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1nwq

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(New page: 200px<br /><applet load="1nwq" size="450" color="white" frame="true" align="right" spinBox="true" caption="1nwq, resolution 2.80&Aring;" /> '''CRYSTAL STRUCTURE OF...)
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[[Image:1nwq.gif|left|200px]]<br /><applet load="1nwq" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1nwq, resolution 2.80&Aring;" />
 
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'''CRYSTAL STRUCTURE OF C/EBPALPHA-DNA COMPLEX'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF C/EBPALPHA-DNA COMPLEX==
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CCAAT/enhancer-binding proteins (C/EBPs) are basic region leucine zipper, (bZIP) transcription factors that regulate cell differentiation, growth, survival, and inflammation. To understand the molecular basis of DNA, recognition by the C/EBP family we determined the x-ray structure of a, C/EBPalpha bZIP polypeptide bound to its cognate DNA site, (A(-5)T(-4)T(-3)G(-2)C(-1)G(1)C(2)A(3)A(4)T(5)) and characterized several, basic region mutants. Binding specificity is provided by interactions of, basic region residues Arg(289), Asn(292), Ala(295), Val(296), Ser(299), and Arg(300) with DNA bases. A striking feature of the C/EBPalpha, protein-DNA interface that distinguishes it from known bZIP-DNA complexes, is the central role of Arg(289), which is hydrogen-bonded to base A(3), phosphate, Asn(292) (invariant in bZIPs), and Asn(293). The conformation, of Arg(289) is also restricted by Tyr(285). In accordance with the, structural model, mutation of Arg(289) or a pair of its interacting, partners (Tyr(285) and Asn(293)) abolished C/EBPalpha binding activity., Val(296) (Ala in most other bZIPs) contributes to C/EBPalpha specificity, by discriminating against purines at position -3 and imposing steric, restraints on the invariant Arg(300). Mutating Val(296) to Ala strongly, enhanced C/EBPalpha binding to cAMP response element (CRE) sites while, retaining affinity for C/EBP sites. Thus, Arg(289) is essential for, formation of the complementary protein-DNA interface, whereas Val(296), functions primarily to restrict interactions with related sequences such, as CRE sites rather than specifying binding to C/EBP sites. Our studies, also help to explain the phenotypes of mice carrying targeted mutations in, the C/EBPalpha bZIP region.
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<StructureSection load='1nwq' size='340' side='right'caption='[[1nwq]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1nwq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NWQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NWQ FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nwq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nwq OCA], [https://pdbe.org/1nwq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nwq RCSB], [https://www.ebi.ac.uk/pdbsum/1nwq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nwq ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/CEBPA_RAT CEBPA_RAT] C/EBP is a DNA-binding protein that recognizes two different motifs: the CCAAT homology common to many promoters and the enhanced core homology common to many enhancers.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nw/1nwq_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1nwq ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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CCAAT/enhancer-binding proteins (C/EBPs) are basic region leucine zipper (bZIP) transcription factors that regulate cell differentiation, growth, survival, and inflammation. To understand the molecular basis of DNA recognition by the C/EBP family we determined the x-ray structure of a C/EBPalpha bZIP polypeptide bound to its cognate DNA site (A(-5)T(-4)T(-3)G(-2)C(-1)G(1)C(2)A(3)A(4)T(5)) and characterized several basic region mutants. Binding specificity is provided by interactions of basic region residues Arg(289), Asn(292), Ala(295), Val(296), Ser(299), and Arg(300) with DNA bases. A striking feature of the C/EBPalpha protein-DNA interface that distinguishes it from known bZIP-DNA complexes is the central role of Arg(289), which is hydrogen-bonded to base A(3), phosphate, Asn(292) (invariant in bZIPs), and Asn(293). The conformation of Arg(289) is also restricted by Tyr(285). In accordance with the structural model, mutation of Arg(289) or a pair of its interacting partners (Tyr(285) and Asn(293)) abolished C/EBPalpha binding activity. Val(296) (Ala in most other bZIPs) contributes to C/EBPalpha specificity by discriminating against purines at position -3 and imposing steric restraints on the invariant Arg(300). Mutating Val(296) to Ala strongly enhanced C/EBPalpha binding to cAMP response element (CRE) sites while retaining affinity for C/EBP sites. Thus, Arg(289) is essential for formation of the complementary protein-DNA interface, whereas Val(296) functions primarily to restrict interactions with related sequences such as CRE sites rather than specifying binding to C/EBP sites. Our studies also help to explain the phenotypes of mice carrying targeted mutations in the C/EBPalpha bZIP region.
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==About this Structure==
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Structural basis for DNA recognition by the basic region leucine zipper transcription factor CCAAT/enhancer-binding protein alpha.,Miller M, Shuman JD, Sebastian T, Dauter Z, Johnson PF J Biol Chem. 2003 Apr 25;278(17):15178-84. Epub 2003 Feb 10. PMID:12578822<ref>PMID:12578822</ref>
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1NWQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NWQ OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structural basis for DNA recognition by the basic region leucine zipper transcription factor CCAAT/enhancer-binding protein alpha., Miller M, Shuman JD, Sebastian T, Dauter Z, Johnson PF, J Biol Chem. 2003 Apr 25;278(17):15178-84. Epub 2003 Feb 10. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12578822 12578822]
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</div>
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[[Category: Rattus norvegicus]]
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<div class="pdbe-citations 1nwq" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Dauter, Z.]]
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[[Category: Johnson, P.F.]]
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[[Category: Miller, M.]]
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[[Category: Sebastian, T.]]
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[[Category: Shuman, J.D.]]
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[[Category: basic leucine zipper]]
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[[Category: protein-dna complex]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:36:54 2007''
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==See Also==
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*[[Tomato aspermy virus protein 2b Suppression of RNA Silencing|Tomato aspermy virus protein 2b Suppression of RNA Silencing]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Rattus norvegicus]]
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[[Category: Dauter Z]]
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[[Category: Johnson PF]]
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[[Category: Miller M]]
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[[Category: Sebastian T]]
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[[Category: Shuman JD]]

Current revision

CRYSTAL STRUCTURE OF C/EBPALPHA-DNA COMPLEX

PDB ID 1nwq

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