Crystal structures of a ddATP-, ddTTP-, ddCTP-, and ddGTP-trapped ternary complex of Klentaq1: Insights into nucleotide incorporation and selectivity

Protein Science

Volumn 10, Issue 6, 2001, Pages 1225-1233

  Li, Ying ^a   Waksman, Gabriel ^a,b  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Crystal structure; DNA polymerase; Fidelity; Klentaq1

Indexed keywords

DNA DIRECTED DNA POLYMERASE BETA;

ARTICLE; BASE PAIRING; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DNA REPLICATION; ENZYME ACTIVE SITE; NUCLEOTIDE SEQUENCE; POLYMERIZATION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN TERTIARY STRUCTURE; STRUCTURE ANALYSIS;

BINDING SITES; COMPUTER SIMULATION; DEOXYADENINE NUCLEOTIDES; DEOXYCYTOSINE NUCLEOTIDES; DEOXYGUANINE NUCLEOTIDES; DNA; DNA-DIRECTED DNA POLYMERASE; KINETICS; MODELS, MOLECULAR; NUCLEOTIDES; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; TAQ POLYMERASE; THYMINE NUCLEOTIDES;

BACTERIA (MICROORGANISMS); THERMUS AQUATICUS;

EID: 0035019856     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.250101     Document Type: Article

References (22)

1. Brandis, J.W., Edwards, S.G., and Johnson, K.A. 1996. Slow rate of phosphodiester bond formation accounts for the strong bias that Taq DNA polymerase shows against 2′,3′-dideoxynucleotide terminators. Biochemistry 35: 2189-2200.
2. Carroll, S.S., Cowan, M., and Benkovic, S.J. 1991. A mutant DNA polymerase 1 (Klenow fragment) with reduced fidelity. Biochemistry 30: 804-813.
3. Carson, M. 1997. Ribbons. Methods Enzymol. 277: 493-505.
4. Doublié, S., Tabor, S., Long, A.M., Richardson, C.C., and Ellenberger, T. 1998. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature 391: 251-258.
5. Echols, H. and Goodman, M.F. 1991. Fidelity mechanisms in DNA replication. Annu. Rev. Biochem. 60: 477-511.
6. Goodman, M.F. 1997. Hydrogen bonding revisited: Geometric selection as a principal determinant of DNA replication fidelity. Proc. Natl. Acad. Sci. 94: 10493-10495.
7. Guckian, K.M., Krugh, T.R., and Kool, E.T. 1998. Solution structure of a DNA duplex containing a replicable difluorotoluene-adenine pair. Nat. Struct. Biol. 5: 954-959.
8. Johnson, K.A. 1993. Conformational coupling in DNA polymerase fidelity. Annu. Rev. Biochem. 62:685-713.
9. Jones, T.A., Zou, J.Y., Cowan, S.W., and Kjeldgaard, M. 1991. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47: 110-119.
10. Kieler, J.R., Mao, C., Braman, J.C., and Beese, L.S. 1998. Visualising DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature 391: 304-307.
11. Klenow, H., Overgaard-Hansen, K., and Patkar, S.A. 1971. Proteolytic cleavage of native DNA polymerase into two different catalytic fragments. Influence of assay conditions on the change of exonuclease activity and polymerase activity accompanying cleavage. Eur. J. Biochem. 22: 371-381.
12. Korolev, S., Nayal, M., Barnes, W.M., Di Cera, E., and Waksman, G. 1995. Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-A resolution: Structural basis for thermostability. Proc. Natl. Acad. Sci. 92: 9264-9268.
13. Kuchta, R.D., Mizrahi, V., Benkovic, P.A., Johnson, K.A., and Benkovic, S.J. 1987. Kinetic mechanism of DNA polymerase I (Klenow). Biochemistry 26: 8410-8417.
14. Kuchta, R.D., Benkovic, P., and Benkovic, S.J. 1988. Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity. Biochemistry 27: 6716-6725.
15. Li, Y., Kong, Y., Korolev, S., and Waksman, G. 1998a. Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates. Protein Sci. 7: 1116-1123.
16. Li, Y., Korolev, S., and Waksman, G. 1998b. Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: Structural basis for nucleotide incorporation. EMBO J. 17: 7514-7525.
17. Li, Y., Mitaxov, V., and Waksman, G. 1999. Structure-based design of Taq polymerases with improved properties of dideoxynucleotide incorporation. Proc. Natl. Acad. Sci. 96: 9491-9496.
18. Moran, S., Ren, R.X.-F., and Kool, E.T. 1997. A thymidine triphosphate shape analog lacking Watson-Crick pairing ability is replicated with high sequence selectivity. Proc. Natl. Acad Sci. 94: 10506-10511.
19. Ollis, D.L., Brick, R.H., Hamlin, R., Xuong, N.G., and Steitz, T.A. 1985. Structure of large fragment of Escherichia coli DNA polymerase 1 complexed with dTMP. Nature 313: 762-766.
20. Patel, S.S., Wong, I., and Johnson, K.A. 1991. Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant. Biochemistry 30: 511-525.
21. Steitz, T.A. 1999. DNA polymerases: Structural diversity and common mechanisms. J. Biol. Chem. 274: 17395-17398.
22. Wong, I., Patel, S.S., and Johnson, K.A. 1991. An induced-fit kinetic mechanism for DNA replication fidelity: Direct measurement by single-turnover kinetics. Biochemistry 30: 526-537.