∅29 DNA polymerase residue Lys383, invariant at motif B of DNA-dependent polymerases, is involved in dNTP binding

Journal of Molecular Biology

Volumn 269, Issue 3, 1997, Pages 313-325

  Saturno, Javier ^a   Lázaro, José M ^a   Esteban, Francisco J ^a   Blanco, Luis ^a   Salas, Margarita ^a  

^a UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

Author keywords

DNA replication; dNTP binding site; Polymerase active site; Site directed mutagenesis; 29 DNA polymerase

Indexed keywords

DNA; DNA POLYMERASE; EXONUCLEASE; LYSINE; MAGNESIUM; MANGANESE; MUTANT PROTEIN; NUCLEOSIDE TRIPHOSPHATE; VIRUS ENZYME; DEOXYRIBONUCLEOTIDE; DNA DIRECTED DNA POLYMERASE; NUCLEOTIDE; PRIMER DNA;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BACTERIOPHAGE; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA SYNTHESIS; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME BINDING; ENZYME KINETICS; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; NONHUMAN; PRIORITY JOURNAL; PROTEIN NUCLEIC ACID INTERACTION; STRUCTURE ACTIVITY RELATION; BACILLUS PHAGE; BINDING SITE; CHEMISTRY; DNA REPLICATION; DNA TEMPLATE; ENZYMOLOGY; GENETICS; METABOLISM; MOLECULAR GENETICS; MUTATION; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; BACILLUS PHAGES; BINDING SITES; DEOXYRIBONUCLEOTIDES; DNA PRIMERS; DNA REPLICATION; DNA-DIRECTED DNA POLYMERASE; LYSINE; MAGNESIUM; MANGANESE; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEOTIDES; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; TEMPLATES, GENETIC;

EID: 0030611410     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1053     Document Type: Article

References (49)

1. Beese L. S., Derbyshire V., Steitz T. A. Structure of DNA polymerase I Klenow fragment bound to duplex DNA. Science. 260:1993;352-355.
2. Bernad A., Blanco L., Lázaro J. M., Martín G., Salas M. A conserved 3′-5′ exonuclease active site in prokaryotic and eukaryotic DNA polymerases. Cell. 59:1989;219-228.
3. Blanco L., Salas M. Characterization and purification of a phage ø29-encoded DNA polymerase required for the initiation of replication. Proc. Natl Acad. Sci. USA. 82:1984;5325-5329.
4. Blanco L., Salas M. Replication of phage ø29 DNA with purified terminal protein and DNA polymerase: synthesis of full-length ø29 DNA. Proc. Natl Acad. Sci. USA. 82:1985;6404-6408.
5. Blanco L., Salas M. Mutational analysis of bacteriophage ø29 DNA polymerase. Methods Enzymol. 262:1995;283-294.
6. Blanco L., Bernad A., Lázaro J. M., Martín G., Garmendia C., Salas M. Highly efficient DNA synthesis by the phage ø29 DNA polymerase. Symmetrical mode of DNA replication. J. Biol. Chem. 264:1989;8935-8940.
7. Blanco L., Bernad A., Blasco M. A., Salas M. A general structure for DNA-dependent DNA polymerases. Gene. 100:1991;27-38.
8. Blanco L., Bernad A., Esteban J. A., Salas M. DNA-independent deoxynucleotidylation of the ø29 terminal protein by the ø29 DNA polymerase. J. Biol. Chem. 267:1992;1225-1230.
9. 390are affected in dNTP binding. J. Biol. Chem. 267:1992;19427-19434.
10. 3NSxYG is involved in template-primer binding and dNTP selection. J. Biol. Chem. 268:1993;16763-16770.
11. Braithwaite D. K., Ito J. Compilation, alignment and phylogenetic relationships of DNA polymerases. Nucl. Acids Res. 21:1993;787-802.
12. Carthew R. W., Chodosh L. A., Sharp P. A. An RNA polymerase II transcription factor binds to an upstream element in the adenovirus major late promoter. Cell. 43:1985;439-448.
13. Cheng C. H., Kuchta R. D. DNA polymerase epsilon: aphidicolin inhibition and the relationship between polymerase and exonuclease activity. Biochemistry. 32:1993;8568-8574.
14. Delarue M., Poch O., Tordo N., Moras D., Argos P. An attempt to unify the structure of polymerases. Protein Eng. 6:1990;461-467.
15. Dong Q., Wang T. S.-F. Mutational studies of DNA polymerase α. Lysine 950 in the third most conserved region of α-like DNA polymerases is involved in binding the deoxynucleoside triphosphate. J. Biol. Chem. 270:1995;21563-21570.
16. Donlin M. J., Johnson J. A. Mutants affecting nucleotide recognition by T7 DNA polymerase. Biochemistry. 33:1994;14908-14917.
17. Eom S. H., Wang J., Steitz T. A. Structure of Taq polymerase with DNA at the polymerase active site. Nature. 382:1996;278-281.
18. Esteban J. A., Salas M, Blanco L. Fidelity of ø29 DNA polymerase. Comparison between protein-primed initiation and DNA polymerization. J. Biol. Chem. 268:1993;2719-2726.
19. Esteban J. A., Soengas M. S., Salas M., Blanco L. 3′ to 5′ exonuclease active site of ø29 DNA polymerase. Evidence favoring a metal ion-assisted reaction mechanism. J. Biol. Chem. 269:1994;31946-31954.
20. Garmendia C., Bernad A., Esteban J. A., Blanco L., Salas M. The bacteriophage ø29 DNA polymerase, a proofreading enzyme. J. Biol. Chem. 267:1992;2594-2599.
21. Inciarte M. R., Lázaro J. M., Salas M., Viñuela E. Physical map of bacteriophage ø29 DNA. Virology. 74:1976;314-323.
22. Jacobo-Molina A., Ding J., Nanni R. G., Clark A. D., Lu X., Tantillo C., Williams R. L., Kamer G., Ferris A. L., Clark P., Hizi A., Hughes S. H., Arnold E. Crystal structure of human inmunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 Å resolution shows bent DNA. Proc. Natl. Acad. Sci. USA. 90:1993;6320-6324.
23. Joyce C. M., Steitz T. A. Function and structure relationships in DNA polymerases. Annu. Rev. Biochem. 63:1994;777-822.
24. Joyce C. M., Steitz T. A. Polymerase structures and function: variations on a theme? J. Bacteriol. 177:1995;6321-6329.
25. Kohlstaedt L. A., Wang J., Friedman J. M., Rice P. A., Steitz T. A. Crystal structure at 3.5 Å resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science. 256:1992;1783-1790.
26. Larder B. A., Kemp S. D., Darby G. Related functional domains in virus DNA polymerases. EMBO J. 6:1987;169-175.
27. Lázaro J. M., Blanco L., Salas M. Purification of bacteriophage ø29 DNA polymerase. Methods Enzymol. 262:1995;42-49.
28. Masters B. S., Stohl L. L., Clayton D. A. Yeast mitochondrial RNA polymerase is homologous to those encoded by bacteriophages T3 and T7. Cell. 51:1987;89-99.
29. McDonell M. W., Simon M. N., Studier F. W. Analysis of restriction fragments of T7 DNA and determination of molecular weights by electrophoresis in neutral and alkaline gels. J. Mol. Biol. 110:1977;119-146.
30. Méndez J., Blanco L., Esteban J. A., Bernad A., Salas M. Initiation of ø29 DNA replication occurs at the second 3′ nucleotide of the linear template: a sliding-back mechanism for protein-primed DNA replication. Proc. Natl. Acad. Sci. USA. 89:1992;9579-9583.
31. 2GR. J. Biol. Chem. 269:1994;30030-30038.
32. Méndez J., Blanco L., Salas M. Protein-primed DNA replication: a transition between two modes of priming by a unique DNA polymerase. EMBO J. 16:1997;2519-2527.
33. Morrison A., Arai H., Clark A. B., Hamatake R. K., Sugino A. A third essential DNA polymerase in S. cerevisiae. Cell. 62:1990;1143-1151.
34. Nakamaye K., Eckstein F. Inhibition of restriction endonuclease NciI cleavage by phosphorothioate groups and its application to oligonucleotide-directed mutagenesis. Nucl. Acids Res. 14:1986;9679-9698.
35. Osumi-Davis P. A., de Aguilera M. C., Woody R. W., Woody A.-Y. M. Asp537, Asp812 are essential and Lys631, His811 are catalytically significant in bacteriophage T7 RNA polymerase activity. J. Mol. Biol. 226:1992;37-45.
36. Pandey V. N., Kaushik N., Modak M. J. Role of lysine 758 of Escherichia coli DNA polymerase I as assessed by site-directed mutagenesis. J. Biol. Chem. 269:1994;13259-13265.
37. Pelletier H., Sawaya M. R., Kumar A., Wilson S. H., Kraut J. Structures of ternary complexes of rat DNA polymerase ß, a DNA template-primer, and ddCTP. Science. 264:1994;1891-1903.
38. Peñalva M. A., Salas M. Initiation of phage ø29 DNA replication in vitro: formation of a covalent complex between the terminal protein p3 and 5′-dAMP. Proc. Natl. Acad. Sci. USA. 79:1982;5522-5526.
39. Polesky A. H., Steitz T. A., Grindley N. D. F., Joyce C. M. Identification of residues critical for the polymerase activity of the Klenow fragment of DNA polymerase I fromEscherichia coli. J. Biol. Chem. 265:1990;14579-14591.
40. Rodríguez J. M., Yáñez R. J., Rodríguez J. F., Viñuela E., Salas M. L. The DNA polymerase encoding gene of African swine fever virus: sequence and transcriptionasl analysis. Gene. 136:1993;103-110.
41. Rush J., Konigsberg W. H. Photoaffinity labeling of the Klenow fragment with 8-azido-dATP. J. Biol. Chem. 265:1990;4821-4827.
42. Saturno J., Blanco L., Salas M., Esteban J. A. A novel kinetic analysis to determine nucleotide affinity for proofreading DNA polymerases. J. Biol. Chem. 270:1995;31235-31243.
43. Sousa R. Structural and mechanistic relationships between nucleic acid polymerases. Trends Biochem. Sci. 21:1996;186-190.
44. Sousa R., Chung Y. J., Rose J. P., Wang B.-C. Crystal structure of bacteriophage T7 RNA polymerase at 3.3 Å resolution. Nature. 364:1993;593-599.
45. Studier F. W. Use of bacteriophage T7 lysozyme to improve an inducible T7 expression system. J. Mol. Biol. 219:1991;37-44.
46. Studier F. W., Moffat B. A. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J. Mol. Biol. 189:1986;113-130.
47. Tabor S., Richardson C. C. A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes. Proc. Natl. Acad. Sci. USA. 82:1985;1074-1078.
48. Zaballos A., Salas M. Functional domains in the bacteriophage ø29 terminal protein for interaction with the ø29 DNA polymerase and with DNA. Nucl Acids Res. 17:1989;10353-10366.
49. Zhu W., Leavitt M. C., Jung G., Ito J. Mutagenesis of a highly conserved lysine 340 of the PRD1 DNA polymerase. Biochim. Biophys. Acta. 1219:1994;260-266.