2es2

From Proteopedia

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

PDB ID 2es2

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Structural highlights

2es2 is a 2 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.78Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CSPB_BACSU Binds to the pentamer sequences ATTGG and CCAAT with highest affinity in single-stranded DNA, and also to other sequences. Has greater affinity for ATTGG than CCAAT. Can act as transcriptional activator of cold shock genes by recognizing putative ATTGG-box elements present in promoter regions of genes induced under cold shock conditions.

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 PubMed

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.

T-rich DNA single strands bind to a preformed site on the bacterial cold shock protein Bs-CspB.,Max KE, Zeeb M, Bienert R, Balbach J, Heinemann U J Mol Biol. 2006 Jul 14;360(3):702-14. Epub 2006 Jun 2. PMID:16780871^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Max KE, 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. 2006 Jul 14;360(3):702-14. Epub 2006 Jun 2. PMID:16780871 doi:10.1016/j.jmb.2006.05.044