2den: Difference between revisions

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-[[Image:2den.gif|left|200px]]<br />
-<applet load="2den" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2den" />
-'''Solution Structure of the Ubiquitin-Associated Domain of Human BMSC-UbP and its Complex with Ubiquitin'''<br />
-==Overview==
+==Solution Structure of the Ubiquitin-Associated Domain of Human BMSC-UbP and its Complex with Ubiquitin==
-Ubiquitin is an important cellular signal that targets proteins for, degradation or regulates their functions. The previously identified, BMSC-UbP protein derived from bone marrow stromal cells contains a, ubiquitin-associated (UBA) domain at the C terminus that has been, implicated in linking cellular processes and the ubiquitin system. Here, we report the solution NMR structure of the UBA domain of human BMSC-UbP, protein and its complex with ubiquitin. The structure determination was, facilitated by using a solubility-enhancement tag (SET) GB1, immunoglobulin G binding domain 1 of Streptococcal protein G. The results, show that BMSC-UbP UBA domain is primarily comprised of three, alpha-helices with a hydrophobic patch defined by residues within the C, terminus of helix-1, loop-1, and helix-3. The M-G-I motif is similar to, the M/L-G-F/Y motifs conserved in most UBA domains. Chemical shift, perturbation study revealed that the UBA domain binds with the conserved, five-stranded beta-sheet of ubiquitin via hydrophobic interactions with, the dissociation constant (KD) of approximately 17 microM. The structural, model of BMSC-UbP UBA domain complexed with ubiquitin was constructed by, chemical shift mapping combined with the program HADDOCK, which is in, agreement with the result from mutagenesis studies. In the complex, structure, three residues (Met76, Ile78, and Leu99) of BMSC-UbP UBA form a, trident anchoring the domain to the hydrophobic concave surface of, ubiquitin defined by residues Leu8, Ile44, His68, and Val70. This complex, structure may provide clues for BMSC-UbP functions and structural insights, into the UBA domains of other ubiquitin-associated proteins that share, high sequence homology with BMSC-UbP UBA domain.
+<StructureSection load='2den' size='340' side='right'caption='[[2den]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2den]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Streptococcus_sp._'group_G' Streptococcus sp. 'group G']. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DEN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DEN FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2den FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2den OCA], [https://pdbe.org/2den PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2den RCSB], [https://www.ebi.ac.uk/pdbsum/2den PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2den ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/UBL7_HUMAN UBL7_HUMAN]
+== 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/de/2den_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=2den ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-DEN is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Streptococcus_sp._and_homo_sapiens Streptococcus sp. and homo sapiens]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2DEN OCA].
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
+__TOC__
-==Reference==
+</StructureSection>
-Solution structure of the ubiquitin-associated domain of human BMSC-UbP and its complex with ubiquitin., Chang YG, Song AX, Gao YG, Shi YH, Lin XJ, Cao XT, Lin DH, Hu HY, Protein Sci. 2006 Jun;15(6):1248-59. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16731964 16731964]
 [[Category: Homo sapiens]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Streptococcus sp. and homo sapiens]]
+[[Category: Streptococcus sp. 'group G']]
-[[Category: Chang, Y.G.]]
+[[Category: Chang YG]]
-[[Category: Hu, H.Y.]]
+[[Category: Hu HY]]
-[[Category: Lin, D.H.]]
+[[Category: Lin DH]]
-[[Category: a:alpha-alpha-alpha]]
-[[Category: b:beta-beta-helix-helix-beta-beta-helix-beta]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 21:31:26 2007''