3dzd: Difference between revisions

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-{{Seed}}
-[[Image:3dzd.png|left|200px]]
-<!--
+==Crystal structure of sigma54 activator NTRC4 in the inactive state==
-The line below this paragraph, containing "STRUCTURE_3dzd", creates the "Structure Box" on the page.
+<StructureSection load='3dzd' size='340' side='right'caption='[[3dzd]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3dzd]] is a 2 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=3DZD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DZD FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_3dzd|  PDB=3dzd  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dzd OCA], [https://pdbe.org/3dzd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dzd RCSB], [https://www.ebi.ac.uk/pdbsum/3dzd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dzd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/O66551_AQUAE O66551_AQUAE]
+<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.
-===Crystal structure of sigma54 activator NTRC4 in the inactive state===
+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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18955063}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3dzd" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18955063 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18955063}}
+__TOC__
+</StructureSection>
-==About this Structure==
-DZD is a 2 chains structure of sequences 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].
-==Reference==
-<ref group="xtra">PMID:18955063</ref><references group="xtra"/>
 [[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]]
-[[Category: Nucleotide-binding]]
-[[Category: Response regulator]]
-[[Category: Sigma43 activator]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Transcription regulator]]
-[[Category: Transcriptional activator]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 10 18:45:55 2009''