1cmx: Difference between revisions

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-{{Seed}}
-[[Image:1cmx.png|left|200px]]
-<!--
+==STRUCTURAL BASIS FOR THE SPECIFICITY OF UBIQUITIN C-TERMINAL HYDROLASES==
-The line below this paragraph, containing "STRUCTURE_1cmx", creates the "Structure Box" on the page.
+<StructureSection load='1cmx' size='340' side='right'caption='[[1cmx]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1cmx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CMX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CMX FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLZ:AMINO-ACETALDEHYDE'>GLZ</scene></td></tr>
-{{STRUCTURE_1cmx|  PDB=1cmx  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1cmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cmx OCA], [https://pdbe.org/1cmx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cmx RCSB], [https://www.ebi.ac.uk/pdbsum/1cmx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cmx ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/UBL1_YEAST UBL1_YEAST] 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 RUB1. Preferentially cleaves ubiquitin from peptides and small adducts.<ref>PMID:2555355</ref> <ref>PMID:12455997</ref> <ref>PMID:17709260</ref> <ref>PMID:21762696</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cm/1cmx_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </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/main_output.php?pdb_ID=1cmx ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The release of ubiquitin from attachment to other proteins and adducts is critical for ubiquitin biosynthesis, proteasomal degradation and other cellular processes. De-ubiquitination is accomplished in part by members of the UCH (ubiquitin C-terminal hydrolase) family of enzymes. We have determined the 2.25 A resolution crystal structure of the yeast UCH, Yuh1, in a complex with the inhibitor ubiquitin aldehyde (Ubal). The structure mimics the tetrahedral intermediate in the reaction pathway and explains the very high enzyme specificity. Comparison with a related, unliganded UCH structure indicates that ubiquitin binding is coupled to rearrangements which block the active-site cleft in the absence of authentic substrate. Remarkably, a 21-residue loop that becomes ordered upon binding Ubal lies directly over the active site. Efficiently processed substrates apparently pass through this loop, and constraints on the loop conformation probably function to control UCH specificity.
-===STRUCTURAL BASIS FOR THE SPECIFICITY OF UBIQUITIN C-TERMINAL HYDROLASES===
+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:10406793<ref>PMID:10406793</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1cmx" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10406793}}, adds the Publication Abstract to the page
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
-(as it appears on PubMed at http://www.pubmed.gov), where 10406793 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10406793}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Homo sapiens]]
-CMX is a [[Protein complex]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CMX OCA].
+[[Category: Large Structures]]
+[[Category: Saccharomyces cerevisiae S288C]]
-==Reference==
+[[Category: Cohen RE]]
-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]
+[[Category: Hill CP]]
-[[Category: Protein complex]]
+[[Category: Johnston SC]]
-[[Category: Ubiquitin thiolesterase]]
+[[Category: Riddle SM]]
-[[Category: Cohen, R E.]]
-[[Category: Hill, C P.]]
-[[Category: Johnston, S C.]]
-[[Category: Riddle, S M.]]
-[[Category: Cysteine protease]]
-[[Category: Deubiquitinating enzyme]]
-[[Category: Enzyme specificity]]
-[[Category: Ubiquitin]]
-[[Category: Ubiquitin hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 20:58:04 2008''