2znv: Difference between revisions

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-[[Image:2znv.png|left|200px]]
-<!--
+==Crystal structure of human AMSH-LP DUB domain in complex with Lys63-linked ubiquitin dimer==
-The line below this paragraph, containing "STRUCTURE_2znv", creates the "Structure Box" on the page.
+<StructureSection load='2znv' size='340' side='right'caption='[[2znv]], [[Resolution|resolution]] 1.60&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'>[[2znv]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZNV 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]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2znv|  PDB=2znv  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2znv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2znv OCA], [https://pdbe.org/2znv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2znv RCSB], [https://www.ebi.ac.uk/pdbsum/2znv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2znv ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/STALP_HUMAN STALP_HUMAN] Zinc metalloprotease that specifically cleaves 'Lys-63'-linked polyubiquitin chains. Does not cleave 'Lys-48'-linked polyubiquitin chains.<ref>PMID:18758443</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/zn/2znv_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2znv ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Deubiquitinating enzymes (DUBs) remove ubiquitin from conjugated substrates to regulate various cellular processes. The Zn(2+)-dependent DUBs AMSH and AMSH-LP regulate receptor trafficking by specifically cleaving Lys 63-linked polyubiquitin chains from internalized receptors. Here we report the crystal structures of the human AMSH-LP DUB domain alone and in complex with a Lys 63-linked di-ubiquitin at 1.2 A and 1.6 A resolutions, respectively. The AMSH-LP DUB domain consists of a Zn(2+)-coordinating catalytic core and two characteristic insertions, Ins-1 and Ins-2. The distal ubiquitin interacts with Ins-1 and the core, whereas the proximal ubiquitin interacts with Ins-2 and the core. The core and Ins-1 form a catalytic groove that accommodates the Lys 63 side chain of the proximal ubiquitin and the isopeptide-linked carboxy-terminal tail of the distal ubiquitin. This is the first reported structure of a DUB in complex with an isopeptide-linked ubiquitin chain, which reveals the mechanism for Lys 63-linkage-specific deubiquitination by AMSH family members.
-===Crystal structure of human AMSH-LP DUB domain in complex with Lys63-linked ubiquitin dimer===
+Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains.,Sato Y, Yoshikawa A, Yamagata A, Mimura H, Yamashita M, Ookata K, Nureki O, Iwai K, Komada M, Fukai S Nature. 2008 Sep 18;455(7211):358-62. Epub 2008 Aug 31. PMID:18758443<ref>PMID:18758443</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_18758443}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2znv" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18758443 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_18758443}}
-==About this Structure==
-[[2znv]] is a 6 chain structure of [[Ubiquitin]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNV OCA].
 ==See Also==
-*[[Ubiquitin]]
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:18758443</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Ubiquitin thiolesterase]]
+[[Category: Azusa Y]]
-[[Category: Azusa, Y.]]
+[[Category: Fukai S]]
-[[Category: Fukai, S.]]
+[[Category: Iwai K]]
-[[Category: Iwai, K.]]
+[[Category: Komada M]]
-[[Category: Komada, M.]]
+[[Category: Mimura H]]
-[[Category: Mimura, H.]]
+[[Category: Nureki O]]
-[[Category: Nureki, O.]]
+[[Category: Ookata K]]
-[[Category: Ookata, K.]]
+[[Category: Sato Y]]
-[[Category: Sato, Y.]]
+[[Category: Wang X]]
-[[Category: Wang, X.]]
+[[Category: Yamagata A]]
-[[Category: Yamagata, A.]]
+[[Category: Yamashita M]]
-[[Category: Yamashita, M.]]
-[[Category: Alternative splicing]]
-[[Category: Cytoplasm]]
-[[Category: Hydrolase]]
-[[Category: Hydrolase/signaling protein complex]]
-[[Category: Metal binding protein]]
-[[Category: Metal-binding]]
-[[Category: Metalloprotease]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Protease]]
-[[Category: Protein complex]]
-[[Category: Ubl conjugation pathway]]
-[[Category: Zinc]]