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4fth

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==Crystal Structure of NtrC4 DNA-binding domain bound to double-stranded DNA==
==Crystal Structure of NtrC4 DNA-binding domain bound to double-stranded DNA==
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<StructureSection load='4fth' size='340' side='right' caption='[[4fth]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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<StructureSection load='4fth' size='340' side='right'caption='[[4fth]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4fth]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FTH FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4fth]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FTH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FTH FirstGlance]. <br>
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</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3e7l|3e7l]]</td></tr>
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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]] 3.004&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aq_164, ntrC4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</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=4fth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fth OCA], [https://pdbe.org/4fth PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fth RCSB], [https://www.ebi.ac.uk/pdbsum/4fth PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fth ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4fth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fth OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fth RCSB], [http://www.ebi.ac.uk/pdbsum/4fth PDBsum]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/O66551_AQUAE O66551_AQUAE]
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Transcription initiation by bacterial sigma(54)-polymerase requires the action of a transcriptional activator protein. Activators bind sequence-specifically upstream of the transcription initiation site via a DNA-binding domain (DBD). The structurally characterized DBDs from activators all belong to the Fis (factor for inversion stimulation) family of helix-turn-helix DNA-binding proteins. We report here structures of the free and DNA-bound forms of the DBD of NtrC4 (4DBD) from Aquifex aeolicus, a member of the NtrC family of sigma(54) activators. Two NtrC4-binding sites were identified upstream (-145 and -85bp) from the start of the lpxC gene, which is responsible for the first committed step in lipid A biosynthesis. This is the first experimental evidence for sigma(54) regulation in lpxC expression. 4DBD was crystallized both without DNA and in complex with the -145-binding site. The structures, together with biochemical data, indicate that NtrC4 binds to DNA in a manner that is similar to that of its close homolog, Fis. The greater sequence specificity for the binding of 4DBD relative to Fis seems to arise from a larger number of base-specific contacts contributing to affinity than for Fis.
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DNA Recognition by a sigma(54) Transcriptional Activator from Aquifex aeolicus.,Vidangos NK, Heideker J, Lyubimov A, Lamers M, Huo Y, Pelton JG, Ton J, Gralla J, Berger J, Wemmer DE J Mol Biol. 2014 Oct 23;426(21):3553-68. doi: 10.1016/j.jmb.2014.08.009. Epub, 2014 Aug 23. PMID:25158097<ref>PMID:25158097</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Aquifex aeolicus huber and stetter 2001]]
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[[Category: Aquifex aeolicus]]
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[[Category: Berger, J M.]]
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[[Category: Large Structures]]
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[[Category: Gralla, J D.]]
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[[Category: Berger JM]]
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[[Category: Heideker, J.]]
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[[Category: Gralla JD]]
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[[Category: Huo, Y.]]
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[[Category: Heideker J]]
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[[Category: Kuriyan, J.]]
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[[Category: Huo Y]]
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[[Category: Lamers, M.]]
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[[Category: Kuriyan J]]
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[[Category: Lyubimov, A Y.]]
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[[Category: Lamers M]]
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[[Category: Pelton, J G.]]
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[[Category: Lyubimov AY]]
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[[Category: Ton, J.]]
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[[Category: Pelton JG]]
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[[Category: Vidangos, N K.]]
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[[Category: Ton J]]
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[[Category: Wemmer, D E.]]
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[[Category: Vidangos NK]]
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[[Category: Dna-binding]]
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[[Category: Wemmer DE]]
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[[Category: Dna-binding domain]]
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[[Category: Fi]]
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[[Category: Helix-turn-helix]]
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[[Category: Ntrc]]
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[[Category: Sigma-54]]
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[[Category: Transcription regulator-dna complex]]
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[[Category: Transcriptional activator]]
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Current revision

Crystal Structure of NtrC4 DNA-binding domain bound to double-stranded DNA

PDB ID 4fth

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