Introduction
Y box binding protein 1 (YBX1) belongs to the YBX family of transcription factors that contain an ancient and evolutionarily conserved cold shock domain (CSD). The name “cold shock” originates from E. coli, which, when exposed to the stress of cold temperature, increases the expression of around 13 proteins containing the CSD by 2–10 folds. This helps the cell survive in low temperature.
This observation found in bacteria is similar to the role of YBX1 in eukaryotic cell's response to stress, indicating the existence of not only structural, but also functional conservation over a wide evolutionary span in the YBX family.
The name ‘YBX’ was coined due to the ability of the YBX protein family to bind the Y box sequence on DNA, defined as 5′-CTGATTGG-3′. The YBX family of proteins has high sequence homology across different species. There are three members of the YBX family: YBX1, YBX2 and YBX3. As shown in Fig. 1, all members have structural commonalities as follows: an N-terminal alanine (A)- and proline (P)-rich domain (A/P domain), a central CSD and a C-terminal domain (CTD) consisting of alternating base/acid amino acid repeats. The A/P domain is thought to be important for the transcriptional activity of YBX1 and has also been shown to interact with tumor suppressor p53 to mediate p53-dependent transcription.
The crystal structure of the human YBX1 CSD domain is known to be comprised of a five-stranded anti-parallel-barrel structure with a long flexible loop and has 40% homology with its bacterial counterpart.