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Volumn 268, Issue 2, 1997, Pages 284-302

Biochemical and mutational studies of the 5'-3' exonuclease of DNA polymerase I of Escherichia coli

Author keywords

5' 3' exonuclease; Carboxylate ligands; DNA polymerase; Structure specific nuclease; Two metal catalysis

Indexed keywords

DNA DIRECTED DNA POLYMERASE BETA; EXONUCLEASE;

EID: 0031547960     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.0967     Document Type: Article
Times cited : (55)

References (55)
  • 1
    • 0023148160 scopus 로고
    • Inducible DNA polymerase I synthesis in a UV hyper-resistant mutant of Escherichia coli
    • Ahmad S. I., van Sluis C. A. Inducible DNA polymerase I synthesis in a UV hyper-resistant mutant of Escherichia coli. Mutat. Res. 190:1987;77-81.
    • (1987) Mutat. Res. , vol.190 , pp. 77-81
    • Ahmad, S.I.1    Van Sluis, C.A.2
  • 2
    • 0026593806 scopus 로고
    • Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops
    • Antao V. P., Tinoco I., Jr. Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucl. Acids Res. 20:1992;819-824.
    • (1992) Nucl. Acids Res. , vol.20 , pp. 819-824
    • Antao, V.P.1    Tinoco, I.2    Jr3
  • 3
    • 0027483668 scopus 로고
    • Cloning, nucleotide sequence, and expression in Escherichia coli of DNA polymerase gene (polA) fromThermus thermophilus
    • Asakura K., Komatsubara H., Soga S., Yomo T., Oka M., Emi S., Urabe I. Cloning, nucleotide sequence, and expression in Escherichia coli of DNA polymerase gene (polA) fromThermus thermophilus. J. Ferment. Bioeng. 76:1993;265-269.
    • (1993) J. Ferment. Bioeng. , vol.76 , pp. 265-269
    • Asakura, K.1    Komatsubara, H.2    Soga, S.3    Yomo, T.4    Oka, M.5    Emi, S.6    Urabe, I.7
  • 4
    • 0026019625 scopus 로고
    • Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: A two metal ion mechanism
    • Beese L. S., Steitz T. A. Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. EMBO J. 10:1991;25-33.
    • (1991) EMBO J. , vol.10 , pp. 25-33
    • Beese, L.S.1    Steitz, T.A.2
  • 5
    • 0027231782 scopus 로고
    • Structure of DNA polymerase I Klenow fragment bound to duplex DNA
    • Beese L. S., Derbyshire V., Steitz T. A. Structure of DNA polymerase I Klenow fragment bound to duplex DNA. Science. 260:1993;352-355.
    • (1993) Science , vol.260 , pp. 352-355
    • Beese, L.S.1    Derbyshire, V.2    Steitz, T.A.3
  • 7
    • 0017184389 scopus 로고
    • A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding
    • Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:1976;248-254.
    • (1976) Anal. Biochem. , vol.72 , pp. 248-254
    • Bradford, M.M.1
  • 9
    • 0030002197 scopus 로고    scopus 로고
    • A helical arch allowing single-stranded DNA to thread through T5 5′ exonuclease
    • Ceska T. A., Sayers J. R., Stier G., Sück D. A helical arch allowing single-stranded DNA to thread through T5 5′ exonuclease. Nature. 382:1996;90-93.
    • (1996) Nature , vol.382 , pp. 90-93
    • Ceska, T.A.1    Sayers, J.R.2    Stier, G.3    Sück, D.4
  • 14
    • 0027305444 scopus 로고
    • Conserved sites in the 5′-3′ exonuclease domain of Escherichia coli DNA polymerase
    • Gutman P. D., Minton K. W. Conserved sites in the 5′-3′ exonuclease domain of Escherichia coli DNA polymerase. Nucl. Acids Res. 21:1993;4406-4407.
    • (1993) Nucl. Acids Res. , vol.21 , pp. 4406-4407
    • Gutman, P.D.1    Minton, K.W.2
  • 15
    • 0028281443 scopus 로고
    • The characterization of a mammalian DNA structure-specific endonuclease
    • Harrington J. J., Lieber M. R. The characterization of a mammalian DNA structure-specific endonuclease. EMBO J. 13:1994a;1235-1246.
    • (1994) EMBO J. , vol.13 , pp. 1235-1246
    • Harrington, J.J.1    Lieber, M.R.2
  • 16
    • 0028335180 scopus 로고
    • Functional domains within FEN-1 and RAD2 define a family of structure-specific endonucleases: Implications for nucleotide excision repair
    • Harrington J. J., Lieber M. R. Functional domains within FEN-1 and RAD2 define a family of structure-specific endonucleases: implications for nucleotide excision repair. Genes Dev. 8:1994b;1344-1355.
    • (1994) Genes Dev. , vol.8 , pp. 1344-1355
    • Harrington, J.J.1    Lieber, M.R.2
  • 18
    • 0016252159 scopus 로고
    • The N-terminal amino-acid sequences of DNA polymerase I from Escherichia coli and of the large and the small fragments obtained by a limited proteolysis
    • Jacobsen H., Klenow H., Overgaard-Hansen K. The N-terminal amino-acid sequences of DNA polymerase I from Escherichia coli and of the large and the small fragments obtained by a limited proteolysis. Eur. J. Biochem. 45:1974;623-627.
    • (1974) Eur. J. Biochem. , vol.45 , pp. 623-627
    • Jacobsen, H.1    Klenow, H.2    Overgaard-Hansen, K.3
  • 19
    • 0014670099 scopus 로고
    • Enzymatic synthesis of deoxyribonucleic acid. XXVI. Physical and chemical studies of a homogeneous deoxyribonucleic acid polymerase
    • Jovin T. M., Englund P. T., Bertsch L. L. Enzymatic synthesis of deoxyribonucleic acid. XXVI. Physical and chemical studies of a homogeneous deoxyribonucleic acid polymerase. J. Biol. Chem. 244:1969;2996-3008.
    • (1969) J. Biol. Chem. , vol.244 , pp. 2996-3008
    • Jovin, T.M.1    Englund, P.T.2    Bertsch, L.L.3
  • 20
    • 0024395470 scopus 로고
    • How DNA travels between the separate polymerase and 3′-5′-exonuclease sites of DNA polymerase I (Klenow fragment)
    • Joyce C. M. How DNA travels between the separate polymerase and 3′-5′-exonuclease sites of DNA polymerase I (Klenow fragment). J. Biol. Chem. 264:1989;10858-10866.
    • (1989) J. Biol. Chem. , vol.264 , pp. 10858-10866
    • Joyce, C.M.1
  • 21
    • 0028827318 scopus 로고
    • Purification of Escherichia coli DNA polymerase I and Klenow fragment
    • Joyce C. M., Derbyshire V. Purification of Escherichia coli DNA polymerase I and Klenow fragment. Methods Enzymol. 262:1995;1-13.
    • (1995) Methods Enzymol. , vol.262 , pp. 1-13
    • Joyce, C.M.1    Derbyshire, V.2
  • 22
    • 0028206048 scopus 로고
    • Function and structure relationships in DNA polymerases
    • Joyce C. M., Steitz T. A. Function and structure relationships in DNA polymerases. Annu. Rev. Biochem. 63:1994;777-822.
    • (1994) Annu. Rev. Biochem. , vol.63 , pp. 777-822
    • Joyce, C.M.1    Steitz, T.A.2
  • 23
    • 0020490301 scopus 로고
    • Nucleotide sequence of the Escherichia colipolA gene and primary structure of DNA polymerase I
    • Joyce C. M., Kelley W. S., Grindley N. D. F. Nucleotide sequence of the Escherichia colipolA gene and primary structure of DNA polymerase I. J. Biol. Chem. 257:1982;1958-1964.
    • (1982) J. Biol. Chem. , vol.257 , pp. 1958-1964
    • Joyce, C.M.1    Kelley, W.S.2    Grindley, N.D.F.3
  • 24
    • 0022368297 scopus 로고
    • Genetic mapping and DNA sequence analysis of mutations in the polA gene of Escherichia coli
    • Joyce C. M., Fujii D. M., Laks H. S., Hughes C. M., Grindley N. D. F. Genetic mapping and DNA sequence analysis of mutations in the polA gene of Escherichia coli. J. Mol. Biol. 186:1985;283-293.
    • (1985) J. Mol. Biol. , vol.186 , pp. 283-293
    • Joyce, C.M.1    Fujii, D.M.2    Laks, H.S.3    Hughes, C.M.4    Grindley, N.D.F.5
  • 25
    • 0029655167 scopus 로고
    • Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. I. Sequence features in the 1 Mb region from map positions 64% to 92% of the genome
    • Kaneko T., Tanaka A., Sato S., Kotani H., Sazuka T., Miyajima N., Sugiura M., Tabata S. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. I. Sequence features in the 1 Mb region from map positions 64% to 92% of the genome. DNA Res. 2:1995;153-166.
    • (1995) DNA Res. , vol.2 , pp. 153-166
    • Kaneko, T.1    Tanaka, A.2    Sato, S.3    Kotani, H.4    Sazuka, T.5    Miyajima, N.6    Sugiura, M.7    Tabata, S.8
  • 26
    • 0020533576 scopus 로고
    • Genetic characterization of early amber mutations in the Escherichia colipolA gene and purification of the amber peptides
    • Kelley W. S., Joyce C. M. Genetic characterization of early amber mutations in the Escherichia colipolA gene and purification of the amber peptides. J. Mol. Biol. 164:1983;529-560.
    • (1983) J. Mol. Biol. , vol.164 , pp. 529-560
    • Kelley, W.S.1    Joyce, C.M.2
  • 27
    • 0017753421 scopus 로고
    • Isolation and characterization of a λpolA transducing phage
    • Kelley W. S., Chalmers K., Murray N. E. Isolation and characterization of a λpolA transducing phage. Proc. Natl Acad. Sci. USA. 74:1977;5632-5636.
    • (1977) Proc. Natl Acad. Sci. USA , vol.74 , pp. 5632-5636
    • Kelley, W.S.1    Chalmers, K.2    Murray, N.E.3
  • 28
    • 0000648854 scopus 로고
    • Excision of thymine dimers and other mismatched sequences by DNA polymerase of Escherichia coli
    • Kelly R. B., Atkinson M. R., Huberman J. A., Kornberg A. Excision of thymine dimers and other mismatched sequences by DNA polymerase of Escherichia coli. Nature. 224:1969;495-501.
    • (1969) Nature , vol.224 , pp. 495-501
    • Kelly, R.B.1    Atkinson, M.R.2    Huberman, J.A.3    Kornberg, A.4
  • 29
    • 0028018381 scopus 로고
    • Acidic carboxyl-terminal domain of gene 2.5 protein of bacteriophage T7 is essential for protein-protein interactions
    • Kim Y. T., Richardson C. C. Acidic carboxyl-terminal domain of gene 2.5 protein of bacteriophage T7 is essential for protein-protein interactions. J. Biol. Chem. 269:1994;5270-5278.
    • (1994) J. Biol. Chem. , vol.269 , pp. 5270-5278
    • Kim, Y.T.1    Richardson, C.C.2
  • 30
    • 0028983795 scopus 로고
    • Crystal structure of Thermus aquaticus DNA polymerase
    • Kim Y., Eom S. H., Wang J., Lee D.-S., Suh S. W., Steitz T. A. Crystal structure of Thermus aquaticus DNA polymerase. Nature. 376:1995;612-616.
    • (1995) Nature , vol.376 , pp. 612-616
    • Kim, Y.1    Eom, S.H.2    Wang, J.3    Lee, D.-S.4    Suh, S.W.5    Steitz, T.A.6
  • 31
    • 0014708426 scopus 로고
    • Selective elimination of the exonuclease activity of the deoxyribonucleic acid polymerase from Escherichia coli B by limited proteolysis
    • Klenow H., Henningsen I. Selective elimination of the exonuclease activity of the deoxyribonucleic acid polymerase from Escherichia coli B by limited proteolysis. Proc. Natl Acad. Sci. USA. 65:1970;168-175.
    • (1970) Proc. Natl Acad. Sci. USA , vol.65 , pp. 168-175
    • Klenow, H.1    Henningsen, I.2
  • 32
    • 0003363169 scopus 로고
    • DNA Replication
    • San Francisco, CA: Freeman
    • Kornberg A., Baker T. A. DNA Replication. 2nd edit. 1992;Freeman, San Francisco, CA.
    • (1992) 2Nd Edit.
    • Kornberg, A.1    Baker, T.A.2
  • 33
    • 0023613953 scopus 로고
    • Rapid and efficient site-specific mutagenesis without phenotypic selection
    • Kunkel T. A., Roberts J. D., Zakour R. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 154:1987;367-382.
    • (1987) Methods Enzymol. , vol.154 , pp. 367-382
    • Kunkel, T.A.1    Roberts, J.D.2    Zakour, R.A.3
  • 34
    • 0020426678 scopus 로고
    • Transient generation of displaced single-stranded DNA during nick translation
    • Lundquist R. C., Olivera B. M. Transient generation of displaced single-stranded DNA during nick translation. Cell. 31:1982;53-60.
    • (1982) Cell , vol.31 , pp. 53-60
    • Lundquist, R.C.1    Olivera, B.M.2
  • 35
    • 0027215222 scopus 로고
    • Structure-specific endonucleolytic cleavage of nucleic acids by eubacterial DNA polymerases
    • Lyamichev V., Brow M. A. D., Dahlberg J. E. Structure-specific endonucleolytic cleavage of nucleic acids by eubacterial DNA polymerases. Science. 260:1993;778-783.
    • (1993) Science , vol.260 , pp. 778-783
    • Lyamichev, V.1    Brow, M.A.D.2    Dahlberg, J.E.3
  • 37
    • 0021264737 scopus 로고
    • Escherichia coli DNA polymerase I. Construction of a polA plasmid for amplification and an improved purification scheme
    • Minkley E., Jr, Leney A. T., Bodner J. B., Panicker M. M., Brown W. E. Escherichia coli DNA polymerase I. Construction of a polA plasmid for amplification and an improved purification scheme. J. Biol. Chem. 259:1984;10386-10392.
    • (1984) J. Biol. Chem. , vol.259 , pp. 10386-10392
    • Minkley, E.1    Jr2    Leney, A.T.3    Bodner, J.B.4    Panicker, M.M.5    Brown, W.E.6
  • 38
    • 0030444635 scopus 로고    scopus 로고
    • Deoxy- and dideoxynucleotide discrimination and identification of critical 5′ nuclease domain residues of the DNA polymerase I from Mycobacterium tuberculosis
    • Mizrahi V., Huberts P. Deoxy- and dideoxynucleotide discrimination and identification of critical 5′ nuclease domain residues of the DNA polymerase I from Mycobacterium tuberculosis. Nucl. Acids Res. 24:1996;4845-4852.
    • (1996) Nucl. Acids Res. , vol.24 , pp. 4845-4852
    • Mizrahi, V.1    Huberts, P.2
  • 39
    • 0027750969 scopus 로고
    • A PCR method for the sequence analysis of the gyrA, polA and rnhA gene segments from mycobacteria
    • Mizrahi V., Huberts P., Dawes S. S., Dudding L. R. A PCR method for the sequence analysis of the gyrA, polA and rnhA gene segments from mycobacteria. Gene. 136:1993;287-290.
    • (1993) Gene , vol.136 , pp. 287-290
    • Mizrahi, V.1    Huberts, P.2    Dawes, S.S.3    Dudding, L.R.4
  • 40
    • 2142860722 scopus 로고    scopus 로고
    • Structure of bacteriophage T4 RNase H, a 5′ to 3′ RNA-DNA and DNA-DNA exonuclease with sequence similarity to the RAD2 family of eukaryotic proteins
    • Mueser T. C., Nossal N. G., Hyde C. C. Structure of bacteriophage T4 RNase H, a 5′ to 3′ RNA-DNA and DNA-DNA exonuclease with sequence similarity to the RAD2 family of eukaryotic proteins. Cell. 85:1996;1101-1112.
    • (1996) Cell , vol.85 , pp. 1101-1112
    • Mueser, T.C.1    Nossal, N.G.2    Hyde, C.C.3
  • 41
    • 0029616338 scopus 로고
    • Calf 5′ to 3′ exo/endonuclease must slide from a 5′ end of the substrate to perform structure-specific cleavage
    • Murante R. S., Rust L., Bambara R. A. Calf 5′ to 3′ exo/endonuclease must slide from a 5′ end of the substrate to perform structure-specific cleavage. J. Biol. Chem. 270:1994;30377-30383.
    • (1994) J. Biol. Chem. , vol.270 , pp. 30377-30383
    • Murante, R.S.1    Rust, L.2    Bambara, R.A.3
  • 42
    • 0021984004 scopus 로고
    • Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP
    • Ollis D. L., Brick P., 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.
    • (1985) Nature , vol.313 , pp. 762-766
    • Ollis, D.L.1    Brick, P.2    Hamlin, R.3    Xuong, N.G.4    Steitz, T.A.5
  • 43
    • 0028049441 scopus 로고
    • Structures of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP
    • 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;1891-1903.
    • (1994) Science , vol.264 , pp. 1891-1903
    • Pelletier, H.1    Sawaya, M.R.2    Kumar, A.3    Wilson, S.H.4    Kraut, J.5
  • 44
    • 0025121103 scopus 로고
    • Identification of residues critical for the polymerase activity of the Klenow fragment of DNA polymerase I fromEscherichia coli
    • 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.
    • (1990) J. Biol. Chem. , vol.265 , pp. 14579-14591
    • Polesky, A.H.1    Steitz, T.A.2    Grindley, N.D.F.3    Joyce, C.M.4
  • 45
    • 0028034508 scopus 로고
    • Structural and functional homology between mammalian DNase IV and the 5′-nuclease domain of Escherichia coli DNA polymerase I
    • Robins P., Pappin D. J., Wood R. D., Lindahl T. Structural and functional homology between mammalian DNase IV and the 5′-nuclease domain of Escherichia coli DNA polymerase I. J. Biol. Chem. 269:1994;28535-28538.
    • (1994) J. Biol. Chem. , vol.269 , pp. 28535-28538
    • Robins, P.1    Pappin, D.J.2    Wood, R.D.3    Lindahl, T.4
  • 46
    • 0020645050 scopus 로고
    • The use of pKC30 and its derivatives for controlled expression of genes
    • Rosenberg M., Ho Y.-S., Shatzman A. The use of pKC30 and its derivatives for controlled expression of genes. Methods Enzymol. 101:1983;123-138.
    • (1983) Methods Enzymol. , vol.101 , pp. 123-138
    • Rosenberg, M.1    Ho, Y.-S.2    Shatzman, A.3
  • 48
    • 0028130380 scopus 로고
    • Computer aided identification of a potential 5′-3′ exonuclease gene encoded by Escherichia coli
    • Sayers J. R. Computer aided identification of a potential 5′-3′ exonuclease gene encoded by Escherichia coli. J. Theoret. Biol. 170:1994;415-421.
    • (1994) J. Theoret. Biol. , vol.170 , pp. 415-421
    • Sayers, J.R.1
  • 49
    • 0025114469 scopus 로고
    • Properties of overexpressed phage T5 D15 exonuclease. Similarities with Escherichia coli DNA polymerase I 5′-3′ exonuclease
    • Sayers J. R., Eckstein F. Properties of overexpressed phage T5 D15 exonuclease. Similarities with Escherichia coli DNA polymerase I 5′-3′ exonuclease. J. Biol. Chem. 265:1990;18311-18317.
    • (1990) J. Biol. Chem. , vol.265 , pp. 18311-18317
    • Sayers, J.R.1    Eckstein, F.2
  • 50
    • 0016018693 scopus 로고
    • DNA polymerase I from Escherichia coli
    • Setlow P. DNA polymerase I from Escherichia coli. Methods Enzymol. 29:1974;3-12.
    • (1974) Methods Enzymol. , vol.29 , pp. 3-12
    • Setlow, P.1
  • 51
    • 0015499986 scopus 로고
    • Deoxyribonucleic acid polymerase: Two distinct enzymes in one polypeptide. II. A proteolytic fragment containing the 5′→3′ exonuclease function. Restoration of intact enzyme functions from the two proteolytic fragments
    • Setlow P., Kornberg A. Deoxyribonucleic acid polymerase: two distinct enzymes in one polypeptide. II. A proteolytic fragment containing the 5′→3′ exonuclease function. Restoration of intact enzyme functions from the two proteolytic fragments. J. Biol. Chem. 247:1972;232-240.
    • (1972) J. Biol. Chem. , vol.247 , pp. 232-240
    • Setlow, P.1    Kornberg, A.2
  • 52
    • 0015499898 scopus 로고
    • Deoxyribonucleic acid polymerase: Two distinct enzymes in one polypeptide. I. A proteolytic fragment containing the polymerase and 3′→5′ exonuclease functions
    • Setlow P., Brutlag D., Kornberg A. Deoxyribonucleic acid polymerase: two distinct enzymes in one polypeptide. I. A proteolytic fragment containing the polymerase and 3′→5′ exonuclease functions. J. Biol. Chem. 247:1972;224-231.
    • (1972) J. Biol. Chem. , vol.247 , pp. 224-231
    • Setlow, P.1    Brutlag, D.2    Kornberg, A.3
  • 53
    • 0030009265 scopus 로고    scopus 로고
    • Essential amino acids for substrate binding and catalysis of human flap endonuclease 1
    • Shen B., Nolan J. P., Sklar L. A., Park M. S. Essential amino acids for substrate binding and catalysis of human flap endonuclease 1. J. Biol. Chem. 271:1996;9173-9176.
    • (1996) J. Biol. Chem. , vol.271 , pp. 9173-9176
    • Shen, B.1    Nolan, J.P.2    Sklar, L.A.3    Park, M.S.4
  • 54
    • 0027184481 scopus 로고
    • A general two-metal-ion mechanism for catalytic RNA
    • Steitz T. A., Steitz J. A. A general two-metal-ion mechanism for catalytic RNA. Proc. Natl Acad. Sci. USA. 90:1993;6498-6502.
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 6498-6502
    • Steitz, T.A.1    Steitz, J.A.2
  • 55
    • 0028864184 scopus 로고
    • DNA strand transfer catalyzed by the 5′-3′ exonuclease domain of Escherichia coli DNA polymerase I
    • Zhang W., Evans D. H. DNA strand transfer catalyzed by the 5′-3′ exonuclease domain of Escherichia coli DNA polymerase I. Nucl. Acids Res. 23:1995;4620-4627.
    • (1995) Nucl. Acids Res. , vol.23 , pp. 4620-4627
    • Zhang, W.1    Evans, D.H.2


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