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Common mode of DNA binding to cold shock domains
Author(s) -
Max Klaas E. A.,
Zeeb Markus,
Bienert Ralf,
Balbach Jochen,
Heinemann Udo
Publication year - 2007
Publication title -
the febs journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 204
eISSN - 1742-4658
pISSN - 1742-464X
DOI - 10.1111/j.1742-4658.2007.05672.x
Subject(s) - cold shock domain , chemistry , dna , dimer , monomer , crystallography , stacking , stereochemistry , oligonucleotide , biophysics , biochemistry , rna , biology , organic chemistry , gene , polymer
Bacterial cold shock proteins (CSPs) regulate cellular adaptation to cold stress. Functions ascribed to CSP include roles as RNA chaperones and in transcription antitermination. We present the crystal structure of the Bacillus caldolyticus CSP ( Bc ‐Csp) in complex with hexathymidine (dT 6 ) at a resolution of 1.29 Å. Bound to dT 6 , crystalline Bc ‐Csp forms a domain‐swapped dimer in which β strands 1–3 associate with strands 4 and 5 from the other subunit to form a closed β barrel and vice versa. The globular units of dimeric Bc ‐Csp closely resemble the well‐known structure of monomeric CSP. Structural reorganization from the monomer to the domain‐swapped dimer involves a strictly localized change in the peptide bond linking Glu36 and Gly37 of Bc ‐Csp. Similar structural reorganizations have not been found in any other CSP or oligonucleotide/oligosaccharide‐binding fold structures. Each dT 6 ligand is bound to one globular unit of Bc ‐Csp via an amphipathic protein surface. Individual binding subsites interact with the DNA bases through stacking and hydrogen bonding. The sugar–phosphate backbone remains solvent exposed. Based on crystallographic and biochemical studies of deoxyoligonucleotide binding to CSP, we suggest a common mode of binding of single‐stranded heptanucleotide motifs to proteins containing cold shock domains, including the eukaryotic Y‐box factors.