1my7: Difference between revisions

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-[[Image:1my7.gif|left|200px]]<br /><applet load="1my7" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1my7, resolution 1.49&Aring;" />
-'''NF-kappaB p65 subunit dimerization domain homodimer N202R mutation'''<br />
-==Overview==
+==NF-kappaB p65 subunit dimerization domain homodimer N202R mutation==
-IkappaBalpha inhibits transcription factor NF-kappaB activity by specific, binding to NF-kappaB heterodimers composed of p65 and p50 subunits. It, binds with slightly lower affinity to p65 homodimers and with, significantly lower affinity to homodimers of p50. We have employed a, structure-based mutagenesis approach coupled with protein-protein, interaction assays to determine the source of this dimer selectivity, exhibited by IkappaBalpha. Mutation of amino acid residues in IkappaBalpha, that contact NF-kappaB only marginally affects complex binding affinity, indicating a lack of hot spots in NF-kappaB/IkappaBalpha complex, formation. Conversion of the weak binding NF-kappaB p50 homodimer into a, high affinity binding partner of IkappaBalpha requires transfer of both, the NLS polypeptide and amino acid residues Asn202 and Ser203 from the, NF-kappaB p65 subunit. Involvement of Asn202 and Ser203 in complex, formation is surprising as these amino acid residues occupy solvent, exposed positions at a distance of 20A from IkappaBalpha in the crystal, structures. However, the same amino acid residue positions have been, genetically isolated as determinants of binding specificity in a, homologous system in Drosophila. X-ray crystallographic and solvent, accessibility experiments suggest that these solvent-exposed amino acid, residues contribute to NF-kappaB/IkappaBalpha complex formation by, modulating the NF-kappaB p65 subunit NLS polypeptide.
+<StructureSection load='1my7' size='340' side='right'caption='[[1my7]], [[Resolution|resolution]] 1.49&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1my7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MY7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MY7 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.49&#8491;</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=1my7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1my7 OCA], [https://pdbe.org/1my7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1my7 RCSB], [https://www.ebi.ac.uk/pdbsum/1my7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1my7 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TF65_MOUSE TF65_MOUSE] NF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. NF-kappa-B is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RELA/p65, RELB, NFKB1/p105, NFKB1/p50, REL and NFKB2/p52 and the heterodimeric p65-p50 complex appears to be most abundant one. The dimers bind at kappa-B sites in the DNA of their target genes and the individual dimers have distinct preferences for different kappa-B sites that they can bind with distinguishable affinity and specificity. Different dimer combinations act as transcriptional activators or repressors, respectively. NF-kappa-B is controlled by various mechanisms of post-translational modification and subcellular compartmentalization as well as by interactions with other cofactors or corepressors. NF-kappa-B complexes are held in the cytoplasm in an inactive state complexed with members of the NF-kappa-B inhibitor (I-kappa-B) family. In a conventional activation pathway, I-kappa-B is phosphorylated by I-kappa-B kinases (IKKs) in response to different activators, subsequently degraded thus liberating the active NF-kappa-B complex which translocates to the nucleus. NF-kappa-B heterodimeric p65-p50 and p65-c-Rel complexes are transcriptional activators. The NF-kappa-B p65-p65 complex appears to be involved in invasin-mediated activation of IL-8 expression (By similarity). The inhibitory effect of I-kappa-B upon NF-kappa-B the cytoplasm is exerted primarily through the interaction with p65. p65 shows a weak DNA-binding site which could contribute directly to DNA binding in the NF-kappa-B complex. Associates with chromatin at the NF-kappa-B promoter region via association with DDX1.<ref>PMID:21131967</ref> <ref>PMID:22244329</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/my/1my7_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=1my7 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-MY7 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1MY7 OCA].
+*[[NF-kB|NF-kB]]
+== References ==
-==Reference==
+<references/>
-Solvent exposed non-contacting amino acids play a critical role in NF-kappaB/IkappaBalpha complex formation., Huxford T, Mishler D, Phelps CB, Huang DB, Sengchanthalangsy LL, Reeves R, Hughes CA, Komives EA, Ghosh G, J Mol Biol. 2002 Dec 6;324(4):587-97. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12460563 12460563]
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Single protein]]
+[[Category: Ghosh G]]
-[[Category: Ghosh, G.]]
+[[Category: Huang D-B]]
-[[Category: Huang, D.B.]]
+[[Category: Hughes CA]]
-[[Category: Hughes, C.A.]]
+[[Category: Huxford T]]
-[[Category: Huxford, T.]]
+[[Category: Komives EA]]
-[[Category: Komives, E.A.]]
+[[Category: Mishler D]]
-[[Category: Mishler, D.]]
+[[Category: Phelps CB]]
-[[Category: Phelps, C.B.]]
+[[Category: Reeves R]]
-[[Category: Reeves, R.]]
+[[Category: Sengchanthalangsy LL]]
-[[Category: Sengchanthalangsy, L.L.]]
-[[Category: activator]]
-[[Category: beta-sandwich]]
-[[Category: beta-sheet]]
-[[Category: homodimerdna-binding]]
-[[Category: ig]]
-[[Category: immunoglobulin]]
-[[Category: nuclear protein]]
-[[Category: phosphorylation]]
-[[Category: transcription regulation]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:48:22 2007''