Summary information and primary citation

PDB-id
2es2; DSSR-derived features in text and JSON formats
Class
gene regulation
Method
X-ray (1.78 Å)
Summary
Crystal structure analysis of the bacillus subtilis cold shock protein bs-cspb in complex with hexathymidine
Reference
Max KE, Zeeb M, Bienert R, Balbach J, Heinemann U (2006): "T-rich DNA single strands bind to a preformed site on the bacterial cold shock protein Bs-CspB." J.Mol.Biol., 360, 702-714. doi: 10.1016/j.jmb.2006.05.044.
Abstract
Bacterial cold shock proteins (CSPs) are involved in cellular adaptation to cold stress. They bind to single-stranded nucleic acids with a KD value in the micro- to nanomolar range. Here we present the structure of the Bacillus subtilis CspB (Bs-CspB) in complex with hexathymidine (dT6) at a resolution of 1.78 A. Bs-CspB binds to dT6 with nanomolar affinity via an amphipathic interface on the protein surface. Individual binding subsites interact with single nucleobases through stacking interactions and hydrogen bonding. The sugar-phosphate backbone and the methyl groups of the thymine nucleobases remain solvent exposed and are not contacted by protein groups. Fluorescence titration experiments monitoring the binding of oligopyrimidines to Bs-CspB reveal binding preferences at individual subsites and allow the design of an optimised heptapyrimidine ligand, which is bound with sub-nanomolar affinity. This study reveals the stoichiometry and sequence determinants of the binding of single-stranded nucleic acids to a preformed site on Bs-CspB and thus provides the structural basis of the RNA chaperone and transcription antitermination activities of the CSP.

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