|PROSITE documentation PDOC00304|
The cold-shock domain (CSD) is an ancient β-barrel fold of about 70 amino acids that binds single-stranded nucleic acids (both RNA and DNA). CSD-containing proteins have been found in all three domains of life and function in a variety of processes that are related, for the most part, to post-translational gene regulation. CSDs were first found in bacterial cold-shock proteins (CSPs). CSPs are small, abundant proteins that are essentially composed of one CSD. Some members of this family are strongly induced after cold shock and are involved in adaptation to low temperatures, while others function during normal growth conditions. Bacterial CSPs bind to single-stranded nucleic acids and function as RNA chaperones, rescuing RNAs trapped in unproductive folding states. This general molecular function enables CSPs to participate in the regulation of practically any step of gene expression involving RNA, including transcription, translation, and RNA turnover. Since their discovery in bacterial CSPs, CSDs have been found in many other bacterial and eukaryotic proteins. In multicellular organisms, CSDs are usually embedded in larger proteins [1,2,3,4,5].
The CSD adopts a five-stranded antiparallel β-barrel structure, which is similar to the oligonucleotide/oligosaccharide fold (OB-fold) (see <PDB:1WFQ>). Many CSDs contain the motifs [YF]-G-F-I and [VF]-[VF]-H, which are known as the ribonucleoprotein (RNP)-1 and RNP-2 motifs and include most of the residues involved in the interaction with nucleic acids. RNP-1 and RNP-2 are located in strands β2 and β3, respectively [2,3,4,6].
Some proteins known to contain a CSD domain are listed below:
We developed both a pattern and a profile for the CSD domain. As a signature pattern for the CSD domain we selected its most conserved region which is located in its N-terminal section and corresponds to the RNP-1 RNA-binding motif . The profile we developed covers the CSD domain.Expert(s) to contact by email:
February 2018 / Text revised; profile added.
PROSITE methods (with tools and information) covered by this documentation:
|1||Authors||Mihailovich M. Militti C. Gabaldon T. Gebauer F.|
|Title||Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression.|
|2||Authors||Goroncy A.K. Koshiba S. Tochio N. Tomizawa T. Inoue M. Watanabe S. Harada T. Tanaka A. Ohara O. Kigawa T. Yokoyama S.|
|Title||The NMR solution structures of the five constituent cold-shock domains (CSD) of the human UNR (upstream of N-ras) protein.|
|Source||J. Struct. Funct. Genomics 11:181-188(2010).|
|3||Authors||Kljashtorny V. Nikonov S. Ovchinnikov L. Lyabin D. Vodovar N. Curmi P. Manivet P.|
|Title||The Cold Shock Domain of YB-1 Segregates RNA from DNA by Non-Bonded Interactions.|
|Source||PLoS ONE 10:E0130318-E0130318(2015).|
|4||Authors||Kloks C.P.A.A. Spronk C.A.E.M. Lasonder E. Hoffmann A. Vuister G.W. Grzesiek S. Hilbers C.W.|
|Title||The solution structure and DNA-binding properties of the cold-shock domain of the human Y-box protein YB-1.|
|Source||J. Mol. Biol. 316:317-326(2002).|
|5||Authors||Doniger J. Landsman D. Gonda M.A. Wistow G.|
|Title||The product of unr, the highly conserved gene upstream of N-ras, contains multiple repeats similar to the cold-shock domain (CSD), a putative DNA-binding motif.|
|Source||New Biol. 4:389-395(1992).|
|Title||RNP-1, an RNA-binding motif is conserved in the DNA-binding cold shock domain.|
|Source||Nucleic Acids Res. 20:2861-2864(1992).|