∅29 DNA polymerase requires the N-terminal domain to bind terminal protein and DNA primer substrates

Journal of Molecular Biology

Volumn 278, Issue 4, 1998, Pages 741-755

  Truniger, Verónica ^a   Lázaro, José M ^a   Salas, Margarita ^a   Blanco, Luis ^a  

^a CENTRO DE BIOLOGÍA MOLECULAR SEVERO OCHOA   (Spain)

Author keywords

C terminal domain; Polymerization module; Strand displacement; Terminal protein; 29 DNA polymerase

Indexed keywords

DNA POLYMERASE; MANGANESE; PRIMER DNA; DNA DIRECTED DNA POLYMERASE; DNA REPLICASE; EXODEOXYRIBONUCLEASE; EXODEOXYRIBONUCLEASE V; PEPTIDE FRAGMENT; RECOMBINANT PROTEIN; TERMINAL PROTEIN, BACILLUS PHAGE PHI29; VIRUS PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; DNA REPLICATION; DNA SYNTHESIS; ENZYME ACTIVITY; NONHUMAN; POLYMERIZATION; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN STRUCTURE; BACILLUS PHAGE; CHEMICAL STRUCTURE; ENZYMOLOGY; ESCHERICHIA COLI; GENETICS; METABOLISM; MOLECULAR CLONING; PROTEIN BINDING; STRUCTURE ACTIVITY RELATION; VIROLOGY;

ESCHERICHIA COLI;

BACILLUS PHAGES; CLONING, MOLECULAR; DNA PRIMERS; DNA REPLICATION; DNA-DIRECTED DNA POLYMERASE; ESCHERICHIA COLI; EXODEOXYRIBONUCLEASE V; EXODEOXYRIBONUCLEASES; MODELS, MOLECULAR; PEPTIDE FRAGMENTS; PROTEIN BINDING; RECOMBINANT PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP; VIRAL PROTEINS;

EID: 0032523226     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1724     Document Type: Article

References (60)

1. Arnold E., Ding J., Hughes S.H., Hostomsky Z. Structures of DNA and RNA polymerases and their interactions with nucleic acid substrates. Curr. Opin. Struct. Biol. 5:1995;27-38
2. Beese L.S., Derbyshire V., Steitz T.A. Structure of DNA polymerase I Klenow fragment bound to duplex DNA. Science. 260:1993;352-355
3. Bernad A., Zaballos A., Salas M., Blanco L. Structural and functional relationships between prokaryotic and eukaryotic DNA polymerases. EMBO J. 6:1987;4219-4225
4. 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
5. Bernad A., Lázaro J.M., Salas M., Blanco L. The highly conserved amino acid sequence motif Tyr-Gly-Asp-Thr-Asp-Ser in α-like DNA polymerases is required by phage ø29 DNA polymerase for protein-primed initiation and polymerization. Proc. Natl Acad. Sci. USA. 87:1990;4610-4614
6. Blanco L., Salas M. Mutational analysis of bacteriophage ø29 DNA polymerase. Methods Enzymol. 262:1995;283-294
7. Blanco L., Salas M. Bacteriophage ø29 DNA polymerase. Nucl. Acids Mol. Biol. 9:1995;328-341
8. Blanco L., Salas M. Relating structure to function in ø29 DNA polymerase. J. Biol. Chem. 271:1996;8509-8512
9. Blanco L., Gutiérrez J., Lázaro J.M., Bernad A., Salas M. Replication of phage ø29 DNA in vitro role of the viral protein p6 in initiation and elongation. Nucl. Acids Res. 14:1986;4923-4937
10. + ions on ø29 DNA-protein p3 replication formation of a complex between the terminal protein and the DNA polymerase. Virology. 61:1987;3983-3991
11. Blanco L., Bernad A., Salas M. Transition from initiation to elongation in protein-primed ø29 DNA replication Salt-dependent stimulation by the viral protein p6. J. Virol. 62:1988;4167-4172
12. 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
13. Blanco L., Bernad A., Salas M. Evidence favoring the hypothesis of a conserved 3′-5′ exonuclease active site in DNA-dependent DNA polymerases. Gene. 112:1992;139-144
14. 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
15. 2SLYP is critical for synthetic activities. J. Biol. Chem. 268:1993;24106-24113
16. 3NSxYG" is involved in template-primer binding and dNTP selection. J. Biol. Chem. 268:1993;16763-16770
17. Blasco M.A., Méndez J., Lázaro J.M., Blanco L., Salas M. Primer-terminus stabilization at the ø29 DNA polymerase active site Mutational analysis of conserved motif KxY. J. Biol. Chem. 270:1995;2735-2740
18. Braithwaite D.K., Ito J. Compilation, alignment and phylogenetic relationships of DNA polymerases. Nucl. Acids Res. 21:1993;787-802
19. Carthew R.W., Chodosch 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
20. Delarue M., Poch O., Tordo N., Moras D., Argos P. An attempt to unify the structure of polymerases. Protein Eng. 3:1990;461-467
21. Derbyshire V., Astatke M., Joyce C.M. Re-engineering the polymerase domain of Klenow fragment and evaluation of overproduction and purification strategies. Nucl. Acids Res. 23:1993;5439-5448
22. Derbyshire V., Pinsonneault J.K., Joyce C.M. Structure-function analysis of 3′-5′ exonucleases of DNA polymerases. Methods Enzymol. 262:1995;363-385
23. de Vega M., Lázaro J.M., Salas M., Blanco L. Primer-terminus stabilization at the 3′-5′ exonuclease active site of ø29 DNA polymerase. Involvement of two amino acid residues highly conserved in proofreading DNA polymerases. EMBO J. 15:1996;1182-1192
24. Esteban J.A., Soengas M.S., Salas M., Blanco L. 3′-5′ exonuclease active site of ø29 DNA polymerase. Evidence favoring a metal ion-assisted reaction mechanism. J. Biol. Chem. 244:1994;31946-31954
25. Freemont P.S., Ollis D.L., Steitz T.A., Joyce C.M. A domain of the Klenow fragment of Escherichia coli DNA polymerase I has polymerase but no exonuclease activity. Proteins: Struct. Funct. Genet. 1:1986;66-73
26. Freire R., Serrano M., Salas M., Hermoso J.M. Activation of replication origins in ø29 - related phages requires the recognition of initiation proteins to specific nucleoprotein complexes. J. Biol. Chem. 271:1996;31000-31007
27. Garmendia C., Bernad A., Esteban J.A., Blanco L., Salas M. The bacteriophage ø29 DNA polymerase, a proof-reading enzyme. J. Biol. Chem. 267:1992;2594-2599
28. Joyce C.M., Steitz T.A. Function and structure relationships in DNA polymerases. Annu. Rev. Biochem. 63:1994;777-822
29. Karawaya E., Swack J., Wilson S.H. Improved conditions for activity gel analysis of DNA polymerase catalytic polypeptides. Anal. Biochem. 135:1983;318-325
30. Kiefer J.R., Mao C., Hansen C., Basehore S., Hogrefe H., Braman J., Beese L.S. Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 Å resolution. Structure. 5:1997;95-108
31. Kohlstaedt L.A., Wang J., Friedman J., Rice P., Steitz T.A. Crystal structure at 3.5 Å resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science. 256:1992;1783-1790
32. Korolev S., Nayal M., Barnes W.M., di Cera E., Waksman G. Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5 å resolution Structural basis of thermostability. Proc. Natl Acad. Sci. USA. 92:1995;9264-9268
33. Lázaro J.M., Blanco L., Salas M. Purification of bacteriophage ø29 DNA polymerase. Methods Enzymol. 262:1995;42-49
34. Lai M.T., Verma I.M. Reverse transcriptase of RNA tumor viruses. J. Virol. 25:1978;652-663
35. Lin T.C., Karam G., Konigsberg W. Isolation, characterization and kinetic properties of truncated forms of T4 DNA polymerase exhibit 3′-5′ exonuclease activity. J. Biol. Chem. 269:1994;19286-19294
36. Matsumoto Y., Kim K. Excission of deoxyribose phosphate residues by DNA polymerase β during DNA repair. Science. 269:1995;699-702
37. 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
38. 2GR" J. Biol. Chem. 269:1994;30030-30038
39. 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
40. Ollis D.L., Brick R., Hamlin R., Xuong N.G., Steitz T.A. Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. Nature. 313:1985;762-766
41. Pastrana R., Lázaro J.M., Blanco L., García J.A., Méndez E., Salas M. Overproduction and purification of protein p6 of Bacillus subtilis phage ø29 role in the initiation of DNA replication. Nucl. Acids Res. 13:1985;3083-3100
42. 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
43. Pisani F.M., Rossi M. Evidence that an archeal α-like DNA polymerase has a modular organization of its associated catalytic activities. J. Biol. Chem. 269:1994;7887-7892
44. Salas M. Protein-priming of DNA replication. Annu. Rev. Biochem. 60:1991;39-71
45. Sawaya M.R., Pelletier H., Kumar A., Wilson S.H., Kraut J. Crystal structure of rat DNA polymerase β evidence for a common polymerase mechanism. Science. 264:1994;1930-1935
46. Sayle R.A., Milnerwhite E.J. RASMOL biomolecular graphics for all. Trends Biochem. Sci. 20:1995;375
47. Serrano M., Salas M., Hermoso J.M. A novel nucleoprotein complex at a replication origin. Science. 248:1990;1012-1016
48. Serrano M., Gutiérrez C., Freire R., Bravo A., Salas M., Hermoso J.M. Phage ø29 protein p6 a viral histone-like protein. Biochimie. 76:1994;981-991
49. Smith J.S., Roth M.J. Purification and characterization of an active human immunodeficiency virus type I RNase H domain. J. Virol. 67:1993;4037-4049
50. Soengas M.S., Esteban J.A., Lázaro J.M., Bernad A., Blasco M.A., Salas M., Blanco L. Site-directed mutagenesis at the Exo III motif of ø29 DNA polymerase. Overlapping structural domains for the 3′-5′ exonuclease and strand-displacement activities. EMBO J. 11:1992;4227-4237
51. Studier F.W. Use of bacteriophage T7 lysozyme to improve an inducible T7 expression system. J. Mol. Biol. 219:1991;37-44
52. Studier F.W., Moffatt B.A. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J. Mol. Biol. 189:1986;113-130
53. 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
54. Tanese N., Telesnitsky A., Goff S.P. Abortive reverse transcription by mutants of Moloney murine leukemia virus deficient in the reverse transcriptase-associated Rnase H function. J. Virol. 65:1991;4387-4397
55. Truniger V., Lázaro J.M., Salas M., Blanco L. A DNA binding motif coordinating synthesis and degradation in proofreading DNA polymerases. EMBO J. 15:1996;3430-3441
56. 2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions. Biochemistry. 35:1996;8110-8119
57. Wang J., Sattar A.K.M.A., Wang C.C., Karam J.D., Konigsberg W.H., Steitz T.A. Crystal structure of a pol α family replication DNA polymerase from bacteriophage RB69. Cell. 89:1997;1087-1099
58. Weisshart K., Kuo A.A., Hwang C.B., Kumura K., Coen D.M. Structural and functional organization of herpes simplex virus DNA polymerase investigated by limited proteolysis. J. Biol. Chem. 269:1994;22788-22796
59. Yang X., Richardson C.C. Structural and functional organization of the DNA polymerase of bacteriophage T7. J. Biol. Chem. 271:1996;24207-24212
60. Zaballos A., Salas M. Functional domains in the bacteriophage ø29 terminal protein for the interaction with the ø29 DNA polymerase and with DNA. Nucl. Acids Res. 17:1989;10353-10366