative stress-induced apoptosis. Stabilizes NFE2L2 by preventing its association with KEAP1 and its subsequent ubiquitination. Binds to OTUD7B and inhibits its deubiquitinating activity. Enhances RELA nuclear translocation. Binds to a number of mRNAs containing multiple copies of GG or CC motifs and partially inhibits their translation but dissociates following oxidative stress. Required for correct mitochondrial morphology and function and for autophagy of dysfunctional mitochondria. Regulates astrocyte inflammatory responses. Acts as a positive regulator of androgen receptor-dependent transcription. Prevents aggregation of SNCA. Plays a role in fertilization. Has no proteolytic activity. Has cell-growth promoting activity and transforming activity. May function as a redox-sensitive chaperone.[9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22]

See Also

References

  1. ↑ Miller DW, Ahmad R, Hague S, Baptista MJ, Canet-Aviles R, McLendon C, Carter DM, Zhu PP, Stadler J, Chandran J, Klinefelter GR, Blackstone C, Cookson MR. L166P mutant DJ-1, causative for recessive Parkinson's disease, is degraded through the ubiquitin-proteasome system. J Biol Chem. 2003 Sep 19;278(38):36588-95. Epub 2003 Jul 8. PMID:12851414 doi:10.1074/jbc.M304272200
  2. ↑ Bonifati V, Rizzu P, van Baren MJ, Schaap O, Breedveld GJ, Krieger E, Dekker MC, Squitieri F, Ibanez P, Joosse M, van Dongen JW, Vanacore N, van Swieten JC, Brice A, Meco G, van Duijn CM, Oostra BA, Heutink P. Mutations in the DJ-1 gene associated with autosomal recessive early-onset parkinsonism. Science. 2003 Jan 10;299(5604):256-9. Epub 2002 Nov 21. PMID:12446870 doi:10.1126/science.1077209
  3. ↑ Moore DJ, Zhang L, Dawson TM, Dawson VL. A missense mutation (L166P) in DJ-1, linked to familial Parkinson's disease, confers reduced protein stability and impairs homo-oligomerization. J Neurochem. 2003 Dec;87(6):1558-67. PMID:14713311
  4. ↑ Abou-Sleiman PM, Healy DG, Quinn N, Lees AJ, Wood NW. The role of pathogenic DJ-1 mutations in Parkinson's disease. Ann Neurol. 2003 Sep;54(3):283-6. PMID:12953260 doi:http://dx.doi.org/10.1002/ana.10675
  5. ↑ Hering R, Strauss KM, Tao X, Bauer A, Woitalla D, Mietz EM, Petrovic S, Bauer P, Schaible W, Muller T, Schols L, Klein C, Berg D, Meyer PT, Schulz JB, Wollnik B, Tong L, Kruger R, Riess O. Novel homozygous p.E64D mutation in DJ1 in early onset Parkinson disease (PARK7). Hum Mutat. 2004 Oct;24(4):321-9. PMID:15365989 doi:10.1002/humu.20089
  6. ↑ Gorner K, Holtorf E, Odoy S, Nuscher B, Yamamoto A, Regula JT, Beyer K, Haass C, Kahle PJ. Differential effects of Parkinson's disease-associated mutations on stability and folding of DJ-1. J Biol Chem. 2004 Feb 20;279(8):6943-51. Epub 2003 Nov 7. PMID:14607841 doi:10.1074/jbc.M309204200
  7. ↑ Clark LN, Afridi S, Mejia-Santana H, Harris J, Louis ED, Cote LJ, Andrews H, Singleton A, Wavrant De-Vrieze F, Hardy J, Mayeux R, Fahn S, Waters C, Ford B, Frucht S, Ottman R, Marder K. Analysis of an early-onset Parkinson's disease cohort for DJ-1 mutations. Mov Disord. 2004 Jul;19(7):796-800. PMID:15254937 doi:10.1002/mds.20131
  8. ↑ Olzmann JA, Li L, Chudaev MV, Chen J, Perez FA, Palmiter RD, Chin LS. Parkin-mediated K63-linked polyubiquitination targets misfolded DJ-1 to aggresomes via binding to HDAC6. J Cell Biol. 2007 Sep 10;178(6):1025-38. PMID:17846173 doi:10.1083/jcb.200611128
  9. ↑ Nagakubo D, Taira T, Kitaura H, Ikeda M, Tamai K, Iguchi-Ariga SM, Ariga H. DJ-1, a novel oncogene which transforms mouse NIH3T3 cells in cooperation with ras. Biochem Biophys Res Commun. 1997 Feb 13;231(2):509-13. PMID:9070310 doi:S0006-291X(97)96132-5
  10. ↑ Takahashi K, Taira T, Niki T, Seino C, Iguchi-Ariga SM, Ariga H. DJ-1 positively regulates the androgen receptor by impairing the binding of PIASx alpha to the receptor. J Biol Chem. 2001 Oct 5;276(40):37556-63. Epub 2001 Jul 26. PMID:11477070 doi:10.1074/jbc.M101730200
  11. ↑ Niki T, Takahashi-Niki K, Taira T, Iguchi-Ariga SM, Ariga H. DJBP: a novel DJ-1-binding protein, negatively regulates the androgen receptor by recruiting histone deacetylase complex, and DJ-1 antagonizes this inhibition by abrogation of this complex. Mol Cancer Res. 2003 Feb;1(4):247-61. PMID:12612053
  12. ↑ Taira T, Saito Y, Niki T, Iguchi-Ariga SM, Takahashi K, Ariga H. DJ-1 has a role in antioxidative stress to prevent cell death. EMBO Rep. 2004 Feb;5(2):213-8. Epub 2004 Jan 23. PMID:14749723 doi:10.1038/sj.embor.7400074
  13. ↑ Shendelman S, Jonason A, Martinat C, Leete T, Abeliovich A. DJ-1 is a redox-dependent molecular chaperone that inhibits alpha-synuclein aggregate formation. PLoS Biol. 2004 Nov;2(11):e362. Epub 2004 Oct 5. PMID:15502874 doi:10.1371/journal.pbio.0020362
  14. ↑ Shinbo Y, Niki T, Taira T, Ooe H, Takahashi-Niki K, Maita C, Seino C, Iguchi-Ariga SM, Ariga H. Proper SUMO-1 conjugation is essential to DJ-1 to exert its full activities. Cell Death Differ. 2006 Jan;13(1):96-108. PMID:15976810 doi:4401704
  15. ↑ Sekito A, Koide-Yoshida S, Niki T, Taira T, Iguchi-Ariga SM, Ariga H. DJ-1 interacts with HIPK1 and affects H2O2-induced cell death. Free Radic Res. 2006 Feb;40(2):155-65. PMID:16390825 doi:10.1080/10715760500456847
  16. ↑ Clements CM, McNally RS, Conti BJ, Mak TW, Ting JP. DJ-1, a cancer- and Parkinson's disease-associated protein, stabilizes the antioxidant transcriptional master regulator Nrf2. Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15091-6. Epub 2006 Oct 2. PMID:17015834 doi:10.1073/pnas.0607260103
  17. ↑ van der Brug MP, Blackinton J, Chandran J, Hao LY, Lal A, Mazan-Mamczarz K, Martindale J, Xie C, Ahmad R, Thomas KJ, Beilina A, Gibbs JR, Ding J, Myers AJ, Zhan M, Cai H, Bonini NM, Gorospe M, Cookson MR. RNA binding activity of the recessive parkinsonism protein DJ-1 supports involvement in multiple cellular pathways. Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):10244-9. doi:, 10.1073/pnas.0708518105. Epub 2008 Jul 14. PMID:18626009 doi:10.1073/pnas.0708518105
  18. ↑ Junn E, Jang WH, Zhao X, Jeong BS, Mouradian MM. Mitochondrial localization of DJ-1 leads to enhanced neuroprotection. J Neurosci Res. 2009 Jan;87(1):123-9. doi: 10.1002/jnr.21831. PMID:18711745 doi:10.1002/jnr.21831
  19. ↑ Chen J, Li L, Chin LS. Parkinson disease protein DJ-1 converts from a zymogen to a protease by carboxyl-terminal cleavage. Hum Mol Genet. 2010 Jun 15;19(12):2395-408. doi: 10.1093/hmg/ddq113. Epub 2010, Mar 18. PMID:20304780 doi:10.1093/hmg/ddq113
  20. ↑ McNally RS, Davis BK, Clements CM, Accavitti-Loper MA, Mak TW, Ting JP. DJ-1 enhances cell survival through the binding of Cezanne, a negative regulator of NF-kappaB. J Biol Chem. 2011 Feb 11;286(6):4098-106. doi: 10.1074/jbc.M110.147371. Epub 2010, Nov 19. PMID:21097510 doi:10.1074/jbc.M110.147371
  21. ↑ Lee SJ, Kim SJ, Kim IK, Ko J, Jeong CS, Kim GH, Park C, Kang SO, Suh PG, Lee HS, Cha SS. Crystal structures of human DJ-1 and Escherichia coli Hsp31, which share an evolutionarily conserved domain. J Biol Chem. 2003 Nov 7;278(45):44552-9. Epub 2003 Aug 25. PMID:12939276 doi:http://dx.doi.org/10.1074/jbc.M304517200
  22. ↑ Canet-Aviles RM, Wilson MA, Miller DW, Ahmad R, McLendon C, Bandyopadhyay S, Baptista MJ, Ringe D, Petsko GA, Cookson MR. The Parkinson's disease protein DJ-1 is neuroprotective due to cysteine-sulfinic acid-driven mitochondrial localization. Proc Natl Acad Sci U S A. 2004 Jun 15;101(24):9103-8. Epub 2004 Jun 4. PMID:15181200 doi:10.1073/pnas.0402959101

4n0m, resolution 1.95Å

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