DNA binding properties of protein TrwA, a possible structural variant of the Arc repressor superfamily

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• 作者：Moncaliá ; n ; Gabriel ; de la Cruz ; Fernando
• 关键词：DNA ; TrwA ; Arc repressor ; RHH ; ribbon-helix-helix ; oriT ; origin of transfer ; IPTG ; isopropyl-β ; -d-thiogalactopyranoside ; IHF ; integration host factor ; DR ; direct repeats ; IR ; inverted repeats ; DMS ; dimethylsulfate
• 刊名：Biochimica et Biophysica Acta - Proteins and Proteomics
• 出版年：2004
• 出版时间：September 1, 2004
• 年：2004
• 卷：1701
• 期：1-2
• 页码：15-23
• 全文大小：444 K

文摘

Conjugative DNA processing of plasmid R388 requires the concerted action of two proteins, the relaxase-helicase TrwC and the relaxase enhancer TrwA. TrwA can be aligned with DNA binding proteins belonging to the ribbon-helix-helix (RHH) protein family. To further analyse TrwA function, the structural domains of the protein have been identified and dissected by limited proteolysis. Two stable domains were found that resulted to be, according to DNA binding experiments and oligomerization analysis, an N-terminal DNA binding domain and a C-terminal tetramerization domain. Using the three-dimensional structure of the Arc repressor as a guide, it was possible to model TrwA DNA binding site with atomic detail. As a result, TrwA polar amino acids Q8, R10 and S12, contained in the polar face of a putative N-terminal β-strand, were found to be directly involved in DNA binding, in a manner analogous to RHH proteins. In this respect, TrwA seemed to be a new member of the RHH family. However, secondary structure analyses underscored the existence of a substantial difference in the architecture of the TrwA–oriT complex when compared to the Arc repressor–operator complex.