2vrr: Difference between revisions

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-{{Seed}}
-[[Image:2vrr.jpg|left|200px]]
-<!--
+==Structure of SUMO modified Ubc9==
-The line below this paragraph, containing "STRUCTURE_2vrr", creates the "Structure Box" on the page.
+<StructureSection load='2vrr' size='340' side='right'caption='[[2vrr]], [[Resolution|resolution]] 2.22&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'>[[2vrr]] is a 2 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=2VRR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VRR 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]] 2.22&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_2vrr|  PDB=2vrr  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vrr OCA], [https://pdbe.org/2vrr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vrr RCSB], [https://www.ebi.ac.uk/pdbsum/2vrr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vrr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/UBC9_MOUSE UBC9_MOUSE] Accepts the ubiquitin-like proteins SUMO1, SUMO2 and SUMO3 from the UBLE1A-UBLE1B E1 complex and catalyzes their covalent attachment to other proteins with the help of an E3 ligase such as RANBP2 or CBX4. Can catalyze the formation of poly-SUMO chains. Essential for nuclear architecture, chromosome segregation and embryonic viability. Necessary for sumoylation of FOXL2 and KAT5 (By similarity).<ref>PMID:16326389</ref> <ref>PMID:17187077</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/vr/2vrr_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=2vrr ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Posttranslational modification with small ubiquitin-related modifier, SUMO, is a widespread mechanism for rapid and reversible changes in protein function. Considering the large number of known targets, the number of enzymes involved in modification seems surprisingly low: a single E1, a single E2, and a few distinct E3 ligases. Here we show that autosumoylation of the mammalian E2-conjugating enzyme Ubc9 at Lys14 regulates target discrimination. While not altering its activity toward HDAC4, E2-25K, PML, or TDG, sumoylation of Ubc9 impairs its activity on RanGAP1 and strongly activates sumoylation of the transcriptional regulator Sp100. Enhancement depends on a SUMO-interacting motif (SIM) in Sp100 that creates an additional interface with the SUMO conjugated to the E2, a mechanism distinct from Ubc9 approximately SUMO thioester recruitment. The crystal structure of sumoylated Ubc9 demonstrates how the newly created binding interface can provide a gain in affinity otherwise provided by E3 ligases.
-===STRUCTURE OF SUMO MODIFIED UBC9===
+Ubc9 sumoylation regulates SUMO target discrimination.,Knipscheer P, Flotho A, Klug H, Olsen JV, van Dijk WJ, Fish A, Johnson ES, Mann M, Sixma TK, Pichler A Mol Cell. 2008 Aug 8;31(3):371-82. PMID:18691969<ref>PMID:18691969</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2vrr" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18691969}}, adds the Publication Abstract to the page
+*[[SUMO 3D Structures|SUMO 3D Structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18691969 is the PubMed ID number.
+*[[SUMO conjugating enzyme Ubc9|SUMO conjugating enzyme Ubc9]]
--->
+== References ==
-{{ABSTRACT_PUBMED_18691969}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-VRR is a [[Protein complex]] structure of sequences 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=2VRR OCA].
-==Reference==
-Ubc9 sumoylation regulates SUMO target discrimination., Knipscheer P, Flotho A, Klug H, Olsen JV, van Dijk WJ, Fish A, Johnson ES, Mann M, Sixma TK, Pichler A, Mol Cell. 2008 Aug 8;31(3):371-82. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18691969 18691969]
 [[Category: Homo sapiens]]
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Protein complex]]
+[[Category: Fish A]]
-[[Category: Ubiquitin--protein ligase]]
+[[Category: Flotho A]]
-[[Category: Dijk, W J.Van.]]
+[[Category: Johnson ES]]
-[[Category: Fish, A.]]
+[[Category: Klug H]]
-[[Category: Flotho, A.]]
+[[Category: Knipscheer P]]
-[[Category: Johnson, E S.]]
+[[Category: Mann M]]
-[[Category: Klug, H.]]
+[[Category: Olsen JV]]
-[[Category: Knipscheer, P.]]
+[[Category: Pichler A]]
-[[Category: Mann, M.]]
+[[Category: Sixma TK]]
-[[Category: Olsen, J V.]]
+[[Category: Van Dijk WJ]]
-[[Category: Pichler, A.]]
-[[Category: Sixma, T K.]]
-[[Category: Cell cycle]]
-[[Category: Cell cycle/ligase]]
-[[Category: Cell division]]
-[[Category: Chromosome partition]]
-[[Category: Cytoplasm]]
-[[Category: Developmental protein]]
-[[Category: E2]]
-[[Category: Host-virus interaction]]
-[[Category: Isopeptide bond]]
-[[Category: Ligase]]
-[[Category: Membrane]]
-[[Category: Mitosis]]
-[[Category: Modification]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Posttranslational modification]]
-[[Category: Sumo]]
-[[Category: Ubc9]]
-[[Category: Ubiquitin like molecule]]
-[[Category: Ubl conjugation pathway]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 20 12:19:24 2008''