T-rich DNA Single Strands Bind to a Preformed Site on the Bacterial Cold Shock Protein Bs-CspB

• Published in: Journal of molecular biology Vol. 360; no. 3; pp. 702 - 714
• Main Authors: Max, Klaas E.A., Zeeb, Markus, Bienert, Ralf, Balbach, Jochen, Heinemann, Udo
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 14-07-2006
• Subjects: Amino Acid Sequence; Bacillus subtilis; Bacillus subtilis - genetics; Bacillus subtilis - metabolism; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Binding Sites; cold shock proteins; cold shock response; DNA binding proteins; DNA, Single-Stranded - metabolism; Heat-Shock Proteins - chemistry; Heat-Shock Proteins - metabolism; Hydrophobic and Hydrophilic Interactions; Ligands; Models, Molecular; Molecular Sequence Data; Mutation - genetics; Oligonucleotides - chemistry; Protein Binding; Protein Structure, Secondary; RNA chaperone activity; Thymine - chemistry; transcription antitermination; ss; CSP; Bc; DNA binding proteins; PDB; Bs; OB; RNP; Tm; RNA chaperone activity; cold shock proteins; cold shock response; Ec; transcription antitermination
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2006.05.044

Bacterial cold shock proteins (CSPs) are involved in cellular adaptation to cold stress. They bind to single-stranded nucleic acids with a
K
D value in the micro- to nanomolar range. Here we present the structure of the
Bacillus subtilis CspB (
Bs-CspB) in complex with hexathymidine (dT
6) at a resolution of 1.78 Å.
Bs-CspB binds to dT
6 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.