The unique QA domain of RUNX2 causes conformational change in the Runt DNA binding domain which may result in alteration in its function

Runt-related transcription factors (RUNX) are a family of proteins expressed by RUNX genes. In mammals, there are three members in this family- RUNX1, RUNX2 and RUNX3. There is high sequence similarity in the three members. However, there is a presence of QA domain in the N-terminal of Runx2. The structural aspect of this domain has not been elucidated till now. Here, we model the structures RUNX1, RUNX2 and RUNX2 without the QA domain (RUNX2Δqa) from its N-terminal to DNA binding domain. It has been found that there is a significant difference in structure of RUNX2 and RUNX2Δqa. The structure of RUNX2Δqa resembles that of RUNX1. Also, RUNX2Δqa seems to bind to the consensus DNA sequence of RUNX1 with higher affinity than that of RUNX2. The presence of QA domain also decreases the affinity of Runx2 towards CBFbeta. Thus, we find that the QA domain structurally and functionally diverts RUNX2 from that of RUNX1.