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| | ==Solution structure of the DNA complex of PhoB DNA-binding/transactivation Domain== | | ==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 == | | == 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> | | </table> |
| | == Function == | | == 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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </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]]
| + | |
| Structural highlights
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
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