View source for 2z33


==Solution structure of the DNA complex of PhoB DNA-binding/transactivation Domain==
<StructureSection load='2z33' size='340' side='right'caption='[[2z33]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2z33]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z33 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z33 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2z33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z33 OCA], [https://pdbe.org/2z33 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z33 RCSB], [https://www.ebi.ac.uk/pdbsum/2z33 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z33 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PHOB_ECOLI PHOB_ECOLI] This protein is a positive regulator for the phosphate regulon. Transcription of this operon is positively regulated by PhoB and PhoR when phosphate is limited.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z3/2z33_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2z33 ConSurf].
<div style="clear:both"></div>
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== Publication Abstract from PubMed ==
The solution structure of the complex between the transcription factor PhoB DNA-binding/transactivation domain and DNA was determined by NMR spectroscopy and simulated annealing in a periodic boundary box of explicit water with the particle mesh Ewald method. The refined structures provided better convergence and better local geometry compared with the structures determined in vacuum. The hydrogen bond interactions between the PhoB domain and DNA in the aqueous environment were fully formed. The complex structure was found to be very similar to the crystal structure, particularly at the PhoB-DNA interface, much more so than expected from the vacuum structure. These results indicate the importance of the proper treatment of electrostatic and hydration influences in describing protein-DNA interactions. The hydration structures observed for the refined structures contained most of the crystal waters as a subset. We observed that various water-mediated PhoB-DNA interactions contributed to the molecular recognition between PhoB and DNA. Proteins 2008. (c) 2008 Wiley-Liss, Inc.

Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment.,Yamane T, Okamura H, Ikeguchi M, Nishimura Y, Kidera A Proteins. 2008 Jan 10;. PMID:18186481<ref>PMID:18186481</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 2z33" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Ikeguchi M]]
[[Category: Kidera A]]
[[Category: Nishimura Y]]
[[Category: Okamura H]]
[[Category: Yamane T]]