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| | ==Crystal structure of sigma54 activator NtrC4's DNA binding domain== | | ==Crystal structure of sigma54 activator NtrC4's DNA binding domain== |
| - | <StructureSection load='3e7l' size='340' side='right' caption='[[3e7l]], [[Resolution|resolution]] 2.25Å' scene=''> | + | <StructureSection load='3e7l' size='340' side='right'caption='[[3e7l]], [[Resolution|resolution]] 2.25Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3e7l]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E7L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E7L FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3e7l]] 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=3E7L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E7L FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.252Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3dzd|3dzd]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ntrC4, aq_164 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])</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=3e7l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e7l OCA], [https://pdbe.org/3e7l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e7l RCSB], [https://www.ebi.ac.uk/pdbsum/3e7l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e7l 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=3e7l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e7l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e7l RCSB], [http://www.ebi.ac.uk/pdbsum/3e7l PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/O66551_AQUAE O66551_AQUAE] |
| - | Genetic changes lead gradually to altered protein function, making deduction of the molecular basis for activity from a sequence difficult. Comparative studies provide insights into the functional consequences of specific changes. Here we present structural and biochemical studies of NtrC4, a sigma-54 activator from Aquifex aeolicus, and compare it with NtrC1 (a paralog) and NtrC (a homolog from Salmonella enterica) to provide insight into how a substantial change in regulatory mechanism may have occurred. Activity assays show that assembly of NtrC4's active oligomer is repressed by the N-terminal receiver domain, and that BeF3- addition (mimicking phosphorylation) removes this repression. Observation of assembly without activation for NtrC4 indicates that it is much less strongly repressed than NtrC1. The crystal structure of the unactivated receiver-ATPase domain combination shows a partially disrupted interface. NMR structures of the regulatory domain show that its activation mechanism is very similar to that of NtrC1. The crystal structure of the NtrC4 DNA-binding domain shows that it is dimeric and more similar in structure to NtrC than NtrC1. Electron microscope images of the ATPase-DNA-binding domain combination show formation of oligomeric rings. Sequence alignments provide insights into the distribution of activation mechanisms in this family of proteins.
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| - | Structure and regulatory mechanism of Aquifex aeolicus NtrC4: variability and evolution in bacterial transcriptional regulation.,Batchelor JD, Doucleff M, Lee CJ, Matsubara K, De Carlo S, Heideker J, Lamers MH, Pelton JG, Wemmer DE J Mol Biol. 2008 Dec 31;384(5):1058-75. Epub 2008 Oct 17. PMID:18955063<ref>PMID:18955063</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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| - | == References ==
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| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Aquifex aeolicus]] | | [[Category: Aquifex aeolicus]] |
| - | [[Category: Batchelor, J D]] | + | [[Category: Large Structures]] |
| - | [[Category: Carlo, S De]] | + | [[Category: Batchelor JD]] |
| - | [[Category: Doucleff, M]] | + | [[Category: De Carlo S]] |
| - | [[Category: Heideker, J]] | + | [[Category: Doucleff M]] |
| - | [[Category: Lamers, M M]] | + | [[Category: Heideker J]] |
| - | [[Category: Lee, C J]] | + | [[Category: Lamers MM]] |
| - | [[Category: Matsubara, K]] | + | [[Category: Lee C-J]] |
| - | [[Category: Pelton, J G]] | + | [[Category: Matsubara K]] |
| - | [[Category: Wemmer, D E]] | + | [[Category: Pelton JG]] |
| - | [[Category: Aaa+ atpase]]
| + | [[Category: Wemmer DE]] |
| - | [[Category: Atp-binding]]
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| - | [[Category: Nucleotide-binding]]
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| - | [[Category: Response regulator]]
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| - | [[Category: Sigma43 activator]]
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| - | [[Category: Transcription]]
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| - | [[Category: Transcription regulator]]
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| - | [[Category: Transcriptional activator]]
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