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| ==Crystal structure of A. aeolicus NtrC1 DNA binding domain== | | ==Crystal structure of A. aeolicus NtrC1 DNA binding domain== |
| <StructureSection load='4l5e' size='340' side='right' caption='[[4l5e]], [[Resolution|resolution]] 1.34Å' scene=''> | | <StructureSection load='4l5e' size='340' side='right'caption='[[4l5e]], [[Resolution|resolution]] 1.34Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[4l5e]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquae Aquae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4L5E FirstGlance]. <br> | | <table><tr><td colspan='2'>[[4l5e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L5E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4L5E FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.34Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4l4u|4l4u]], [[2m8g|2m8g]]</td></tr>
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ntrC1, aq_1117 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</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=4l5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l5e OCA], [https://pdbe.org/4l5e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4l5e RCSB], [https://www.ebi.ac.uk/pdbsum/4l5e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4l5e ProSAT]</span></td></tr> |
| <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=4l5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l5e OCA], [http://pdbe.org/4l5e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4l5e RCSB], [http://www.ebi.ac.uk/pdbsum/4l5e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4l5e ProSAT]</span></td></tr> | |
| </table> | | </table> |
| <div style="background-color:#fffaf0;">
| | == Function == |
| == Publication Abstract from PubMed == | | [https://www.uniprot.org/uniprot/O67198_AQUAE O67198_AQUAE] |
| We compare the structure, activity and linkage of DNA binding domains from sigma54 transcriptional activators, and discuss how the properties of the DNA binding domains and the linker to the neighboring domain are affected by the overall properties and requirements of the full proteins. These transcriptional activators bind upstream of specific promoters that utilize sigma54 -polymerase. Upon receiving a signal the activators assemble into hexamers, which then, through ATP hydrolysis, drive a conformational change in polymerase that enables transcription initiation. We present structures of the DNA-binding domains of activators NtrC1 and Nlh2 from the thermophile A. aeolicus. The structures of these domains, and their relationship to other parts of the activators are discussed. These structures are compared with previously determined structures of the DNA-binding domains of NtrC4, NtrC, ZraR, and FIS. The N-terminal linkers that connect the DNA-binding domains to the central domains in NtrC1 and Nlh2 were studied and found to be unstructured. Additionally, a crystal structure of full-length NtrC1 was solved, but density for the DNA-binding domains was extremely weak, further indicating that the linker between ATPase and DNA binding domains functions as a flexible tether. Flexible linking of ATPase and DNA binding domains is likely necessary to allow assembly of the active hexameric ATPase ring. The comparison of this set of activators also shows clearly that strong dimerization of the DNA binding domain only occurs when other domains do not dimerize strongly.
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| Structure, function, and tethering of DNA-binding domains in sigma transcriptional activators.,Vidangos N, Maris AE, Young A, Hong E, Pelton JG, Batchelor JD, Wemmer DE Biopolymers. 2013 Jul 2. doi: 10.1002/bip.22333. PMID:23818155<ref>PMID:23818155</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 4l5e" style="background-color:#fffaf0;"></div>
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| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Aquae]] | | [[Category: Aquifex aeolicus VF5]] |
| [[Category: Batchelor, J D]] | | [[Category: Large Structures]] |
| [[Category: Hong, E]] | | [[Category: Batchelor JD]] |
| [[Category: Maris, A E]] | | [[Category: Hong E]] |
| [[Category: Pelton, J G]] | | [[Category: Maris AE]] |
| [[Category: Vidangos, N K]] | | [[Category: Pelton JG]] |
| [[Category: Wemmer, D E]] | | [[Category: Vidangos NK]] |
| [[Category: Young, A]] | | [[Category: Wemmer DE]] |
| [[Category: Dna binding]]
| | [[Category: Young A]] |
| [[Category: Helix-turn-helix dna binding domain]]
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| [[Category: Protein binding]]
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