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| | <StructureSection load='3by4' size='340' side='right'caption='[[3by4]], [[Resolution|resolution]] 1.55Å' scene=''> | | <StructureSection load='3by4' size='340' side='right'caption='[[3by4]], [[Resolution|resolution]] 1.55Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3by4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824] and [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BY4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BY4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3by4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BY4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BY4 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3CN:3-AMINOPROPANE'>3CN</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]] 1.55Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3c0r|3c0r]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3CN:3-AMINOPROPANE'>3CN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Otu1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), ubiquitin B ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ubiquitinyl_hydrolase_1 Ubiquitinyl hydrolase 1], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.12 3.4.19.12] </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=3by4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3by4 OCA], [https://pdbe.org/3by4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3by4 RCSB], [https://www.ebi.ac.uk/pdbsum/3by4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3by4 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=3by4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3by4 OCA], [https://pdbe.org/3by4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3by4 RCSB], [https://www.ebi.ac.uk/pdbsum/3by4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3by4 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/OTU1_YEAST OTU1_YEAST]] Hydrolase that can remove conjugated ubiquitin from proteins and may therefore play an important regulatory role at the level of protein turnover by preventing degradation. Participates in the regulation of the ubiquin conjugation pathway involving CDC48 by hindering multiubiquitination of substrates at the CDC48 chaperone. May be indireclty involved in PIS1 gene expression.<ref>PMID:15755922</ref> <ref>PMID:16427015</ref>
| + | [https://www.uniprot.org/uniprot/OTU1_YEAST OTU1_YEAST] Hydrolase that can remove conjugated ubiquitin from proteins and may therefore play an important regulatory role at the level of protein turnover by preventing degradation. Participates in the regulation of the ubiquin conjugation pathway involving CDC48 by hindering multiubiquitination of substrates at the CDC48 chaperone. May be indireclty involved in PIS1 gene expression.<ref>PMID:15755922</ref> <ref>PMID:16427015</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/by/3by4_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/by/3by4_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 18824]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Human]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ubiquitinyl hydrolase 1]] | + | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Marmorstein, R]] | + | [[Category: Marmorstein R]] |
| - | [[Category: Messick, T E]] | + | [[Category: Messick TE]] |
| - | [[Category: Cell cycle]]
| + | |
| - | [[Category: Deubiquitinase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Ubiquitin hydrolase]]
| + | |
| Structural highlights
Function
OTU1_YEAST Hydrolase that can remove conjugated ubiquitin from proteins and may therefore play an important regulatory role at the level of protein turnover by preventing degradation. Participates in the regulation of the ubiquin conjugation pathway involving CDC48 by hindering multiubiquitination of substrates at the CDC48 chaperone. May be indireclty involved in PIS1 gene expression.[1] [2]
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
Ubiquitination of proteins modifies protein function by either altering their activities, promoting their degradation, or altering their subcellular localization. Deubiquitinating enzymes are proteases that reverse this ubiquitination. Previous studies demonstrate that proteins that contain an ovarian tumor (OTU) domain possess deubiquitinating activity. This domain of approximately 130 amino acids is weakly similar to the papain family of proteases and is highly conserved from yeast to mammals. Here we report structural and functional studies on the OTU domain-containing protein from yeast, Otu1. We show that Otu1 binds polyubiquitin chain analogs more tightly than monoubiquitin and preferentially hydrolyzes longer polyubiquitin chains with Lys(48) linkages, having little or no activity on Lys(63)- and Lys(29)-linked chains. We also show that Otu1 interacts with Cdc48, a regulator of the ER-associated degradation pathway. We also report the x-ray crystal structure of the OTU domain of Otu1 covalently complexed with ubiquitin and carry out structure-guided mutagenesis revealing a novel mode of ubiquitin recognition and a variation on the papain protease catalytic site configuration that appears to be conserved within the OTU family of ubiquitin hydrolases. Together, these studies provide new insights into ubiquitin binding and hydrolysis by yeast Otu1 and other OTU domain-containing proteins.
Structural basis for ubiquitin recognition by the Otu1 ovarian tumor domain protein.,Messick TE, Russell NS, Iwata AJ, Sarachan KL, Shiekhattar R, Shanks JR, Reyes-Turcu FE, Wilkinson KD, Marmorstein R J Biol Chem. 2008 Apr 18;283(16):11038-49. Epub 2008 Feb 12. PMID:18270205[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Gardocki ME, Bakewell M, Kamath D, Robinson K, Borovicka K, Lopes JM. Genomic analysis of PIS1 gene expression. Eukaryot Cell. 2005 Mar;4(3):604-14. PMID:15755922 doi:10.1128/EC.4.3.604-614.2005
- ↑ Rumpf S, Jentsch S. Functional division of substrate processing cofactors of the ubiquitin-selective Cdc48 chaperone. Mol Cell. 2006 Jan 20;21(2):261-9. PMID:16427015 doi:S1097-2765(05)01897-6
- ↑ Messick TE, Russell NS, Iwata AJ, Sarachan KL, Shiekhattar R, Shanks JR, Reyes-Turcu FE, Wilkinson KD, Marmorstein R. Structural basis for ubiquitin recognition by the Otu1 ovarian tumor domain protein. J Biol Chem. 2008 Apr 18;283(16):11038-49. Epub 2008 Feb 12. PMID:18270205 doi:http://dx.doi.org/10.1074/jbc.M704398200
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