title: 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 τ subunit.
abstract: PolC is one of two essential replicative DNA polymerases in Bacillus subtilis 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 τ subunit, which is part of the bacterial DNA polymerase III holoenzyme. Despite their common homology to τ, 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 τ subunit, however, the region responsible for this interaction is unknown. We propose that the PolC N-terminus is involved in mediating the PolC-τ interaction and possibly also in binding DNA.
authors: Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.
authors: Kęstutis
authors: K
authors: Timinskas
authors: Česlovas
authors: Č
authors: Venclovas
mesh_terms: D000595:Amino Acid Sequence; D001412:Bacillus subtilis / Q000201:enzymology*; D001426:Bacterial Proteins / Q000737:chemistry*; D017124:Conserved Sequence; D004258:DNA Polymerase III / Q000737:chemistry*; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry*; D016208:Databases, Factual; D030562:Databases, Protein; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D055672:Static Electricity; D013499:Surface Properties; D014157:Transcription Factors / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D014157:Transcription Factors; C446929:PolC protein, bacteria; C041273:transcription factor tau; D004258:DNA Polymerase III; D004259:DNA-Directed DNA Polymerase