7DWM

Crystal structure of the phage VqmA-DPO complex

Summary for 7DWM

• Entry DOI: 10.2210/pdb7dwm/pdb
• Descriptor: Transcriptional regulator, 3,5-dimethylpyrazin-2-ol (3 entities in total)
• Functional Keywords: vqma, 3, 5-dimethylpyrazin-2-ol(dpo), bacteriophage vp882, transcription
• Biological source: Vibrio virus VP882
• Total number of polymer chains: 2
• Total formula weight: 53519.18

Authors

Gu, Y.,Yang, W.S. (deposition date: 2021-01-17, release date: 2021-05-05, Last modification date: 2023-11-29)

Primary citation

Gu, Y.,Zhi, S.X.,Yang, N.,Yang, W.S.
Understanding the mechanism of asymmetric gene regulation determined by the VqmA of vibriophage.
Biochem.Biophys.Res.Commun., 558:51-56, 2021

PubMed Abstract: The quorum-sensing (QS) system between the phages and their hosts is important for the phage lysis-lysogeny decision. In Vibrio cholerae, the QS system consists of a LuxR-type receptor VqmA (VqmA) and an autoinducer molecule 3,5-dimethylpyrazin-2-ol (DPO). A VqmA homolog encoded by vibriophage VP882 (VqmA) can intervene the host QS system via binding to both the host-produced DPO and its cognate promoter (Pqtip) to induce the phage lysogeny-to-lysis transition, whereas VqmA cannot influence the VqmA-induced pathway, suggesting an asymmetry regulation. In this study, we report the crystal structure of VqmA-DPO complex at 2.65 Å and reveal that the mechanism of DPO recognition is conserved in VqmA homologs. Besides, we identify a non-classical palindrome sequence in Pqtip, which can be effectively recognized by VqmA but not VqmA. The sequence contains an interval longer than that in the vqmR promoter recognized by VqmA. In addition, the two DBD regions in the VqmA dimer exhibit more relaxed architecture than that of the reported VqmA, which is likely to be in the conformation that may easily bind to target promoter containing a longer interval. In summary, our findings provide a structural and biochemical basis for the DBD-dependent DNA recognition in different promoter regions in the phage lysogeny-to-lysis decision communication system, and provide clues for developing phage therapies against Vibrio cholerae infection.

PubMed: 33895551
DOI: 10.1016/j.bbrc.2021.04.036

Experimental method

X-RAY DIFFRACTION (2.65 Å)