A single tyrosine prevents insertion of ribonucleotides in the eukaryotic-type φ29 DNA polymerase

Journal of Molecular Biology

Volumn 290, Issue 1, 1999, Pages 241-251

  Bonnin, Ana ^a   Lázaro, José M ^a   Blanco, Luis ^a   Salas, Margarita ^a  

^a UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

Author keywords

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

Indexed keywords

DEOXYRIBONUCLEOTIDE; DNA POLYMERASE; RIBONUCLEOTIDE; TYROSINE; VALINE;

AMINO ACID SUBSTITUTION; ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; ENZYME BINDING; PRIORITY JOURNAL;

EUKARYOTA;

EID: 0345188651     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2900     Document Type: Article

References (36)

1. Arnold E., Ding J., Hughes S. H., Hostomsky A. Structures of DNA and RNA polymerases and their interactions with nucleic acid substrates. Curr. Opin. Struct. Biol. 5:1995;27-38.
2. Astatke M., Ng K. M., Grindley N. D. F., Joyce C. M. A single side-chain prevents E. coli DNA polymerase I (Klenow fragment) from incorporating ribonucleotides. Proc. Natl Acad. Sci. USA. 95:1998;3402-3407.
3. Bebenek K., Kunkel T. A. Analyzing fidelity of DNA polymerases. Methods Enzymol. 262:1995;217-232.
4. Beese L. S., Derbyshire V., Steitz T. A. Structure of DNA polymerase I Klenow fragment bound to duplex DNA. Science. 260:1993;352-355.
5. Blanco L., Salas M. Mutational analysis of bacteriophage φ29 DNA polymerase. Methods Enzymol. 262:1995;283-294.
6. Blanco L., Salas M. Relating structure to function in φ29 DNA polymerase. J. Biol. Chem. 217:1996;721-729.
7. 390are affected in dNTP binding. J. Biol. Chem. 267:1992;19427-19434.
8. Bordo D., Argos P. Suggestions for "safe" residue substitutions in site-directed mutagenesis. J. Biol. Chem. 217:1991;721-729.
9. Braithwaite D. K., Ito J. Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucl. Acids Res. 21:1993;787-802.
10. Chou P. Y., Fasman G. D. Prediction of the secondary structures of proteins from their amino acid sequence. Advan. Enzymol. 47:1978;45-48.
11. Delarue M., Poch O., Tordo N., Moras D., Argos P. An attempt to unify the structure of polymerases. Protein Eng. 6:1990;461-467.
12. Doublié S., Tabor S., Long A. M., Richardson C. C., Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature. 391:1998;251-258.
13. Eom S. H., Wang J., Steitz T. A. Structure of Taq polymerase with DNA at the polymerase active site. Nature. 382:1996;278-281.
14. Gao G., Goff S. P. Replication defect of Moloney Murine Leukemia Virus with a mutant reverse transcriptase that can incorporate ribonucleotides and deoxyribonucleotides. J. Virol. 72:1998;5905-5911.
15. Gao G., Orlova M., Georgiadis M. M., Hendrickson W. A., Goff S. P. Conferring RNA polymerase activity to a DNA polymerase: a single residue in reverse transcriptase controls sub strate selection. Proc. Natl Acad. Sci. USA. 94:1997;407-411.
16. Garnier J., Osguthorpe D. J., Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol. 120:1978;97-120.
17. Ho S. N., Hunt H. D., Horton R. M., Pullen J. K., Pease L. R. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene. 77:1989;51-59.
18. 2+and deoxynucleoside monophosphate incorporation into transcripts. Biochemistry. 36:1997;13718-13728.
19. 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 strusture of human immunodeficiency 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.
20. Joyce C. M. Choosing the right sugar: How polymerases select a nucleotide substrate. Proc. Natl Acad. Sci. USA. 94:1997;1619-1622.
21. Joyce C. M., Steitz T. A. Function and structure relationships in DNA polymerases. Annu. Rev. Biochem. 63:1994;777-822.
22. Kiefer J. R., Mao C., Braman J. C., Beese L. S. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature. 391:1998;304-307.
23. Kornberg A., Baker T. DNA Replication. 1992;Freeman and Company, New York.
24. Lázaro J. M., Blanco L., Salas M. Purification of φ29 DNA polymerase. Methods Enzymol. 262:1995;42-49.
25. Pelletier H., Sawaya M. R., Kumar A., Wilson S. H., Kraut J. Structures of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP. Science. 264:1994;1891-1902.
26. Pelletier H., Sawaya M. R., Wolfe W., Wilson S. H., Kraut J. Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity. Biochemistry. 35:1996;12742-12761.
27. Saturno J., Blanco L., Salas M., Esteban J. A. A novel kinetic analysis to calculate nucleotide affinity of proofreading DNA polymerases. J. Biol. Chem. 270:1995;31235-31243.
28. 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.
29. Sousa R. Structural and mechanistic relationships between nucleic acid polymerases. Trends Biochem. Sci. 21:1996;186-190.
30. Sousa R., Padilla R. A mutant T7 RNA polymerase as a DNA polymerase. EMBO J. 14:1995;4609-4621.
31. Steitz T. A., Smerdon S. J., Jäger J., Joyce C. M. A unified polymerase mechanism for nonhomologous DNA and RNA polymerases. Science. 266:1994;2022-2025.
32. Studier F. W. Use of bacteriophage T7 lysozyme to improve an inducible T7 expression system. J. Mol. Biol. 219:1991;37-44.
33. 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.
34. 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.
35. Tabor S., Richardson C. C. Effect of manganese ions on the incorporation of dideoxynucleotides by bacteriophage T7 DNA polymerase andEscherichia coli DNA polymerase I. Proc. Natl Acad. Sci. USA. 86:1989;4076-4080.
36. Wang J., Sattar A. K. M. A., Wang C. C., Karam J. D., Konisberg W. H., Steitz T. A. Crystal structure of a pol α family replication DNA polymerase from bacteriophage RB69. Cell. 89:1997;1087-1089.