2z33
From Proteopedia
Solution structure of the DNA complex of PhoB DNA-binding/transactivation Domain
Structural highlights
FunctionPHOB_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 PubMedThe 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
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