2Z33

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

Summary for 2Z33

• Entry DOI: 10.2210/pdb2z33/pdb
• Related: 1qqi
• Descriptor: 5'-D(*AP*CP*TP*GP*TP*CP*AP*TP*AP*AP*AP*TP*CP*TP*GP*T)-3', 5'-D(*AP*CP*AP*GP*AP*TP*TP*TP*AP*TP*GP*AP*CP*AP*GP*T)-3', Phosphate regulon transcriptional regulatory protein phoB (3 entities in total)
• Functional Keywords: winged helix-turn-helix, transcription-dna complex, transcription/dna
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P0AFJ5
• Total number of polymer chains: 3
• Total formula weight: 21967.32

Authors

Yamane, T.,Okamura, H.,Ikeguchi, M.,Nishimura, Y.,Kidera, A. (deposition date: 2007-05-31, release date: 2008-04-22, Last modification date: 2024-05-29)

Primary citation

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, 71:1970-1983, 2008

PubMed Abstract: 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.

PubMed: 18186481
DOI: 10.1002/prot.21874

Experimental method

SOLUTION NMR