1c3t: Difference between revisions

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-[[Image:1c3t.gif|left|200px]]<br /><applet load="1c3t" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1c3t" />
-'''ROTAMER STRAIN AS A DETERMINANT OF PROTEIN STRUCTURAL SPECIFICITY'''<br />
-==Overview==
+==ROTAMER STRAIN AS A DETERMINANT OF PROTEIN STRUCTURAL SPECIFICITY==
-We present direct evidence for a change in protein structural specificity due to hydrophobic core packing. High resolution structural analysis of a designed core variant of ubiquitin reveals that the protein is in slow exchange between two conformations. Examination of side-chain rotamers indicates that this dynamic response and the lower stability of the protein are coupled to greater strain and mobility in the core. The results suggest that manipulating the level of side-chain strain may be one way of fine tuning the stability and specificity of proteins.
+<StructureSection load='1c3t' size='340' side='right'caption='[[1c3t]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1c3t]] is a 1 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=1C3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C3T 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=1c3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c3t OCA], [https://pdbe.org/1c3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c3t RCSB], [https://www.ebi.ac.uk/pdbsum/1c3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c3t ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/UBC_HUMAN UBC_HUMAN] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</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/c3/1c3t_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=1c3t ConSurf].
+<div style="clear:both"></div>
-==Disease==
+==See Also==
-Known disease associated with this structure: Cleft palate, isolated OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=191339 191339]]
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
+== References ==
-==About this Structure==
+<references/>
-C3T is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence 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=1C3T OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Rotamer strain as a determinant of protein structural specificity., Lazar GA, Johnson EC, Desjarlais JR, Handel TM, Protein Sci. 1999 Dec;8(12):2598-610. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10631975 10631975]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Desjarlais, J R.]]
+[[Category: Desjarlais JR]]
-[[Category: Handel, T M.]]
+[[Category: Handel TM]]
-[[Category: Johnson, E C.]]
+[[Category: Johnson EC]]
-[[Category: Lazar, G A.]]
+[[Category: Lazar GA]]
-[[Category: de novo protein]]
-[[Category: hydrophobic core]]
-[[Category: packing]]
-[[Category: protein design]]
-[[Category: roc]]
-[[Category: rotamers]]
-[[Category: ubiquitin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:02:07 2008''