3dzd: Difference between revisions
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[[ | ==Crystal structure of sigma54 activator NTRC4 in the inactive state== | ||
<StructureSection load='3dzd' size='340' side='right' caption='[[3dzd]], [[Resolution|resolution]] 2.40Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3dzd]] is a 2 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=3DZD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DZD FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | |||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3e7l|3e7l]]</td></tr> | |||
<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])</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=3dzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dzd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dzd RCSB], [http://www.ebi.ac.uk/pdbsum/3dzd PDBsum]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
< | |||
[[Category: Aquifex aeolicus]] | [[Category: Aquifex aeolicus]] | ||
[[Category: Batchelor, J D | [[Category: Batchelor, J D]] | ||
[[Category: Carlo, S De | [[Category: Carlo, S De]] | ||
[[Category: Doucleff, M | [[Category: Doucleff, M]] | ||
[[Category: Heideker, J | [[Category: Heideker, J]] | ||
[[Category: Lamers, M M | [[Category: Lamers, M M]] | ||
[[Category: Lee, C J | [[Category: Lee, C J]] | ||
[[Category: Matsubara, K | [[Category: Matsubara, K]] | ||
[[Category: Pelton, J G | [[Category: Pelton, J G]] | ||
[[Category: Wemmer, D E | [[Category: Wemmer, D E]] | ||
[[Category: Aaa+ atpase]] | [[Category: Aaa+ atpase]] | ||
[[Category: Atp-binding]] | [[Category: Atp-binding]] | ||