title: DNA polymerase I of Mycobacterium tuberculosis: functional role of a conserved aspartate in the hinge joining the M and N helices.
abstract: The highly conserved GXD sequence present in the Mycobacterium tuberculosis DNA polymerase I corresponds to a hinge region in the finger subdomain connecting M and N helices of Escherichia coli pol I. An examination of the crystal structures of pol I family polymerases reveals that the invariant aspartate of the hinge forms a salt bridge with the conserved arginine of the O-helix and an H-bond with Gln-708. To clarify the role of this region, we generated and characterized conserved and nonconserved mutant derivatives of this aspartate, the preceding glutamate and the Gln in TB pol I. For comparison, D732A mutein of pol I was also included. The muteins representing conserved aspartate (Asp-707 of TB pol I or Asp-732 of pol I) showed a strong K(m)((dNTP)) effect and minor alteration in K(d)((DNA)), with about 10-20-fold decrease in overall catalytic efficiency. The TB muteins, E706A and Q683A, have less pronounced deviations from the wild-type enzyme. Further examination of D707A of TB pol I showed no alteration in the processivity or the dideoxynucleotide sensitivity patterns. However, both TB pol D707A and homologous E. coli D732A failed to form a stable E.DNA.dNTP ternary complex. These results suggest that the aspartate in the hinge region is catalytically important and is required for dNTP binding and in the formation of a prepolymerase ternary complex.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry, New Jersey Medical School and Graduate School of Biomedical Sciences, Newark, New Jersey 07103, USA.
authors.forename: Cindy Jo
authors.initials: CJ
authors.lastname: Arrigo
authors.forename: Kamalendra
authors.initials: K
authors.lastname: Singh
authors.forename: Mukund J
authors.initials: MJ
authors.lastname: Modak
mesh_terms: D000595:Amino Acid Sequence; D001224:Aspartic Acid / Q000378:metabolism*; D001483:Base Sequence; D002384:Catalysis; D018360:Crystallography, X-Ray; D004256:DNA Polymerase I / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017931:DNA Primers; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009169:Mycobacterium tuberculosis / Q000378:metabolism*; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid
chemical_list: D017931:DNA Primers; D001224:Aspartic Acid; D004256:DNA Polymerase I