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1xd3

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{{Seed}}
 
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[[Image:1xd3.png|left|200px]]
 
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==Crystal structure of UCHL3-UbVME complex==
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The line below this paragraph, containing "STRUCTURE_1xd3", creates the "Structure Box" on the page.
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<StructureSection load='1xd3' size='340' side='right'caption='[[1xd3]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1xd3]] is a 4 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=1XD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XD3 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.45&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GVE:METHYL+4-AMINOBUTANOATE'>GVE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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{{STRUCTURE_1xd3| PDB=1xd3 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xd3 OCA], [https://pdbe.org/1xd3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xd3 RCSB], [https://www.ebi.ac.uk/pdbsum/1xd3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xd3 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/UCHL3_HUMAN UCHL3_HUMAN] Deubiquitinating enzyme (DUB) that controls levels of cellular ubiquitin through processing of ubiquitin precursors and ubiquitinated proteins. Thiol protease that recognizes and hydrolyzes a peptide bond at the C-terminal glycine of either ubiquitin or NEDD8. Has a 10-fold preference for Arg and Lys at position P3", and exhibits a preference towards 'Lys-48'-linked Ubiquitin chains. Deubiquitinates ENAC in apical compartments, thereby regulating apical membrane recycling. Indirectly increases the phosphorylation of IGFIR, AKT and FOXO1 and promotes insulin-signaling and insulin-induced adipogenesis. Required for stress-response retinal, skeletal muscle and germ cell maintenance. May be involved in working memory. Can hydrolyze UBB(+1), a mutated form of ubiquitin which is not effectively degraded by the proteasome and is associated with neurogenerative disorders.<ref>PMID:2530630</ref> <ref>PMID:9790970</ref> <ref>PMID:19154770</ref> <ref>PMID:21762696</ref> <ref>PMID:22689415</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xd/1xd3_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1xd3 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Ubiquitin C-terminal hydrolases (UCHs) comprise a family of small ubiquitin-specific proteases of uncertain function. Although no cellular substrates have been identified for UCHs, their highly tissue-specific expression patterns and the association of UCH-L1 mutations with human disease strongly suggest a critical role. The structure of the yeast UCH Yuh1-ubiquitin aldehyde complex identified an active site crossover loop predicted to limit the size of suitable substrates. We report the 1.45 A resolution crystal structure of human UCH-L3 in complex with the inhibitor ubiquitin vinylmethylester, an inhibitor that forms a covalent adduct with the active site cysteine of ubiquitin-specific proteases. This structure confirms the predicted mechanism of the inhibitor and allows the direct comparison of a UCH family enzyme in the free and ligand-bound state. We also show the efficient hydrolysis by human UCH-L3 of a 13-residue peptide in isopeptide linkage with ubiquitin, consistent with considerable flexibility in UCH substrate size. We propose a model for the catalytic cycle of UCH family members which accounts for the hydrolysis of larger ubiquitin conjugates.
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===Crystal structure of UCHL3-UbVME complex===
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Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate.,Misaghi S, Galardy PJ, Meester WJ, Ovaa H, Ploegh HL, Gaudet R J Biol Chem. 2005 Jan 14;280(2):1512-20. Epub 2004 Nov 5. PMID:15531586<ref>PMID:15531586</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1xd3" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_15531586}}, adds the Publication Abstract to the page
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*[[Thioesterase 3D structures|Thioesterase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 15531586 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_15531586}}
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__TOC__
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</StructureSection>
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==About this Structure==
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1XD3 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XD3 OCA].
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==Reference==
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Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate., Misaghi S, Galardy PJ, Meester WJ, Ovaa H, Ploegh HL, Gaudet R, J Biol Chem. 2005 Jan 14;280(2):1512-20. Epub 2004 Nov 5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15531586 15531586]
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Chemistry-based functional proteomics reveals novel members of the deubiquitinating enzyme family., Borodovsky A, Ovaa H, Kolli N, Gan-Erdene T, Wilkinson KD, Ploegh HL, Kessler BM, Chem Biol. 2002 Oct;9(10):1149-59. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12401499 12401499]
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A novel active site-directed probe specific for deubiquitylating enzymes reveals proteasome association of USP14., Borodovsky A, Kessler BM, Casagrande R, Overkleeft HS, Wilkinson KD, Ploegh HL, EMBO J. 2001 Sep 17;20(18):5187-96. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11566882 11566882]
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Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 A resolution., Johnston SC, Larsen CN, Cook WJ, Wilkinson KD, Hill CP, EMBO J. 1997 Jul 1;16(13):3787-96. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9233788 9233788]
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Structural basis for the specificity of ubiquitin C-terminal hydrolases., Johnston SC, Riddle SM, Cohen RE, Hill CP, EMBO J. 1999 Jul 15;18(14):3877-87. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10406793 10406793]
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Ubiquitinyl hydrolase 1]]
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[[Category: Galardy PJ]]
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[[Category: Galardy, P J.]]
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[[Category: Gaudet R]]
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[[Category: Gaudet, R.]]
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[[Category: Meester WJN]]
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[[Category: Meester, W J.N.]]
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[[Category: Misaghi S]]
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[[Category: Misaghi, S.]]
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[[Category: Ovaa H]]
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[[Category: Ovaa, H.]]
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[[Category: Ploegh HL]]
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[[Category: Ploegh, H L.]]
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[[Category: Active site crossover loop]]
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[[Category: Enzyme-ligand complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 04:09:01 2008''
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Current revision

Crystal structure of UCHL3-UbVME complex

PDB ID 1xd3

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