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2z33

From Proteopedia

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

Structural highlights

2z33 is a 3 chain structure with sequence from Escherichia coli. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Yamane T, Okamura H, Ikeguchi M, Nishimura Y, Kidera A. Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment. Proteins. 2008 Jan 10;. PMID:18186481 doi:10.1002/prot.21874

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2z33"

@@ Line 1: / Line 1: @@
 ==Solution structure of the DNA complex of PhoB DNA-binding/transactivation Domain==
-<StructureSection load='2z33' size='340' side='right' caption='[[2z33]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
+<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 [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z33 FirstGlance]. <br>
+<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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1qqi|1qqi]]</td></tr>
+</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">phoB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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>
-<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=2z33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z33 OCA], [http://pdbe.org/2z33 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z33 RCSB], [http://www.ebi.ac.uk/pdbsum/2z33 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z33 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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.
+[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>
+    <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>
@@ Line 33: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Ikeguchi, M]]
+[[Category: Large Structures]]
-[[Category: Kidera, A]]
+[[Category: Ikeguchi M]]
-[[Category: Nishimura, Y]]
+[[Category: Kidera A]]
-[[Category: Okamura, H]]
+[[Category: Nishimura Y]]
-[[Category: Yamane, T]]
+[[Category: Okamura H]]
-[[Category: Transcription-dna complex]]
+[[Category: Yamane T]]
-[[Category: Winged helix-turn-helix]]

2z33

From Proteopedia

Current revision

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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