2kjh: Difference between revisions

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-[[Image:2kjh.png|left|200px]]
-<!--
+==NMR based structural model of the UBCH8-UBIQUITIN complex==
-The line below this paragraph, containing "STRUCTURE_2kjh", creates the "Structure Box" on the page.
+<StructureSection load='2kjh' size='340' side='right'caption='[[2kjh]]' 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'>[[2kjh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KJH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KJH 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">Solution NMR, 16 models</td></tr>
--->
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2kjh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kjh OCA], [https://pdbe.org/2kjh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kjh RCSB], [https://www.ebi.ac.uk/pdbsum/2kjh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kjh ProSAT]</span></td></tr>
-{{STRUCTURE_2kjh|  PDB=2kjh  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/UB2L6_HUMAN UB2L6_HUMAN] Catalyzes the covalent attachment of ubiquitin or ISG15 to other proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Promotes ubiquitination and subsequent proteasomal degradation of FLT3.<ref>PMID:15131269</ref> <ref>PMID:16428300</ref> <ref>PMID:20508617</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/kj/2kjh_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=2kjh ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Ubiquitin-mediated proteolysis utilizes a series of three key enzymes (E1, E2, and E3) to transfer and then covalently modify a substrate with ubiquitin. E2 conjugating enzymes are central proteins in this pathway responsible for the acceptance of a ubiquitin from the E1 enzyme and association with an E3 protein. All E2 enzymes covalently bind ubiquitin through a thiolester linkage between a conserved active-site cysteine on E2 and the C-terminal glycine on ubiquitin. It is not known whether E2 enzymes utilize similar surfaces and residues to coordinate a ubiquitin molecule and how this might contribute to any substrate specificity. In this work, we determined the structure of the human E2 enzyme UbcH8 (UBE2L6) covalently bound to ubiquitin by NMR spectroscopy. A disulfide bond mimicking the short-lived thiolester was formed between the two proteins providing a stable complex. Overall, the structure of UbcH8 does not undergo a significant conformational change upon forming a complex with ubiquitin. Chemical shift perturbation and cross-saturation experiments were used to identify contacts between UbcH8 and ubiquitin and those contacts used as inputs for HADDOCK molecular docking to produce the structure of the UbcH8-ubiquitin complex. An ensemble of 16 structures (root-mean-square deviation of 0.83 A) showed that ubiquitin interacts with the linker region prior to the alpha5 helix as well as residues near the catalytic site. This region corresponds to an area of negative potential on the UbcH8 surface and is considerably different from other E2-ubiquitin interaction sites. Our findings indicate the positioning of ubiquitin on UbcH8 would still allow interaction with E1 and E3 enzymes. Together, the results suggest the UbcH8-ubiquitin complex may provide an additional level of specificity in the ubiquitination pathway.
-===NMR based structural model of the UBCH8-UBIQUITIN complex===
+The Structure of the UbcH8-Ubiquitin Complex Shows a Unique Ubiquitin Interaction Site.,Serniwka SA, Shaw GS Biochemistry. 2009 Dec 4. PMID:19928833<ref>PMID:19928833</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_19928833}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2kjh" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 19928833 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_19928833}}
-==About this Structure==
-[[2kjh]] is a 2 chain structure of [[Ubiquitin]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KJH OCA].
 ==See Also==
-*[[Ubiquitin]]
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
+*[[3D structures of ubiquitin conjugating enzyme|3D structures of ubiquitin conjugating enzyme]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:19928833</ref><references group="xtra"/>
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Ubiquitin--protein ligase]]
+[[Category: Large Structures]]
-[[Category: Serniwka, S A.]]
+[[Category: Serniwka SA]]
-[[Category: Shaw, G S.]]
+[[Category: Shaw GS]]
-[[Category: Atp-binding]]
-[[Category: Cytoplasm]]
-[[Category: E2 enzyme]]
-[[Category: Haddock model]]
-[[Category: Isopeptide bond]]
-[[Category: Ligase]]
-[[Category: Ligase/protein binding complex]]
-[[Category: Nucleotide-binding]]
-[[Category: Nucleus]]
-[[Category: Protein-protein interaction]]
-[[Category: Ubl conjugation]]
-[[Category: Ubl conjugation pathway]]