Journal:Acta Cryst D:S2059798321009633
From Proteopedia
Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR familyMarketa Soltysova, Irena Sieglova, Milan Fabry, Jirı Brynda, Jana Skerlova and Pavlına Rezacova [1] Molecular Tour So far (2021), several 3D structures of SorC EBDs have been determined. They belong to the so-called NagB-like family for their homology with glucosamine 6 phosphate deaminases from the NagB family, characterized by the central Rossman fold (3,8,9). On the other hand, information on the structure of DNA-binding domains of SorC-family proteins is rather limited. SorC DBDs belong to the most abundant helix turn helix (HTH) superfamily and, by their sequences and structures, they cluster into two subfamilies: SorC/DeoR and SorC/CggR. SorC/DeoR DBD is smaller and consists of the HTH bundle followed by a "β linker" (9), and the bigger SorC/CggR belong to the winged HTH family (10). In this paper, we present the first structure of SorC DBDs bound to DNA duplexes. We show DBD structures of representatives of each subfamily, DeoR and CggR, and compare their binding mode, which is likely common to all SorC family members. References: 2. Chaix, D., Ferguson, M.L., Atmanene, C., Dorsselaer, A.V., Sanglier-Cianférani, S., Royer, C.A. and Declerck, N. (2010) Physical basis of the inducer-dependent cooperativity of the Central glycolytic genes Repressor/DNA complex. Nucleic Acids Res, 38, 5944-5957. 3. Rezacova, P., Kozisek, M., Moy, S.F., Sieglova, I., Joachimiak, A., Machius, M. and Otwinowski, Z. (2008) Crystal structures of the effector-binding domain of repressor Central glycolytic gene Regulator from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates. Molecular Microbiology, 69, 895-910. 4. Zorilla, S., Doan, T., Alfonso, C., Margeat, E., Ortega, A., Rivas, G., Aymerich, S., Royer, C.A. and Declerck, N. (2007) Inducer-Modulated Cooperative Binding of the Tetrameric CggR Repressor to Operator DNA. Biohysical Journal, 92, 3215-3227. 5. Xavier, K.B. and Bassler, B.L. (2005) Regulation of uptake and processing of the quorum-sensing autoinducer AI-2 in Escherichia coli. J Bacteriol, 187, 238-248. 6. Ha, J.H., Eo, Y., Grishaev, A., Guo, M., Smith, J.A., Sintim, H.O., Kim, E.H., Cheong, H.K., Bentley, W.E. and Ryu, K.S. (2013) Crystal structures of the LsrR proteins complexed with phospho-AI-2 and two signal-interrupting analogues reveal distinct mechanisms for ligand recognition. J Am Chem Soc, 135, 15526-15535. 7. Zeng, X., Saxild, H.H. and Switzer, R.L. (2000) Purification and Characterization of the DeoR Repressor of Bacillus subtilis. Journal of Bacteriology, 182, 1916-1922. 8. Skerlova, J., Fabry, M., Hubalek, M., Otwinowski, Z. and Rezacova, P. (2014) Structure of the effectorâ€binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis. The FEBS Journal, 281, 4280-4292. 9. de Sanctis, D., McVey, C.E., Enguita, F.J. and Carrondo, M.A. (2009) Crystal structure of the full-length sorbitol operon regulator SorC from Klebsiella pneumoniae: structural evidence for a novel transcriptional regulation mechanism. J Mol Biol, 387, 759-770. 10. Doan, T. and Aymerich, S. (2003) Regulation of the central glycolytic genes in Bacillus subtilis: binding of the repressor CggR to its single DNA target sequence is modulated by fructose-1,6-bisphosphate. Mol Microbiol, 47, 1709-1721. References
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