2z33

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{{Seed}}
 
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[[Image:2z33.png|left|200px]]
 
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==Solution structure of the DNA complex of PhoB DNA-binding/transactivation Domain==
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The line below this paragraph, containing "STRUCTURE_2z33", creates the "Structure Box" on the page.
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<StructureSection load='2z33' size='340' side='right'caption='[[2z33]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<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>
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{{STRUCTURE_2z33| PDB=2z33 | SCENE= }}
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</table>
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== Function ==
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z3/2z33_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Solution structure of the DNA complex of PhoB DNA-binding/transactivation Domain===
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_18186481}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2z33" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 18186481 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18186481}}
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__TOC__
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</StructureSection>
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==About this Structure==
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2Z33 is a [[Protein complex]] structure of sequences from [http://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].
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==Reference==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/18186481 18186481]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Ikeguchi, M.]]
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[[Category: Ikeguchi M]]
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[[Category: Kidera, A.]]
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[[Category: Kidera A]]
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[[Category: Nishimura, Y.]]
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[[Category: Nishimura Y]]
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[[Category: Okamura, H.]]
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[[Category: Okamura H]]
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[[Category: Yamane, T.]]
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[[Category: Yamane T]]
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[[Category: Transcription/dna complex]]
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[[Category: Winged helix-turn-helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 08:42:14 2008''
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Current revision

Solution structure of the DNA complex of PhoB DNA-binding/transactivation Domain

PDB ID 2z33

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