2ES2

Crystal Structure Analysis of the Bacillus Subtilis Cold Shock Protein Bs-CspB in Complex with Hexathymidine

Summary for 2ES2

• Entry DOI: 10.2210/pdb2es2/pdb
• Related: 1CSP 1CSQ
• Descriptor: 5'-D(*TP*TP*TP*TP*TP*T)-3', Cold shock protein cspB, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: beta barrel, protein-dna complex, single-stranded dna, gene regulation
• Biological source: Bacillus subtilis; More
• Cellular location: Cytoplasm: P32081
• Total number of polymer chains: 2
• Total formula weight: 9232.48

Authors

Max, K.E.A.,Bienert, M.,Heinemann, U. (deposition date: 2005-10-25, release date: 2006-09-05, Last modification date: 2023-08-23)

Primary citation

Max, K.E.,Zeeb, M.,Bienert, R.,Balbach, J.,Heinemann, U.
T-rich DNA single strands bind to a preformed site on the bacterial cold shock protein Bs-CspB.
J.Mol.Biol., 360:702-714, 2006

PubMed 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.

PubMed: 16780871
DOI: 10.1016/j.jmb.2006.05.044

Experimental method

X-RAY DIFFRACTION (1.78 Å)