2io2: 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:2io2.gif|left|200px]]
- {{Structure
+==Crystal structure of human Senp2 in complex with RanGAP1-SUMO-1==
-|PDB= 2io2 |SIZE=350|CAPTION= <scene name='initialview01'>2io2</scene>, resolution 2.900&Aring;
+<StructureSection load='2io2' size='340' side='right'caption='[[2io2]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND=
+<table><tr><td colspan='2'>[[2io2]] is a 3 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=2IO2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IO2 FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
-|GENE= SENP2, KIAA1331 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), SUMO1, SMT3C, SMT3H3, UBL1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), RANGAP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2io2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2io2 OCA], [https://pdbe.org/2io2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2io2 RCSB], [https://www.ebi.ac.uk/pdbsum/2io2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2io2 ProSAT]</span></td></tr>
-|DOMAIN=
+</table>
-|RELATEDENTRY=[[1tgz|1TGZ]], [[2io0|2IO0]], [[2io1|2IO1]], [[2io3|2IO3]]
+== Function ==
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2io2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2io2 OCA], [http://www.ebi.ac.uk/pdbsum/2io2 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2io2 RCSB]</span>
+[https://www.uniprot.org/uniprot/SENP2_HUMAN SENP2_HUMAN] Protease that catalyzes two essential functions in the SUMO pathway: processing of full-length SUMO1, SUMO2 and SUMO3 to their mature forms and deconjugation of SUMO1, SUMO2 and SUMO3 from targeted proteins. May down-regulate CTNNB1 levels and thereby modulate the Wnt pathway (By similarity).<ref>PMID:12192048</ref> <ref>PMID:11896061</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/io/2io2_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=2io2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+SUMO processing and deconjugation are essential proteolytic activities for nuclear metabolism and cell-cycle progression in yeast and higher eukaryotes. To elucidate the mechanisms used during substrate lysine deconjugation, SUMO isoform processing and SUMO isoform interactions, X-ray structures were determined for a catalytically inert SENP2 protease domain in complex with conjugated RanGAP1-SUMO-1 or RanGAP1-SUMO-2, or in complex with SUMO-2 or SUMO-3 precursors. Common features within the active site include a 90 degrees kink proximal to the scissile bond that forces C-terminal amino acid residues or the lysine side chain toward a protease surface that appears optimized for lysine deconjugation. Analysis of this surface reveals SENP2 residues, particularly Met497, that mediate, and in some instances reverse, in vitro substrate specificity. Mutational analysis and biochemistry provide a mechanism for SENP2 substrate preferences that explains why SENP2 catalyzes SUMO deconjugation more efficiently than processing.
-'''Crystal structure of human Senp2 in complex with RanGAP1-SUMO-1'''
+Structural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates.,Reverter D, Lima CD Nat Struct Mol Biol. 2006 Dec;13(12):1060-8. Epub 2006 Nov 12. PMID:17099700<ref>PMID:17099700</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2io2" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-SUMO processing and deconjugation are essential proteolytic activities for nuclear metabolism and cell-cycle progression in yeast and higher eukaryotes. To elucidate the mechanisms used during substrate lysine deconjugation, SUMO isoform processing and SUMO isoform interactions, X-ray structures were determined for a catalytically inert SENP2 protease domain in complex with conjugated RanGAP1-SUMO-1 or RanGAP1-SUMO-2, or in complex with SUMO-2 or SUMO-3 precursors. Common features within the active site include a 90 degrees kink proximal to the scissile bond that forces C-terminal amino acid residues or the lysine side chain toward a protease surface that appears optimized for lysine deconjugation. Analysis of this surface reveals SENP2 residues, particularly Met497, that mediate, and in some instances reverse, in vitro substrate specificity. Mutational analysis and biochemistry provide a mechanism for SENP2 substrate preferences that explains why SENP2 catalyzes SUMO deconjugation more efficiently than processing.
+*[[Sentrin-specific protease|Sentrin-specific protease]]
+== References ==
-==About this Structure==
+<references/>
-IO2 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=2IO2 OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Structural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates., Reverter D, Lima CD, Nat Struct Mol Biol. 2006 Dec;13(12):1060-8. Epub 2006 Nov 12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17099700 17099700]
 [[Category: Homo sapiens]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Lima, C D.]]
+[[Category: Lima CD]]
-[[Category: Reverter, D.]]
+[[Category: Reverter D]]
-[[Category: complex]]
-[[Category: senp]]
-[[Category: sumo]]
-[[Category: ubiquitin]]
-[[Category: ulp]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:46:37 2008''