The mechanism of action of T7 DNA polymerase

Current Opinion in Structural Biology

Volumn 8, Issue 6, 1998, Pages 704-712

  Doublié, Sylvie ^a   Ellenberger, Tom ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE;

BACTERIOPHAGE T7; BINDING SITE; CRYSTAL STRUCTURE; DNA SYNTHESIS; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME CONFORMATION; ENZYME MECHANISM; ENZYME SUBSTRATE COMPLEX; HYDROGEN BOND; NONHUMAN; PRIORITY JOURNAL; REVIEW;

UNIDENTIFIED BACTERIOPHAGE;

EID: 0032425080     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(98)80089-4     Document Type: Article

References (73)

1. 1. Joyce CM, Steitz TA: Function and structure relationships in DNA polymerases. Annu Rev Biochem 1994, 63:777-822.
2. 2. Korolev S, Nayal M, Barnes WM, Di Cera E, Waksman G: Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-Å resolution: structural basis for thermostability. Proc Natl Acad Sci USA 1995, 92:9264-9268.
3. 3. Kim Y, Eom SH, Wang J, Lee DS, Sun SW, Steitz TA: Crystal structure of Thermus aquaticus DNA polymerase. Nature 1995, 376:612-616.
4. 4. Eom SH, Wang J, Steitz TA: Structure of Taq polymerase with DNA at the polymerase active site. Nature 1996, 382:278-281.
5. 5. Kiefer JR, Mao C, Hansen CJ, Basehore SL, Hogrefe HH, Braman JC, Beese LS: Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 Å resolution. Structure 1997, 5:95-108.
6. 6. Kiefer JR, Mao C, Braman JC, Beese LS: Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature 1998, 391:304-307. The authors describe several structures of the Bst DNA polymerase in complex with a DNA primer-template that had been extended by several cycles of nucleotide addition actually in the crystals. Polymerization and translocation of the DNA occur within the crystal lattice and the resulting DNA product is shown in the polymerase active site.
7. 7. Doublié S, Tabor S, Long AM, Richardson CC, Ellenberger T: Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature 1998, 391:251-258. The authors describe the first structure determination of a processive polymerase complexed with DNA primer-template and incoming nucleotide. The fingers subdomain of the polymerase closes onto the incoming nucleotide, creating a very tight binding site that can only accommodate Watson-Crick base pairs. The closing of the fingers aligns the incoming nucleotide vis-a-vis both the 3′-end of the primer and the two metals in the active site that are poised to participate in phosphoryl transfer.
8. 8. Baker TA, Bell SP: Polymerases and the replisome: machines within machines. Cell 1998, 92:295-305.
9. 9. Kunkel TA, Wilson SH: DNA polymerases on the move. Nat Struct Biol 1998, 5:95-99.
10. 10. Brautigam CA, Steitz TA: Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes. Curr Opin Struct Biol 1998, 8:54-63.
11. 11. Kelman Z, Hurwitz J, O'Donnell M: Processivity of DNA polymerases: two mechanisms, one goal. Structure 1998, 6:121-125.
12. 12. Tabor S, Richardson CC: A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy-and dideoxyribonucleotides. Proc Natl Acad Sci USA 1995, 92:6339-6343.
13. 13. Astatke M, Grindley ND, Joyce CM: How E. coli DNA polymerase I (Klenow fragment) distinguishes between deoxy-and dideoxynucleotides. J Mol Biol 1998, 278:147-165. Residues in the active site of a Klenow fragment polymerase were examined for their effects on the efficiency of ddNTP incorporation, relative to normal dNTP substrates. Of the many mutant polymerases examined, only residue substitutions involving Phe762 selectively relieved discrimination against ddNTPs, primarily by increasing their rate of incorporation.
14. 14. Astatke M, Ng K, Grindley ND, Joyce CM: A single side chain prevents Escherichia coli DNA polymerase I (Klenow fragment) from incorporating ribonucleotides. Proc Natl Acad Sci USA 1998, 95:3402-3407. The authors demonstrate the crucial role of the Klenow fragment residue Glu710 as a 'steric gate' that discriminates against ribonucleotide incorporation. A mutant polymerase with alanine substituted for Glu710 is permissive for the addition of a single ribonucleotide, but it cannot synthesize RNA, implying that additional barriers prevent the incorporation of successive ribonucleotides.
15. 15. Bell JB, Eckert KA, Joyce CM, Kunkel TA: Base miscoding and strand misalignment errors by mutator Klenow polymerases with amino acid substitutions at tyrosine 766 in the O helix of the fingers subdomain. J Biol Chem 1997, 272:7345-7351.
16. 16. Moran S, Ren RX, Kool ET: A thymidine triphosphate shape analog lacking Watson-Crick pairing ability is replicated with high sequence selectivity. Proc Natl Acad Sci USA 1997, 94:10506-10511. The authors demonstrate that the Klenow fragment selectively incorporates a nonpolar thymine analog opposite a template adenine. This thymine isostere has little or no capacity to hydrogen bond with adenine, demonstrating that nucleotide shape contributes greatly to the accuracy of template-directed DNA synthesis.
17. 17. Minnick DT, Bebenek K, Osheroff WR Turner RM Jr, Astatke M, Liu L, Kunkel TA, Joyce CM: Side chains that influence fidelity at the polymerase active site of Escherichia coli DNA polymerase I (Klenow fragment). J Biol Chem 1999, in press. Five residues in the Klenow fragment polymerase active site are shown to influence the fidelity of DNA synthesis in distinctive ways. Alanine substitutions at these positions cause characteristic error specificities, with differential effects on nucleotide incorporation and the extension of a mismatched primer-template. These residues contact the bound DNA and/or nucleotide in crystal structures of Pol I family polymerases.
18. 18. Wang J, Sattar AK, Wang CC, Karam JD, Konigsberg WH, Steitz TA: Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69. Cell 1997, 89:1087-1099. The first crystal structure determination of a pol α family-type polymerase reveals similarities, but also considerable differences to the Pol I family polymerases, including the position of the proofreading exonuclease domain with respect to the polymerase domain.
19. 19. Pelletier H, Sawaya MR, Kumar A, Wilson SH, Kraut J: Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP. Science 1994, 264:1891-1903.
20. 20. Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H: Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism. Biochemistry 1997, 36:11205-11215. Three structures of DNA polymerase β complexed to DNA substrates are described, each of which represent intermediates of the gap-filling reaction catalyzed by this repair polymerase. The C-terminal domain of the polymerase closes towards the active site only when the correct nucleotide is bound. The authors discuss an induced fit mechanism used by polymerase β to increase fidelity.
21. 21. Kornberg A, Baker T: DNA Replication, edn 2. New York: WH Freeman and Co.; 1992.
22. 22. Steitz TA: DNA-and RNA-dependent DNA polymerases. Curr Opin Struct Biol 1993, 3:31-38.
23. 23. Narlikar GJ, Herschlag D: Mechanistic aspects of enzymatic catalysis: lessons from comparison of RNA and protein enzymes. Annu Rev Biochem 1997, 66:19-59.
24. 24. Matte A, Tari LW, Delbaere LT: How do kinases transfer phosphoryl groups? Structure 1998, 6:413-419.
25. 2+ clusters in enzyme-catalyzed phosphoryl-transfer reactions. Nat Struct Biol 1997, 4:990-994.
26. 26. Sloan DL, Loeb LA, Mildvan AS: Conformation of deoxynucleoside triphosphate substrates on DNA polymerase I from Escherichia coli as determined by nuclear magnetic relaxation. J Biol Chem 1975, 250:8913-8920.
27. 27. Burgers PM, Eckstein F: A study of the mechanism of DNA polymerase I from Escherichia coli with diastereomeric phosphorothioate analogs of deoxyadenosine triphosphate. J Biol Chem 1979, 254:6889-6893.
28. 28. Beese LS, Steitz TA: Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. EMBO J 1991, 10:25-33.
29. 29. Brautigam CA, Steitz TA: Structural principles for the inhibition of the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates. J Mol Biol 1998, 277:363-377.
30. 30. Glusker JP: Structural aspects of metal liganding to functional groups in proteins. Adv Protein Chem 1991, 42:1-76.
31. 31. Brody RS, Frey PA: Unambiguous determination of the stereochemistry of nucleotidyl transfer catalyzed by DNA polymerase I from Escherichia coli. Biochemistry 1981, 20:1245-1252.
32. 32. Brody RS, Adler S, Modrich P, Stec WJ, Leznikowski ZJ, Frey PA: Stereochemical course of nucleotidyl transfer catalyzed by bacteriophage T7 induced DNA polymerase. Biochemistry 1982, 21:2570-2572.
33. 33. Jencks WP: Catalysis in Chemistry and Enzymology. New York: McGraw-Hill; 1969.
34. 34. Schray KJ, Benkovic SJ, Benkovic PA, Rose IA: Catalytic reactions of phosphoglucose isomerase with cyclic forms of glucose 6-phosphate and fructose 6-phosphate. J Biol Chem 1973, 248:2219-2224.
35. 35. Knowles JR: Enzyme-catalyzed phosphoryl transfer reactions. Annu Rev Biochem 1980, 49:877-919.
36. 36. Herschlag D, Jencks WP: Phosphoryl transfer to anionic oxygen nucleophiles. Nature of the transition state and electrostatic repulsion. J Am Chem Soc 1989, 111:7587-7596.
37. 37. Admiraal SJ, Herschlag D: Mapping the transition state for ATP hydrolysis: implications for enzymatic catalysis. Chem Biol 1995, 2:729-739.
38. 38. Delarue M, Poch O, Tordo N, Moras D, Argos P: An attempt to unify the structure of polymerases. Protein Eng 1990, 3:461-467.
39. 39. Beese LS, Friedman JM, Steitz TA: Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate. Biochemistry 1993, 32:14095-14101.
40. 40. McClure WR, Jovin TM: The steady state kinetic parameters and non-processivity of Escherichia coli deoxyribonucleic acid polymerase I. J Biol Chem 1975, 250:4073-4080.
41. 41. Kuchta RD, Benkovic P, Benkovic SJ: Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity. Biochemistry 1988, 27:6716-6725.
42. 42. Dahlberg ME, Benkovic SJ: Kinetic mechanism of DNA polymerase I (Klenow fragment): identification of a second conformational change and evaluation of the internal equilibrium constant. Biochemistry 1991, 30:4835-4843.
43. 43. Patel SS, Wong I, Johnson KA: Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant. Biochemistry 1991, 30:51-525.
44. 44. Wong I, Patel SS, Johnson KA: An induced-fit kinetic mechanism for DNA replication fidelity: direct measurement by single-turnover kinetics. Biochemistry 1991, 30:526-537.
45. 45. Beese LS, Derbyshire V, Steitz TA: Structure of DNA polymerase I Klenow fragment bound to duplex DNA. Science 1993, 260:352-355.
46. 46. Sawaya MR, Pelletier H, Kumar A, Wilson SH, Kraut J: Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism. Science 1994, 264:1930-1935.
47. 47. Polesky AH, Dahlberg ME, Benkovic SJ, Grindley ND, Joyce CM: Side chains involved in catalysis of the polymerase reaction of DNA polymerase I from Escherichia coli. J Biol Chem 1992, 267:8417-8428.
48. 48. Astatke M, Grindley ND, Joyce CM: Deoxynucleoside triphosphate and pyrophosphate binding sites in the catalytically competent ternary complex for the polymerase reaction catalyzed by DNA polymerase I (Klenow fragment). J Biol Chem 1995, 270:1945-1954.
49. 49. Kaushik N, Pandey VN, Modak MJ: Significance of the O-helix residues of Escherichia coli DNA polymerase I in DNA synthesis: dynamics of the dNTP binding pocket Biochemistry 1996, 35:7256-7266.
50. 50. Carroll SS, Cowart M, Benkovic SJ: A mutant of DNA polymerase I (Klenow fragment) with reduced fidelity. Biochemistry 1991, 30:804-813.
51. 51. Donlin MJ, Johnson KA: Mutants affecting nucleotide recognition by T7 DNA polymerase. Biochemistry 1994, 33:14908-14917.
52. 52. Li Y, Kong Y, Korolev S, Waksman G: Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates. Protein Sci 1998, 7:1116-1123. Four structures of Taq DNA polymerase complexed to each of the natural dNTPs are described. The interactions of basic residues with the triphosphate group of the bound nucleotide are nearly identical in all four Taq polymerase structures and are similar to those in the T7 polymerase complex. The sidechain of Tyr671 (Tyr530 of T7 polymerase) does not contact the nucleotide and is not in a fixed conformation in the absence of a DNA primer-template.
53. 53. Echols H, Goodman MF: Fidelity mechanisms in DNA replication. Annu Rev Biochem 1991, 60:477-511.
54. 54. Johnson KA: Conformational coupling in DNA polymerase fidelity. Annu Rev Biochem 1993, 62:685-713.
55. 55. Goodman MF, Creighton S, Bloom LB, Petruska J: Biochemical basis of DNA replication fidelity. Crit Rev Biochem Mol Biol 1993, 28:83-126.
56. 56. Beckman RA, Loeb LA: Multi-stage proofreading in DNA replication. O Rev Biophys 1993, 26:225-331.
57. 57. Goodman MF: Hydrogen bonding revisited: geometric selection as a principal determinant of DNA replication fidelity. Proc Natl Acad Sci USA 1997, 94:10493-10495.
58. 58. Goodman MF, Fygenson KD: DNA polymerase fidelity: from genetics toward a biochemical understanding. Genetics 1998, 148:1475-1482.
59. 59. Engel JD, von Hippel PH: D(M6ATP) as a probe of the fidelity of base incorporation into polynucleotides by Escherichia coli DNA polymerase I. J Biol Chem 1978, 253:935-939.
60. 60. Sloane DL, Goodman MF, Echols H: The fidelity of base selection by the polymerase subunit of DNA polymerase III holoenzyme. Nucleic Acids Res 1988, 16:6465-6475.
61. 61. Herschlag D: The role of induced fit and conformational changes of enzymes in specificity and catalysis. Bioorg Chemistry 1988, 16:62-96.
62. 62. Post CB, Ray WJ Jr: Reexamination of induced fit as a determinant of substrate specificity in enzymatic reactions. Biochemistry 1995, 34:15881-15885.
63. 63. Petruska J, Sowers LC, Goodman MF: Comparison of nucleotide interactions in water, proteins, and vacuum: model for DNA polymerase fidelity. Proc Natl Acad Sci USA 1986, 83:1559-1562.
64. 64. Morales JC, Kool ET: Efficient replication between non-hydrogen bonded nucleoside shape analogues. Nat Struct Biol 1998, in press. The Klenow fragment of E. coli DNA polymerase I selectively incorporates a deoxyribonucleotide of the adenine-shaped mimic 4-methylbenzimidazole (compound Z) opposite the thymine analog difluorotoluene (compound F), which is located in the template strand. Thus, the polymerase recognizes the shape of the nonpolar Z-F base pair, despite a lack of Watson-Crick hydrogen bonds. Conversely, the nucleoside monophosphate of compound F is incorporated opposite a templating Z, in preference to any of the four naturally occurring deoxyribonucleotides.
65. 65. Lam WC, Van der Schans EJ, Joyce CM, Millar DP: Effects of mutations on the partitioning of DNA substrates between the polymerase and 3′-5′ exonuclease sites of DNA polymerase I (Klenow fragment). Biochemistry 1998, 37:1513-1522. Residues affecting the partitioning of DNA between the polymerase and exonuclease active sites of the Klenow fragment were identified by time-resolved fluorescence spectroscopy of mutant polymerases with residue substitutions in the exonuclease domain.
66. 66. Stocki SA, Nonay RL, Reha-Krantz LJ: Dynamics of bacteriophage T4 DNA polymerase function: identification of amino acid residues that affect switching between polymerase and 3′→5′ exonuclease activities. J Mol Biol 1995, 254:15-28.
67. 67. Polesky AH, Steitz TA, Grindley ND, Joyce CM: Identification of residues critical for the polymerase activity of the Klenow fragment of DNA polymerase I from Escherichia coli. J Biol Chem 1990, 265:14579-14591.
68. 68. Tabor S, Huber HE, Richardson CC: Escherichia coli thioredoxin confers processivity on the DNA polymerase activity of the gene 5 protein of bacteriophage T7. J Biol Chem 1987, 262:16212-16223.
69. 69. Huber HE, Russel M, Model P, Richardson CC: Interaction of mutant thioredoxins of Escherichia coli with the gene 5 protein of phage T7. The redox capacity of thioredoxin is not required for stimulation of DNA polymerase activity. J Biol Chem 1986, 261:15006-15012.
70. 70. Huber HE, Tabor S, Richardson CC: Escherichia coli thioredoxin stabilizes complexes of bacteriophage T7 DNA polymerase and primed templates. J Biol Chem 1987, 262:16224-16232.
71. 71. Yang XM, Richardson CC: Amino acid changes in a unique sequence of bacteriophage T7 DNA polymerase alter the processivity of nucleotide polymerization. J Biol Chem 1997, 272:6599-6606.
72. 72. Bedford E, Tabor S, Richardson CC: The thioredoxin binding domain of bacteriophage T7 DNA polymerase confers processivity on Escherichia coli DNA polymerase I. Proc Natl Acad Sci USA 1997, 94:479-484. The Klenow fragment was rendered more processive in the presence of thioredoxin after grafting the thioredoxin-binding domain of T7 DNA polymerase onto the tip of its thumb subdomain. The processivity function is portable and is mainly localized to this small domain.
73. 73. Gottlieb J, Marcy Al, Coen DM, Challberg MD: The Herpes simplex virus type 1 UL42 gene product: a subunit of DNA polymerase that functions to increase processivity. J Virol 1990, 64:5976-5987.