Loop II of DNA polymerase beta is important for discrimination during substrate binding

DNA Repair

Volumn 8, Issue 2, 2009, Pages 182-189

  Lin, George C ^a   Jaeger, Joachim ^b   Eckert, Kristin A ^c   Sweasy, Joann B ^a  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b WADSWORTH CENTER   (United States)

^c PENN STATE CANCER INSTITUTE   (United States)

Author keywords

Base excision repair; DNA polymerase beta; DNA repair; Structure and function

Indexed keywords

AMINO ACID; DEOXYGUANOSINE TRIPHOSPHATE; DNA DIRECTED DNA POLYMERASE BETA; PARATHION;

ARTICLE; DNA BINDING; DNA SYNTHESIS; ENZYME SUBSTRATE; GENE SEQUENCE; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; RIBOSOMAL FRAMESHIFTING; WILD TYPE;

ADENOSINE; AMINO ACID SEQUENCE; ANIMALS; BASE PAIR MISMATCH; BASE SEQUENCE; DNA; DNA POLYMERASE BETA; FRAMESHIFT MUTATION; GUANOSINE TRIPHOSPHATE; HERPESVIRUS 1, HUMAN; KINETICS; MOLECULAR SEQUENCE DATA; MUTANT PROTEINS; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; RATS; SEQUENCE DELETION; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY; THYMIDINE KINASE;

EID: 58149170452     PISSN: 15687864     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dnarep.2008.10.006     Document Type: Article

References (18)

1. Aravind L., and Koonin E.V. DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history. Nucleic Acids Res. 27 (1999) 1609-1618
2. Sobol R.W., Horton J.K., Kuhn R., Gu H., Singhal R.K., Prasad R., Rajewsky K., and Wilson S.H. Requirement of mammalian DNA polymerase-beta in base-excision repair. Nature 379 (1996) 183-186
3. Matsumoto Y., and Kim K. Excision of deoxyribose phosphate residues by DNA polymerase beta during DNA repair. Science 269 (1995) 699-702
4. Liu Y., Prasad R., Beard W.A., Kedar P.S., Hou E.W., Shock D.D., and Wilson S.H. Coordination of steps in single-nucleotide base excision repair mediated by apurinic/apyrimidinic endonuclease 1 and DNA polymerase beta. J. Biol. Chem. 282 (2007) 13532-13541
5. Sawaya M.R., Pelletier H., Kumar A., Wilson S.H., and Kraut J. Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism. Science 264 (1994) 1930-1935
6. Kosa J.L., and Sweasy J.B. 3′-Azido-3′-deoxythymidine-resistant mutants of DNA polymerase beta identified by in vivo selection. J. Biol. Chem. 274 (1999) 3851-3858
7. Kosa J.L., and Sweasy J.B. The E249K mutator mutant of DNA polymerase beta extends mispaired termini. J. Biol. Chem. 274 (1999) 35866-35872
8. Dalal S., Kosa J.L., and Sweasy J.B. The D246V mutant of DNA polymerase beta misincorporates nucleotides: evidence for a role for the flexible loop in DNA positioning within the active site. J. Biol. Chem. 279 (2004) 577-584
9. Lin G.C., Jaeger J., and Sweasy J.B. Loop II of DNA polymerase beta is important for polymerization activity and fidelity. Nucleic Acids Res. 35 (2007) 2924-2935
10. Opresko P.L., Sweasy J.B., and Eckert K.A. The mutator form of polymerase beta with amino acid substitution at tyrosine 265 in the hinge region displays an increase in both base substitution and frame shift errors. Biochemistry 37 (1998) 2111-2119
11. Eckert K.A., Hile S.E., and Vargo P.L. Development and use of an in vitro HSV-tk forward mutation assay to study eukaryotic DNA polymerase processing of DNA alkyl lesions. Nucleic Acids Res. 25 (1997) 1450-1457
12. Bebenek K., and Kunkel T.A. Streisinger revisited: DNA synthesis errors mediated by substrate misalignments. Cold Spring Harb. Symp. Quant. Biol. 65 (2000) 81-91
13. Kunkel T.A. The mutational specificity of DNA polymerase-beta during in vitro DNA synthesis. Production of frameshift, base substitution, and deletion mutations. J. Biol. Chem. 260 (1985) 5787-5796
14. Eckert K.A., Mowery A., and Hile S.E. Misalignment-mediated DNA polymerase beta mutations: comparison of microsatellite and frame-shift error rates using a forward mutation assay. Biochemistry 41 (2002) 10490-10498
15. Kunkel T.A. Frameshift mutagenesis by eucaryotic DNA polymerases in vitro. J. Biol. Chem. 261 (1986) 13581-13587
16. Beard W.A., and Wilson S.H. Structural design of a eukaryotic DNA repair polymerase: DNA polymerase beta. Mutat. Res. 460 (2000) 231-244
17. Beard W.A., and Wilson S.H. Structure and mechanism of DNA polymerase beta. Chem. Rev. 106 (2006) 361-382
18. Batra V.K., Beard W.A., Shock D.D., Pederson L.C., and Wilson S.H. Structures of DNA polymerase beta with active site mismatches suggest a transient base site intermediate during misincorporation. Mol. Cell. 9 (2008) 315-324