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| | ==Crystal Structure of E. coli protein YajL (ThiJ)== | | ==Crystal Structure of E. coli protein YajL (ThiJ)== |
| - | <StructureSection load='2ab0' size='340' side='right' caption='[[2ab0]], [[Resolution|resolution]] 1.10Å' scene=''> | + | <StructureSection load='2ab0' size='340' side='right'caption='[[2ab0]], [[Resolution|resolution]] 1.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2ab0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AB0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AB0 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2ab0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AB0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AB0 FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">thiJ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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]] 1.1Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ab0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ab0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ab0 RCSB], [http://www.ebi.ac.uk/pdbsum/2ab0 PDBsum]</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=2ab0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ab0 OCA], [https://pdbe.org/2ab0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ab0 RCSB], [https://www.ebi.ac.uk/pdbsum/2ab0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ab0 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/THIJ_ECOLI THIJ_ECOLI]] Involved in biogenesis of ribosomal proteins, probably as a ribosomal protein-folding chaperone. Interacts with ribosomal subunits, ribosomes and polysomes. Confers resistance to oxidative stress.<ref>PMID:9592144</ref> <ref>PMID:20889753</ref> <ref>PMID:20124404</ref> | + | [https://www.uniprot.org/uniprot/YAJL_ECOLI YAJL_ECOLI] Protein deglycase that repairs methylglyoxal- and glyoxal-glycated amino acids and proteins, and releases repaired proteins and lactate or glycolate, respectively. Deglycates cysteines, arginines and lysines residues in proteins, and thus reactivates these proteins by reversing glycation by glyoxals. Acts on early glycation intermediates (hemithioacetals and aminocarbinols), preventing the formation of advanced glycation endproducts (AGE) (PubMed:25416785) (By similarity). Displays a covalent chaperone activity with sulfenylated thiol proteins by forming mixed disulfides with members of the thiol proteome, and preferentially with sulfenylated cellular proteins, upon oxidative stress; these mixed disulfides can be subsequently reduced by low-molecular-weight thiols to regenerate YajL and reduced proteins (PubMed:22157000, PubMed:22321799). Involved in biogenesis of ribosomal proteins, probably as a ribosomal protein-folding chaperone. Confers resistance to oxidative stress. The chaperone activity reported for YajL is probably recruited to execute its deglycase activity, to interact with non-native glycated proteins and gain access to partially buried glycated sites.[UniProtKB:Q99497]<ref>PMID:20124404</ref> <ref>PMID:20889753</ref> <ref>PMID:22157000</ref> <ref>PMID:22321799</ref> <ref>PMID:25416785</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ab/2ab0_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ab/2ab0_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
| - | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf]. | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ab0 ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 2ab0" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Escherichia coli]] | | [[Category: Escherichia coli]] |
| - | [[Category: Petsko, G A]] | + | [[Category: Large Structures]] |
| - | [[Category: Ringe, D]] | + | [[Category: Petsko GA]] |
| - | [[Category: Wilson, M A]] | + | [[Category: Ringe D]] |
| - | [[Category: Alpha-beta hydrolase fold]] | + | [[Category: Wilson MA]] |
| - | [[Category: Dj-1/thij superfamily]]
| + | |
| - | [[Category: Unknown function]]
| + | |
| Structural highlights
Function
YAJL_ECOLI Protein deglycase that repairs methylglyoxal- and glyoxal-glycated amino acids and proteins, and releases repaired proteins and lactate or glycolate, respectively. Deglycates cysteines, arginines and lysines residues in proteins, and thus reactivates these proteins by reversing glycation by glyoxals. Acts on early glycation intermediates (hemithioacetals and aminocarbinols), preventing the formation of advanced glycation endproducts (AGE) (PubMed:25416785) (By similarity). Displays a covalent chaperone activity with sulfenylated thiol proteins by forming mixed disulfides with members of the thiol proteome, and preferentially with sulfenylated cellular proteins, upon oxidative stress; these mixed disulfides can be subsequently reduced by low-molecular-weight thiols to regenerate YajL and reduced proteins (PubMed:22157000, PubMed:22321799). Involved in biogenesis of ribosomal proteins, probably as a ribosomal protein-folding chaperone. Confers resistance to oxidative stress. The chaperone activity reported for YajL is probably recruited to execute its deglycase activity, to interact with non-native glycated proteins and gain access to partially buried glycated sites.[UniProtKB:Q99497][1] [2] [3] [4] [5]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The Escherichia coli protein YajL (ThiJ) is a member of the DJ-1 superfamily with close homologues in many prokaryotes. YajL also shares 40% sequence identity with human DJ-1, an oncogene and neuroprotective protein whose loss-of-function mutants are associated with certain types of familial, autosomal recessive Parkinsonism. We report the 1.1 angstroms resolution crystal structure of YajL in a crystal form with two molecules in the asymmetric unit. The structure of YajL is remarkably similar to that of human DJ-1 (0.9 angstroms C(alpha) RMSD) and both proteins adopt the same dimeric structure. The conserved cysteine residue located in the "nucleophile elbow" is oxidized to either cysteine sulfenic or sulfinic acid in the two molecules in the asymmetric unit, and a mechanism for this oxidation is proposed that may be valid for other proteins in the DJ-1 superfamily as well. Rosenfield difference matrix analysis of the refined anisotropic displacement parameters in the YajL structure reveals significant differences in the intramolecular flexibility of the two non-crystallographic symmetry-related molecules in the asymmetric unit. Lastly, a comparison of the crystal structures of the four different E.coli members of the DJ-1 superfamily indicates that the variable oligomerization in this superfamily is due to a combination of protein-specific insertions into the core fold that form specific interfaces while occluding others plus optimization of residues in the structurally invariant regions of the core fold that facilitate protein-protein interactions.
The atomic resolution crystal structure of the YajL (ThiJ) protein from Escherichia coli: a close prokaryotic homologue of the Parkinsonism-associated protein DJ-1.,Wilson MA, Ringe D, Petsko GA J Mol Biol. 2005 Oct 28;353(3):678-91. Epub 2005 Sep 2. PMID:16181642[6]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kthiri F, Le HT, Gautier V, Caldas T, Malki A, Landoulsi A, Bohn C, Bouloc P, Richarme G. Protein aggregation in a mutant deficient in yajL, the bacterial homolog of the Parkinsonism-associated protein DJ-1. J Biol Chem. 2010 Apr 2;285(14):10328-36. doi: 10.1074/jbc.M109.077529. Epub 2010, Feb 2. PMID:20124404 doi:http://dx.doi.org/10.1074/jbc.M109.077529
- ↑ Kthiri F, Gautier V, Le HT, Prere MF, Fayet O, Malki A, Landoulsi A, Richarme G. Translational defects in a mutant deficient in YajL, the bacterial homolog of the parkinsonism-associated protein DJ-1. J Bacteriol. 2010 Dec;192(23):6302-6. doi: 10.1128/JB.01077-10. Epub 2010 Oct 1. PMID:20889753 doi:http://dx.doi.org/10.1128/JB.01077-10
- ↑ Le HT, Gautier V, Kthiri F, Malki A, Messaoudi N, Mihoub M, Landoulsi A, An YJ, Cha SS, Richarme G. YajL, prokaryotic homolog of parkinsonism-associated protein DJ-1, functions as a covalent chaperone for thiol proteome. J Biol Chem. 2012 Feb 17;287(8):5861-70. doi: 10.1074/jbc.M111.299198. Epub 2011 , Dec 7. PMID:22157000 doi:http://dx.doi.org/10.1074/jbc.M111.299198
- ↑ Gautier V, Le HT, Malki A, Messaoudi N, Caldas T, Kthiri F, Landoulsi A, Richarme G. YajL, the prokaryotic homolog of the Parkinsonism-associated protein DJ-1, protects cells against protein sulfenylation. J Mol Biol. 2012 Aug 24;421(4-5):662-70. doi: 10.1016/j.jmb.2012.01.047. Epub, 2012 Feb 1. PMID:22321799 doi:http://dx.doi.org/10.1016/j.jmb.2012.01.047
- ↑ Richarme G, Mihoub M, Dairou J, Bui LC, Leger T, Lamouri A. Parkinsonism-associated protein DJ-1/Park7 is a major protein deglycase that repairs methylglyoxal- and glyoxal-glycated cysteine, arginine, and lysine residues. J Biol Chem. 2015 Jan 16;290(3):1885-97. doi: 10.1074/jbc.M114.597815. Epub 2014 , Nov 21. PMID:25416785 doi:http://dx.doi.org/10.1074/jbc.M114.597815
- ↑ Wilson MA, Ringe D, Petsko GA. The atomic resolution crystal structure of the YajL (ThiJ) protein from Escherichia coli: a close prokaryotic homologue of the Parkinsonism-associated protein DJ-1. J Mol Biol. 2005 Oct 28;353(3):678-91. Epub 2005 Sep 2. PMID:16181642 doi:10.1016/j.jmb.2005.08.033
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