tailieunhanh - Báo cáo khoa học: The N-terminal region of the bacterial DNA polymerase PolC features a pair of domains, both distantly related to domain V of the DNA polymerase III s subunit

PolC is one of two essential replicative DNA polymerases inBacillus subtil-is and other Gram-positive bacteria. The 3D structure of PolC has recently been solved, yet it lacks the N-terminal region. For this PolC region of 230 residues, both the structure and function are unknown. | IFEBS Journal The N-terminal region of the bacterial DNA polymerase PolC features a pair of domains both distantly related to domain V of the DNA polymerase III s subunit Kẹstutis Timinskas and Ceslovas Venclovas Institute of Biotechnology Vilnius University Lithuania Keywords clamp loader DNA polymerase DNA replication homology detection templatebased modeling Correspondence C. Venclovas Institute of Biotechnology Vilnius University Graiciuno 8 LT-02241 Vilnius Lithuania Fax 370 5 260 2116 Tel 370 5 269 1881 E-mail venclovas@ Website http bioinformatics Received 27 May 2011 revised 30 June 2011 accepted 6 July 2011 doi PolC is one of two essential replicative DNA polymerases in Bacillus subtil-is and other Gram-positive bacteria. The 3D structure of PolC has recently been solved yet it lacks the N-terminal region. For this PolC region of 230 residues both the structure and function are unknown. In the present study using sensitive homology detection and comparative protein structure modeling we identified in this enigmatic region two consecutive globular domains PolC-NI and PolC-NII which are followed by an apparently unstructured linker. Unexpectedly we found that both domains are related to domain V of the s subunit which is part of the bacterial DNA polymerase III holoenzyme. Despite their common homology to s PolC-NI and PolC-NII exhibit very little sequence similarity to each other. This observation argues against simple tandem duplication within PolC as the origin of the two-domain structure. Using the derived structural models we analyzed residue conservation and the surface properties of both PolC N-terminal domains. We detected a surface patch of positive electrostatic potential in PolC-NI and a hydrophobic surface patch in PolC-NII suggesting their possible involvement in nucleic acid and protein binding respectively. PolC is known to interact with the s subunit however the region responsible for this .