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Biochim Biophys Acta. 2004 Sep 1;1701(1-2):15-23.

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

Author information

1
Departamento de Biología Molecular (Unidad Asociada al C.I. B., C.S.I.C.), Universidad de Cantabria, C/Herrera Oria s/n, Santander 39011, Spain.

Abstract

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 beta-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.

PMID:
15450172
DOI:
10.1016/j.bbapap.2004.05.009
[Indexed for MEDLINE]

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