2ayo: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2ayo.png|left|200px]]
-<!--
+==Structure of USP14 bound to ubquitin aldehyde==
-The line below this paragraph, containing "STRUCTURE_2ayo", creates the "Structure Box" on the page.
+<StructureSection load='2ayo' size='340' side='right'caption='[[2ayo]], [[Resolution|resolution]] 3.50&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'>[[2ayo]] is a 2 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=2AYO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AYO 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]] 3.5&#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_2ayo|  PDB=2ayo  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ayo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ayo OCA], [https://pdbe.org/2ayo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ayo RCSB], [https://www.ebi.ac.uk/pdbsum/2ayo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ayo ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/UBP14_HUMAN UBP14_HUMAN] Proteasome-associated deubiquitinase which releases ubiquitin from the proteasome targeted ubiquitinated proteins. Ensures the regeneration of ubiquitin at the proteasome. Is a reversibly associated subunit of the proteasome and a large fraction of proteasome-free protein exists within the cell. Required for the degradation of the chemokine receptor CXCR4 which is critical for CXCL12-induced cell chemotaxis. Serves also as a physiological inhibitor of endoplasmic reticulum-associated degradation (ERAD) under the non-stressed condition by inhibiting the degradation of unfolded endoplasmic reticulum proteins via interaction with ERN1. Indispensable for synaptic development and function at neuromuscular junctions (NMJs).<ref>PMID:18162577</ref> <ref>PMID:19135427</ref> <ref>PMID:19106094</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/ay/2ayo_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=2ayo ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The ubiquitin-specific processing protease (UBP) family of deubiquitinating enzymes plays an essential role in numerous cellular processes. Mammalian USP14 (Ubp6 in yeast) is unique among known UBP enzymes in that it is activated catalytically upon specific association with the 26S proteasome. Here, we report the crystal structures of the 45-kDa catalytic domain of USP14 in isolation and in a complex with ubiquitin aldehyde, which reveal distinct structural features. In the absence of ubiquitin binding, the catalytic cleft leading to the active site of USP14 is blocked by two surface loops. Binding by ubiquitin induces a significant conformational change that translocates the two surface loops thereby allowing access of the ubiquitin C-terminus to the active site. These structural observations, in conjunction with biochemical characterization, identify important regulatory mechanisms for USP14.
-===Structure of USP14 bound to ubquitin aldehyde===
+Structure and mechanisms of the proteasome-associated deubiquitinating enzyme USP14.,Hu M, Li P, Song L, Jeffrey PD, Chenova TA, Wilkinson KD, Cohen RE, Shi Y EMBO J. 2005 Nov 2;24(21):3747-56. Epub 2005 Oct 6. PMID:16211010<ref>PMID:16211010</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16211010}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2ayo" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16211010 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_16211010}}
-==About this Structure==
-[[2ayo]] is a 2 chain structure of [[Ubiquitin]] with sequence 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=2AYO OCA].
 ==See Also==
-*[[Ubiquitin]]
+*[[Thioesterase 3D structures|Thioesterase 3D structures]]
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:16211010</ref><references group="xtra"/>
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Ubiquitin thiolesterase]]
+[[Category: Large Structures]]
-[[Category: Hu, M.]]
+[[Category: Hu M]]
-[[Category: Jeffrey, P D.]]
+[[Category: Jeffrey PD]]
-[[Category: Li, P.]]
+[[Category: Li P]]
-[[Category: Shi, Y.]]
+[[Category: Shi Y]]
-[[Category: Deubiquitinating enzyme]]
-[[Category: Dub]]
-[[Category: Enzyme mechanism]]
-[[Category: Hydrolase]]
-[[Category: Proteasome]]
-[[Category: Usp14]]