DNA polymerase I

Summary

Gene Symbol: DNA polymerase I
Description: 5' to 3' DNA polymerase and 3' to 5'/5' to 3' exonuclease
Alias: ECK3855, JW3835, resA
Species: Escherichia coli str. K-12 substr. MG1655

Top Publications

  1. pmc The 3'-5' exonuclease of DNA polymerase I of Escherichia coli: contribution of each amino acid at the active site to the reaction
    V Derbyshire
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510
    EMBO J 10:17-24. 1991
  2. ncbi Metal binding to DNA polymerase I, its large fragment, and two 3',5'-exonuclease mutants of the large fragment
    G P Mullen
    Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
    J Biol Chem 265:14327-34. 1990
  3. ncbi Studies on the mechanism of Escherichia coli DNA polymerase I large fragment. Effect of template sequence and substrate variation on termination of synthesis
    J Abbotts
    Laboratory of Biochemistry, National Cancer Institute, Bethesda, Maryland 20892
    J Biol Chem 263:15094-103. 1988
  4. ncbi Biochemical and mutational studies of the 5'-3' exonuclease of DNA polymerase I of Escherichia coli
    Y Xu
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    J Mol Biol 268:284-302. 1997
  5. ncbi Interaction of DNA polymerase I (Klenow fragment) with the single-stranded template beyond the site of synthesis
    Robert M Turner
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
    Biochemistry 42:2373-85. 2003
  6. pmc Overproduction of DnaE protein (alpha subunit of DNA polymerase III) restores viability in a conditionally inviable Escherichia coli strain deficient in DNA polymerase I
    E M Witkin
    Waksman Institute, Rutgers State University of New Jersey, Piscataway, New Jersey 08854
    J Bacteriol 174:4166-8. 1992
  7. pmc Interaction of the beta sliding clamp with MutS, ligase, and DNA polymerase I
    F J Lopez de Saro
    Howard Hughes Medical Institute and The Rockefeller University, 1230 York Avenue, Box 228, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 98:8376-80. 2001
  8. ncbi Spontaneous and cisplatin-induced recombination in Escherichia coli
    Anetta Nowosielska
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, LRB823 Worcester, MA 01655, USA
    DNA Repair (Amst) 3:719-28. 2004
  9. pmc The Escherichia coli dnaN159 mutant displays altered DNA polymerase usage and chronic SOS induction
    Mark D Sutton
    Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, 3435 Main St, 140 Farber Hall, Buffalo, NY 14214
    J Bacteriol 186:6738-48. 2004
  10. pmc Role of accessory DNA polymerases in DNA replication in Escherichia coli: analysis of the dnaX36 mutator mutant
    Damian Gawel
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
    J Bacteriol 190:1730-42. 2008

Research Grants

  1. DNA REPAIR AND ITS RELATIONSHIP TO CARCINOGENESIS
    Errol Friedberg; Fiscal Year: 2001
  2. DNA REPAIR AND CANCER PRONE HEREDITARY HUMAN DISEASE
    Errol Friedberg; Fiscal Year: 2002
  3. Effects of Formamidopyrimidine Lesions on DNA
    Marc Greenberg; Fiscal Year: 2006
  4. Combined Substrate Polymerase Inhibitors
    MICHAEL DOUGHTY; Fiscal Year: 2007
  5. Non-natural Nucleoside Inhibitors of DNA Polymerases
    Anthony Berdis; Fiscal Year: 2009
  6. Regulation of DNA Replication and Repair
    Mark Sutton; Fiscal Year: 2008
  7. MOUSE MODELS OF DNA REPAIR - DEFECTIVE HUMAN DISEASES
    Errol Friedberg; Fiscal Year: 2011

Scientific Experts

  • Manel Camps
  • T E Spratt
  • Stephan Uphoff
  • Mark Sutton
  • Alvin Markovitz
  • Catherine M Joyce
  • Anthony R Poteete
  • Michael B Doughty
  • Errol Friedberg
  • Shinya Shibutani
  • Marc Greenberg
  • Lauri Saks
  • W W Steiner
  • Kamalendra Singh
  • F J Lopez de Saro
  • Anthony Berdis
  • Masaru Imai
  • Yu ichiro Tago
  • Anetta Nowosielska
  • M Astatke
  • Makoto Ihara
  • Kazuo Yamamoto
  • Yuki Nagata
  • Daniel R Garalde
  • N D Grindley
  • Kate R Lieberman
  • Mark Akeson
  • Lee M Allen
  • Abu Amar M Al Mamun
  • Brett Gyarfas
  • Gil Tae Hwang
  • Janina Cramer
  • Laura Zietlow
  • Y Xu
  • Damian Gawel
  • Helen Ting
  • Asim Sheriff
  • Ern Loh
  • Sanae Fukushima
  • Michael F Bailey
  • Samer Lone
  • Robert W Maul
  • Olga Potapova
  • Robert A Rieger
  • Tomoyuki Furukawa
  • Louis J Romano
  • Angie M Kretulskie
  • Masakado Kawata
  • Eric T Kool
  • Melodie D McCain
  • Joshua P Gill
  • M G Marinus
  • Kelly M Winterberg
  • Gudrun Stengel
  • Tae Woo Kim
  • Nigel D F Grindley
  • John M Essigmann
  • O K Kaboev
  • I R Lehman
  • Robert M Turner
  • Olga Kornyushyna
  • Molly Chiaramonte
  • Rajiv Gangurde
  • Christopher A Simon
  • Joseph M Dahl
  • Hongyun Wang
  • M Reddy
  • S Tuske
  • M Zafri Humayun
  • Seico Benner
  • Michael R G Hodskinson
  • Felix Olasagasti
  • Jon R Sayers
  • Daniel Garalde
  • Tadayoshi Bessho
  • C A Brautigam
  • Piotr Jonczyk
  • Floyd E Romesberg
  • Andreas Marx
  • Edward Motea
  • Elena A Kouzminova
  • Iwona J Fijalkowska
  • Y Agemizu
  • Roel M Schaaper
  • Gopinath Rangam
  • Tobias Restle
  • Irene Lee
  • Phuong T Pham
  • Andrei Kuzminov
  • Laurie H Sanders

Detail Information

Publications111 found, 100 shown here

  1. pmc The 3'-5' exonuclease of DNA polymerase I of Escherichia coli: contribution of each amino acid at the active site to the reaction
    V Derbyshire
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510
    EMBO J 10:17-24. 1991
    ..The pH-dependence of the 3'-5' exonuclease reaction is consistent with a mechanism in which nucleophilic attack on the terminal phosphodiester bond is initiated by a hydroxide ion coordinated to one of the enzyme-bound metal ions...
  2. ncbi Metal binding to DNA polymerase I, its large fragment, and two 3',5'-exonuclease mutants of the large fragment
    G P Mullen
    Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
    J Biol Chem 265:14327-34. 1990
    b>DNA polymerase I (Pol I) is an enzyme of DNA replication and repair containing three active sites, each requiring divalent metal ions such as Mg2+ or Mn2+ for activity...
  3. ncbi Studies on the mechanism of Escherichia coli DNA polymerase I large fragment. Effect of template sequence and substrate variation on termination of synthesis
    J Abbotts
    Laboratory of Biochemistry, National Cancer Institute, Bethesda, Maryland 20892
    J Biol Chem 263:15094-103. 1988
    Termination of Escherichia coli DNA polymerase I large fragment after processive synthesis on natural and other well-defined template.primer systems has been examined...
  4. ncbi Biochemical and mutational studies of the 5'-3' exonuclease of DNA polymerase I of Escherichia coli
    Y Xu
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    J Mol Biol 268:284-302. 1997
    In order to improve our understanding of the 5'-3' exonuclease reaction catalyzed by Escherichia coli DNA polymerase I, we have constructed expression plasmids and developed purification methods for whole DNA polymerase I and its 5'-3' ..
  5. ncbi Interaction of DNA polymerase I (Klenow fragment) with the single-stranded template beyond the site of synthesis
    Robert M Turner
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
    Biochemistry 42:2373-85. 2003
    ..Overall, the data are most consistent with the template strand following a path over the fingers subdomain, close to the side chain of R836 and a neighboring cluster of positively charged residues...
  6. pmc Overproduction of DnaE protein (alpha subunit of DNA polymerase III) restores viability in a conditionally inviable Escherichia coli strain deficient in DNA polymerase I
    E M Witkin
    Waksman Institute, Rutgers State University of New Jersey, Piscataway, New Jersey 08854
    J Bacteriol 174:4166-8. 1992
    A polA12 recA718 double mutant of Escherichia coli, in which DNA polymerase I is temperature sensitive, was unable to maintain normal DNA synthesis or to form colonies on rich media at 42 degrees C...
  7. pmc Interaction of the beta sliding clamp with MutS, ligase, and DNA polymerase I
    F J Lopez de Saro
    Howard Hughes Medical Institute and The Rockefeller University, 1230 York Avenue, Box 228, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 98:8376-80. 2001
    ..Thus, beta interacts with MutS, DNA ligase, and DNA polymerase I. Given the diverse use of these proteins in repair and other DNA transactions, this expanded list of beta ..
  8. ncbi Spontaneous and cisplatin-induced recombination in Escherichia coli
    Anetta Nowosielska
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, LRB823 Worcester, MA 01655, USA
    DNA Repair (Amst) 3:719-28. 2004
    ..The lack of recombination induction by trans-DDP suggests that the recombinogenic lesions for cisplatin are purine-purine intrastrand crosslinks...
  9. pmc The Escherichia coli dnaN159 mutant displays altered DNA polymerase usage and chronic SOS induction
    Mark D Sutton
    Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, 3435 Main St, 140 Farber Hall, Buffalo, NY 14214
    J Bacteriol 186:6738-48. 2004
    ..These findings are discussed in terms of a model to describe how the beta clamp might help to coordinate protein traffic at the replication fork...
  10. pmc Role of accessory DNA polymerases in DNA replication in Escherichia coli: analysis of the dnaX36 mutator mutant
    Damian Gawel
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
    J Bacteriol 190:1730-42. 2008
    ..Overall, the results provide insight into the interplay of the various DNA polymerases, and of tau subunit, in securing a high fidelity of replication...
  11. ncbi Facile polymerization of dNTPs bearing unnatural base analogues by DNA polymerase alpha and Klenow fragment (DNA polymerase I)
    Molly Chiaramonte
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
    Biochemistry 42:10472-81. 2003
    ..We have found that human DNA polymerase alpha (pol alpha) and the Klenow fragment of Escherichia coli DNA polymerase I (KF) incorporate all four nucleotide analogues opposite all four canonical bases up to 4000-fold more ..
  12. ncbi Escherichia coli mutator (Delta)polA is defective in base mismatch correction: the nature of in vivo DNA replication errors
    Yu ichiro Tago
    Graduate School of Life Sciences, Tohoku University, Sendai 980 8577, Japan
    J Mol Biol 351:299-308. 2005
    ..coli strains containing deletions in genes encoding three SOS polymerases, and defective in MutS and DNA polymerase I (PolI) mismatch repair, and estimated the rate and specificity of spontaneous endogenous tonB(+)-->tonB- ..
  13. pmc Reassessment of the in vivo functions of DNA polymerase I and RNase H in bacterial cell growth
    Sanae Fukushima
    Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka 1 1 1 Setagaya ku, Tokyo 156 8502, Japan
    J Bacteriol 189:8575-83. 2007
    A major factor in removing RNA primers during the processing of Okazaki fragments is DNA polymerase I (Pol I). Pol I is thought to remove the RNA primers and to fill the resulting gaps simultaneously...
  14. pmc DNA polymerase I modulates inducible stable DNA replication in Escherichia coli
    T Ruscitti
    Division of Biochemistry and Molecular Biology, University of California, Berkeley 94720
    J Bacteriol 174:6311-3. 1992
    ..We report here that mutants deleted for the polA gene express induced stable DNA replication at approximately 25-fold the rate of wild-type cells, whereas constitutive stable DNA replication is not enhanced...
  15. ncbi Reactions at the polymerase active site that contribute to the fidelity of Escherichia coli DNA polymerase I (Klenow fragment)
    C M Joyce
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510
    J Biol Chem 267:24485-500. 1992
    ..and the rates of extension from the resulting mismatched base pairs, catalyzed by the Klenow fragment of DNA polymerase I. Using a combination of semi-quantitative and qualitative approaches, we have studied each of the 12 possible ..
  16. ncbi The affinity of the Klenow fragment of E. coli DNA-polymerase 1 to primers containing bases noncomplementary to the template and hairpin-like elements
    M V Ljach
    Novosibirsk Institute of Bioorganic Chemistry, Siberian Division of the USSR Academy of Sciences
    FEBS Lett 300:18-20. 1992
    ..For example, the Km value (1.1 nM) for d(pT)4 (pCpG)5 (pT)4 is about 14,000 and 200 times lower than those for d(pT)4 and d(pT)8, respectively. Possible reasons for such an abnormally high affinity of the above primers are discussed...
  17. pmc Segregation of relaxed replicated dimers when DNA ligase and DNA polymerase I are limited during oriC-specific DNA replication
    B R Munson
    Experimental Biology Department, Roswell Park Memorial Institute, Buffalo, New York 14263
    J Bacteriol 171:3803-9. 1989
    ..The results also show that decatenation of dimers occurs readily on nicked dimer and represents an efficient pathway for processing replication intermediates in vitro...
  18. pmc Cocrystal structure of an editing complex of Klenow fragment with DNA
    P S Freemont
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
    Proc Natl Acad Sci U S A 85:8924-8. 1988
    ..crystal structures of editing complexes of both duplex and single-stranded DNA bound to Escherichia coli DNA polymerase I large fragment (Klenow fragment) show four nucleotides of single-stranded DNA bound to the 3'-5' exonuclease ..
  19. ncbi Genetic characterization of early amber mutations in the Escherichia coli polA gene and purification of the amber peptides
    W S Kelley
    J Mol Biol 164:529-60. 1983
    ..The peptides are immunologically related and react weakly but specifically with antibody to whole DNA polymerase I. In their purified form the peptides are less heat-labile than the whole enzyme or the Klenow fragment ..
  20. ncbi Deoxynucleoside triphosphate and pyrophosphate binding sites in the catalytically competent ternary complex for the polymerase reaction catalyzed by DNA polymerase I (Klenow fragment)
    M Astatke
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
    J Biol Chem 270:1945-54. 1995
    ..Mutations of Arg682, His734, and Tyr766 affect the binding of DNA, suggesting that these mutations, whose effect on dNTP binding is small, may influence dNTP binding indirectly via the positioning of the DNA template-primer...
  21. ncbi Sequential proton NMR resonance assignments, circular dichroism, and structural properties of a 50-residue substrate-binding peptide from DNA polymerase I
    G P Mullen
    Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
    Arch Biochem Biophys 301:174-83. 1993
    Peptide I, a 50-amino acid synthetic peptide based on residues 728 to 777 of DNA polymerase I, binds dNTP substrates and duplex DNA (G. Mullen, P. Shenbagamurthi, and A.S. Mildvan, J. Biol. Chem. 264, 19637-19647, 1988)...
  22. pmc DNA strand transfer catalyzed by the 5'-3' exonuclease domain of Escherichia coli DNA polymerase I
    W Zhang
    Department of Molecular Biology and Genetics, University of Guelph, Ontario, Canada
    Nucleic Acids Res 23:4620-7. 1995
    ..coli. The protein is DNA polymerase I. Strand transfer activity residues in the small fragment encoding the 5'-3' exonuclease and can be detected ..
  23. pmc Differential discrimination of DNA polymerase for variants of the non-standard nucleobase pair between xanthosine and 2,4-diaminopyrimidine, two components of an expanded genetic alphabet
    M J Lutz
    Department of Chemistry, Swiss Federal Institute of Technology, Zurich, Switzerland
    Nucleic Acids Res 24:1308-13. 1996
    Mammalian DNA polymerases alpha and epsilon, the Klenow fragment of Escherichia coli DNA polymerase I and HIV-1 reverse transcriptase (RT) were examined for their ability to incorporate components of an expanded genetic alphabet in ..
  24. ncbi A thumb subdomain mutant of the large fragment of Escherichia coli DNA polymerase I with reduced DNA binding affinity, processivity, and frameshift fidelity
    D T Minnick
    Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    J Biol Chem 271:24954-61. 1996
    ..The results are discussed in light of remarkably similar observations with T7 DNA polymerase in the presence or absence of thioredoxin, an accessory subunit that affects these same properties...
  25. ncbi DNA strand exchange proteins: a biochemical and physical comparison
    P R Bianco
    Section of Microbiology and of Molecular and Cellular Biology, USC School of Medicine, 1441 Eastlake Ave, Los Angeles, CA 90033, USA
    Front Biosci 3:D570-603. 1998
    ..coli, UvsX protein from Bacteriophage T4, and RAD51 protein from Saccharomyces cerevisiae...
  26. ncbi DNA sequence analysis of spontaneous tonB deletion mutations in a polA1 strain of Escherichia coli K12
    Y Agemizu
    Graduate School of Science, Tohoku University, Sendai, 980 8578, Japan
    Biochem Biophys Res Commun 261:584-9. 1999
    ..In contrast to previous reports, we did not frequently observe a 5'-GTGG-3' sequence in the vicinity of the deletions and frameshifts. The results presented here indicated an anti-deletion and anti-frameshift role for DNA polymerase I.
  27. ncbi Identification of hydrogen bonds between Escherichia coli DNA polymerase I (Klenow fragment) and the minor groove of DNA by amino acid substitution of the polymerase and atomic substitution of the DNA
    T E Spratt
    American Health Foundation, 1 Dana Road, Valhalla, New York 10595, USA
    Biochemistry 40:2647-52. 2001
    ..we have studied these interactions using a combination of site-specific mutagenesis of Escherichia coli DNA polymerase I (Klenow fragment) and atomic substitution of the DNA...
  28. pmc Probing the active site tightness of DNA polymerase in subangstrom increments
    Tae Woo Kim
    Department of Chemistry, Stanford University, Stanford, CA 94305 5080, USA
    Proc Natl Acad Sci U S A 102:15803-8. 2005
    ..In addition, the results suggest that even high-fidelity replicative enzymes have more steric room than necessary, possibly to allow for an evolutionarily advantageous mutation rate...
  29. ncbi Highly tolerated amino acid substitutions increase the fidelity of Escherichia coli DNA polymerase I
    Ern Loh
    Joseph Gottstein Memorial Cancer Research Laboratory, Department of Pathology, University of Washington, Seattle, Washington 98195, USA
    J Biol Chem 282:12201-9. 2007
    ..coli DNA polymerase I and have determined the effects of these substitutions on the fidelity of DNA synthesis...
  30. ncbi The role of specific amino acid residues in the active site of Escherichia coli DNA polymerase I on translesion DNA synthesis across from and past an N-2-aminofluorene adduct
    Samer Lone
    Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
    Biochemistry 46:2599-607. 2007
    ..on replication across from this type of bulky DNA adduct, three active-site mutants of Escherichia coli DNA polymerase I (Klenow fragment) were used to study DNA synthesis on DNA modified with the carcinogen N-2-aminofluorene (AF)...
  31. doi DNA polymerase I-mediated translesion synthesis in RecA-independent DNA interstrand cross-link repair in E. coli
    Laura Zietlow
    The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, Nebraska 68198 6805, USA
    Biochemistry 47:5460-4. 2008
    ..We demonstrated that the Klenow fragment (DNA polymerase I) performs translesion synthesis on this model substrate...
  32. pmc Synthetic lethality with the dut defect in Escherichia coli reveals layers of DNA damage of increasing complexity due to uracil incorporation
    Helen Ting
    Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    J Bacteriol 190:5841-54. 2008
    ..We conclude that genetic interactions with dut can be explained by redundancy, by defect-damage-repair cycles, or as compensation...
  33. doi Spontaneous mutagenesis is elevated in protease-defective cells
    Abu Amar M Al Mamun
    University of Medicine and Dentistry of New Jersey New Jersey Medical School, Department of Microbiology and Molecular Genetics, International Center for Public Health, Newark, NJ 07101, USA
    Mol Microbiol 71:629-39. 2009
    ..These findings suggest that in normal cells, Clp-mediated proteolysis plays an important role in preventing gratuitous mutagenesis...
  34. ncbi Characterization of lambdapolA transducing phages; effective expression of the E. coli polA gene
    N E Murray
    Mol Gen Genet 175:77-87. 1979
    ..coli or induction of lysogens. Lytic infection gave consistently better amplification of DNA polymerase I than that obtained by induction of a lysogen...
  35. ncbi Identification of residues critical for the polymerase activity of the Klenow fragment of DNA polymerase I from Escherichia coli
    A H Polesky
    Department of Molecular Biophysics and Biochemistry, Yale University Medical School, New Haven, Connecticut 06510
    J Biol Chem 265:14579-91. 1990
    ....
  36. ncbi How DNA travels between the separate polymerase and 3'-5'-exonuclease sites of DNA polymerase I (Klenow fragment)
    C M Joyce
    Department of Molecular Biophysics and Biochemistry, Yale University Medical School, New Haven, Connecticut 06510
    J Biol Chem 264:10858-66. 1989
    The polymerase and 3'-5'-exonuclease activities of the Klenow fragment of DNA polymerase I are located on separate structural domains of the protein, separated by about 30 A...
  37. ncbi Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity
    R D Kuchta
    Department of Chemistry, Pennsylvania State University, University Park 16802
    Biochemistry 27:6716-25. 1988
    ..kinetic scheme describing the polymerization of correct and incorrect dNTPs by the Klenow fragment (KF) of DNA polymerase I has been developed by using short DNA oligomers of defined sequence...
  38. ncbi Mechanisms of error discrimination by Escherichia coli DNA polymerase I
    W S El-Deiry
    Department of Medicine, University of Miami School of Medicine, Florida 33101
    Biochemistry 27:546-53. 1988
    The mechanism of base selection by DNA polymerase I of Escherichia coli has been investigated by kinetic analysis...
  39. ncbi Toxicity, mutagenesis and stress responses induced in Escherichia coli by hydrogen peroxide
    S Linn
    Department of Biochemistry, University of California, Berkeley 94720
    J Cell Sci Suppl 6:289-301. 1987
    ..Mode-two killing is accompanied by enhanced mutagenesis, but strains with DNA repair defects were not observed to be especially sensitive to this mode of killing...
  40. ncbi Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP
    D L Ollis
    Nature 313:762-6. 1985
    The 3.3-A resolution crystal structure of the large proteolytic fragment of Escherichia coli DNA polymerase I complexed with deoxythymidine monophosphate consists of two domains, the smaller of which binds zinc-deoxythymidine ..
  41. pmc Identification of two genes immediately downstream from the polA gene of Escherichia coli
    C M Joyce
    J Bacteriol 152:1211-9. 1982
    ..Sequence analysis of this region of the E. coli genome suggests that it contains little, if any, redundant DNA...
  42. ncbi Isolation and characterization of a mutant of Escherichia coli K12 synthesizing DNA polymerase I and endonuclease I constitutively
    S I Ahmad
    J Gen Microbiol 117:419-22. 1980
    ..The mutant strain apparently repairs its damaged DNA more efficiently than wild-type E. coli K12 strains and, to do so, constitutively produces 35 times more DNA polymerase I and 12 times more endonuclease I than the wild-type strain.
  43. pmc Mapping of the polA locus of Escherichia coli K12: genetic fine structure of the cistron
    W S Kelley
    Genetics 95:15-38. 1980
    ..All four of these mutations are known to alter the 5' leads to 3' exonuclease activity of DNA polymerase I and three of them result in the conditional lethal polA- phenotype...
  44. ncbi Escherichia coli DNA polymerase I. Sequence characterization and secondary structure prediction
    W E Brown
    J Biol Chem 257:1965-72. 1982
    The primary sequence of DNA polymerase I from Escherichia coli K12 as derived from the DNA sequence (Joyce, C. M., Kelley, W. S., and Grindley, N. D. F. (1982) J. Biol. Chem. 257, 1958-1964) has been verified...
  45. pmc Suppression of ColE1 high-copy-number mutants by mutations in the polA gene of Escherichia coli
    Y L Yang
    Department of Biology, Indiana University, Bloomington 47405
    J Bacteriol 175:428-37. 1993
    ..All of the mutations were genetically mapped to the chromosomal polA gene, which encodes DNA polymerase I. The suppressor mutational changes were identified by DNA sequencing and found to alter single nucleotides in ..
  46. ncbi How E. coli DNA polymerase I (Klenow fragment) distinguishes between deoxy- and dideoxynucleotides
    M Astatke
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, 06520, USA
    J Mol Biol 278:147-65. 1998
    ....
  47. ncbi Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli
    C A Brautigam
    Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520 8114, USA
    Biochemistry 38:696-704. 1999
    ..in conjunction with various metal ions at the 3'-5' exonucleolytic active site of the Klenow fragment (KF) of DNA polymerase I from Escherichia coli...
  48. pmc Characterization of the uup locus and its role in transposon excisions and tandem repeat deletions in Escherichia coli
    M Reddy
    Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
    J Bacteriol 182:1978-86. 2000
    ..It is suggested that the differential response of mini-Tn10 and Tn10 to the second category of mutations is related to the presence, respectively, of perfect and of imperfect terminal inverted repeats in them...
  49. ncbi Presence of 18-A long hydrogen bond track in the active site of Escherichia coli DNA polymerase I (Klenow fragment). Its requirement in the stabilization of enzyme-template-primer complex
    Kamalendra Singh
    Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry, New Jersey Medical School, Newark, New Jersey 07103, USA
    J Biol Chem 278:11289-302. 2003
    ..The examination of the interactive environment of individual residues of this track further clarifies the mode of cooperation in various functional domains of pol I...
  50. pmc Targeted gene evolution in Escherichia coli using a highly error-prone DNA polymerase I
    Manel Camps
    The Joseph Gottstein Memorial Cancer Research Laboratory, Department of Pathology, University of Washington, Seattle, WA 98195 7705, USA
    Proc Natl Acad Sci U S A 100:9727-32. 2003
    ..To increase error rates of DNA polymerase I (Pol I) replication, we introduced point mutations in three structural domains that govern Pol I fidelity...
  51. ncbi In vitro replication and repair of DNA containing a C2'-oxidized abasic site
    Marc M Greenberg
    Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
    Biochemistry 43:15217-22. 2004
    ....
  52. ncbi Fidelity of mispair formation and mispair extension is dependent on the interaction between the minor groove of the primer terminus and Arg668 of DNA polymerase I of Escherichia coli
    Melodie D McCain
    American Health Foundation Cancer Center, Institute for Cancer Prevention, One Dana Road, Valhalla, New York 10595, USA
    Biochemistry 44:5647-59. 2005
    The hydrogen bonding interactions between the Klenow fragment of Escherichia coli DNA polymerase I with the proofreading exonuclease inactivated (KF(-)) and the minor groove of DNA were examined with modified oligodeoxynucleotides in ..
  53. ncbi Absence of strand bias for deletion mutagenesis during chromosomal leading and lagging strand replication in Escherichia coli
    Yuki Nagata
    Graduate School of Life Sciences, Tohoku University, Sendai, Japan
    Genes Genet Syst 80:1-8. 2005
    ..The results suggested that the two strands were replicated with equal or similar accuracy for deletion formation...
  54. ncbi Viscoelastic modeling of template-directed DNA synthesis
    Gudrun Stengel
    Anal Chem 77:3709-14. 2005
    ..to study the replication of surface attached oligonucleotide template strands using Escherichia coli DNA polymerase I (Klenow fragment, KF)...
  55. ncbi Contribution of polar residues of the J-helix in the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I (Klenow fragment): Q677 regulates the removal of terminal mismatch
    Kamalendra Singh
    Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, New Jersey 07103, USA
    Biochemistry 44:8101-10. 2005
    ....
  56. pmc DNA polymerase catalysis in the absence of Watson-Crick hydrogen bonds: analysis by single-turnover kinetics
    Olga Potapova
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Biochemistry 45:890-8. 2006
    ..consequences of a lack of hydrogen bonds in the polymerase reaction catalyzed by the Klenow fragment of DNA polymerase I from Escherichia coli...
  57. ncbi Structure of purine-purine mispairs during misincorporation and extension by Escherichia coli DNA polymerase I
    Angie M Kretulskie
    Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, 500 University Drive, Hershey, Pennsylvania 17033, USA
    Biochemistry 45:3740-6. 2006
    ..mispairs are formed and extended was examined with the high-fidelity Klenow fragment of Escherichia coli DNA polymerase I with the proofreading exonuclease activity inactivated...
  58. pmc Homologous recombination prevents methylation-induced toxicity in Escherichia coli
    Anetta Nowosielska
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
    Nucleic Acids Res 34:2258-68. 2006
    ..Cells deleted for the polA (DNA polymerase I) or priA (primosome) genes are as sensitive to MMS and MNNG as alkA tag bacteria...
  59. ncbi Participation of the fingers subdomain of Escherichia coli DNA polymerase I in the strand displacement synthesis of DNA
    Kamalendra Singh
    Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry New Jersey Medical School, Newark, New Jersey 07103, USA
    J Biol Chem 282:10594-604. 2007
    ..In prokaryotes, this process is completed by DNA polymerase I by means of strand displacement DNA synthesis and 5 '-nuclease activity...
  60. ncbi Role of the 5' --> 3' exonuclease and Klenow fragment of Escherichia coli DNA polymerase I in base mismatch repair
    Masaru Imai
    Graduate School of Life Sciences, Tohoku University, Sendai, 980 8577, Japan
    Mol Genet Genomics 278:211-20. 2007
    ..We argued that DNA polymerase I (PolI) corrects transition mismatches...
  61. doi Varied active-site constraints in the klenow fragment of E. coli DNA polymerase I and the lesion-bypass Dbh DNA polymerase
    Janina Cramer
    Max Planck Institut fur molekulare Physiologie, Abteilung Physikalische Biochemie, Otto Hahn Strasse 11, 44227 Dortmund, Germany
    Chembiochem 9:1243-50. 2008
    We report on comparative pre-steady-state kinetic analyses of exonuclease-deficient Escherichia coli DNA polymerase I (Klenow fragment, KF-) and the archaeal Y-family DinB homologue (Dbh) of Sulfolobus solfataricus...
  62. doi Fingers-closing and other rapid conformational changes in DNA polymerase I (Klenow fragment) and their role in nucleotide selectivity
    Catherine M Joyce
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Biochemistry 47:6103-16. 2008
    ..a FRET-based assay for the fingers-closing conformational transition that occurs when a binary complex of DNA polymerase I (Klenow fragment) with a primer-template binds a complementary dNTP and have used this and other fluorescence ..
  63. pmc Mechanism and dynamics of translesion DNA synthesis catalyzed by the Escherichia coli Klenow fragment
    Asim Sheriff
    Departments of Pharmacology and Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
    Biochemistry 47:8527-37. 2008
    ..These biophysical differences argue against a unified mechanism of translesion DNA synthesis and suggest that polymerases employ different catalytic strategies during the misreplication of damaged DNA...
  64. pmc Unnatural substrate repertoire of A, B, and X family DNA polymerases
    Gil Tae Hwang
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    J Am Chem Soc 130:14872-82. 2008
    ..The unnatural pairs were developed based on intensive studies using the Klenow fragment of DNA polymerase I from E. coli (Kf) and found to be recognized to varying degrees...
  65. pmc Expansion of a chromosomal repeat in Escherichia coli: roles of replication, repair, and recombination functions
    Anthony R Poteete
    Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, MA, USA
    BMC Mol Biol 10:14. 2009
    ..To explore the mechanism of expansion, a 7 kbp duplication in the chromosome containing a leaky mutant version of the lac operon was constructed, and its expansion into an amplified array was studied...
  66. doi Mapping the position of DNA polymerase-bound DNA templates in a nanopore at 5 A resolution
    Brett Gyarfas
    Department of Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA
    ACS Nano 3:1457-66. 2009
    ..bearing inserts of abasic (1',2'-dideoxy) residues, bound to the Klenow fragment of Escherichia coli DNA polymerase I (KF) or to bacteriophage T7 DNA polymerase...
  67. pmc Distinct complexes of DNA polymerase I (Klenow fragment) for base and sugar discrimination during nucleotide substrate selection
    Daniel R Garalde
    Department of Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064, USA
    J Biol Chem 286:14480-92. 2011
    ..The Klenow fragment of Escherichia coli DNA polymerase I (KF) achieves this through a series of conformational transitions that precede the chemical step of ..
  68. ncbi Post-incision steps of nucleotide excision repair in Escherichia coli. Disassembly of the UvrBC-DNA complex by helicase II and DNA polymerase I
    D K Orren
    Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill 27599
    J Biol Chem 267:780-8. 1992
    ..helicase II to such reaction mixtures turns over UvrC; UvrB turnover requires the addition of helicase II, DNA polymerase I, and deoxynucleoside triphosphates...
  69. ncbi Kinetic mechanism of DNA polymerase I (Klenow fragment): identification of a second conformational change and evaluation of the internal equilibrium constant
    M E Dahlberg
    Department of Chemistry, Pennsylvania State University, University Park 16802
    Biochemistry 30:4835-43. 1991
    ..minimal kinetic scheme for DNA polymerization catalyzed by the Klenow fragment (KF) of Escherichia coli DNA polymerase I, a nonchemical step that interconverted the KF'.DNAn+1.PPi and KF...
  70. pmc DNA polymerase I and a protein complex bind specifically to E. coli palindromic unit highly repetitive DNA: implications for bacterial chromosome organization
    E Gilson
    Unite de Programmation Moleculaire et Toxicologie Genetique, CNRS UA271 INSERM U163, Institut Pasteur, Paris, France
    Nucleic Acids Res 18:3941-52. 1990
    ..We show that one of these activities is due to the DNA polymerase I (Pol I). This constitutes the first indication for a specific interaction between Pol I and a duplex DNA...
  71. pmc Role of DNA polymerase I in postreplication repair: a reexamination with Escherichia coli delta polA
    R C Sharma
    Department of Therapeutic Radiology, Stanford University School of Medicine, California 94305
    J Bacteriol 169:4559-64. 1987
    Using strains of Escherichia coli K-12 that are deleted for the polA gene, we have reexamined the role of DNA polymerase I (encoded by polA) in postreplication repair after UV irradiation...
  72. ncbi Structure of DNA polymerase I Klenow fragment bound to duplex DNA
    L S Beese
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
    Science 260:352-5. 1993
    Klenow fragment of Escherichia coli DNA polymerase I, which was cocrystallized with duplex DNA, positioned 11 base pairs of DNA in a groove that lies at right angles to the cleft that contains the polymerase active site and is adjacent to ..
  73. ncbi The J-helix of Escherichia coli DNA polymerase I (Klenow fragment) regulates polymerase and 3'- 5'-exonuclease functions
    S Tuske
    Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry New Jersey Medical School and Graduate School of Biomedical Sciences, Newark, New Jersey 07103, USA
    J Biol Chem 275:23759-68. 2000
    To assess the functional importance of the J-helix region of Escherichia coli DNA polymerase I, we performed site-directed mutagenesis of the following five residues: Asn-675, Gln-677, Asn-678, Ile-679, and Pro-680...
  74. ncbi Contacts between the 5' nuclease of DNA polymerase I and its DNA substrate
    Y Xu
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    J Biol Chem 276:30167-77. 2001
    The 5' nuclease of DNA polymerase I (Pol I) of Escherichia coli is a member of an important class of prokaryotic and eukaryotic nucleases, involved in DNA replication and repair, with specificity for the junction between single-stranded ..
  75. ncbi Participation of active-site carboxylates of Escherichia coli DNA polymerase I (Klenow fragment) in the formation of a prepolymerase ternary complex
    Rajiv Gangurde
    Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, New Jersey 07103, USA
    Biochemistry 41:14552-9. 2002
    ..of four active-site carboxylates in the formation of a prepolymerase ternary complex of Escherichia coli DNA polymerase I (Klenow fragment), containing the template-primer and dNTP...
  76. ncbi Discovery of DNA polymerase
    I R Lehman
    Department of Biochemistry, Beckman Center, Stanford University, Stanford, California 94305, USA
    J Biol Chem 278:34733-8. 2003
  77. ncbi Effect of the oxidized guanosine lesions spiroiminodihydantoin and guanidinohydantoin on proofreading by Escherichia coli DNA polymerase I (Klenow fragment) in different sequence contexts
    Olga Kornyushyna
    Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112 0850, USA
    Biochemistry 42:13008-18. 2003
    ..The absence of a sequence effect for the Gh- and Sp-containing duplexes can be attributed to the severe destabilization of the lesion-containing duplexes that promotes interaction with the exonuclease domain of the Klenow fragment...
  78. ncbi Template-free primer-independent DNA synthesis by bacterial DNA polymerases I using the DnaB protein from Escherichia coli
    O K Kaboev
    St Petersburg Institute of Nuclear Physics, Russian Academy of Sciences, Gatchina, Leningradskaya oblast, 188300, Russia
    Dokl Biochem Biophys 398:265-7. 2004
  79. pmc Phenotypic screening of Escherichia coli K-12 Tn5 insertion libraries, using whole-genome oligonucleotide microarrays
    Kelly M Winterberg
    Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Dr, Madison, WI 53706 1544, USA
    Appl Environ Microbiol 71:451-9. 2005
    ..coli chromosome were identified. Tn5 insertions were detected in 15 genes for which no previous insertions have been reported. Other applications of this method are discussed...
  80. ncbi Mechanism for N-acetyl-2-aminofluorene-induced frameshift mutagenesis by Escherichia coli DNA polymerase I (Klenow fragment)
    Joshua P Gill
    Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
    Biochemistry 44:15387-95. 2005
    ..extension and gel shift binding assays were used to study the mechanism of bypass by the Escherichia coli DNA polymerase I (Klenow fragment) in the presence of these templates...

Research Grants7

  1. DNA REPAIR AND ITS RELATIONSHIP TO CARCINOGENESIS
    Errol Friedberg; Fiscal Year: 2001
    ..There is reason to believe that the proteins encoded by these genes operate in a different chromatin-modulating complex, and it is proposed to isolate and characterize this putative complex as well. ..
  2. DNA REPAIR AND CANCER PRONE HEREDITARY HUMAN DISEASE
    Errol Friedberg; Fiscal Year: 2002
    ....
  3. Effects of Formamidopyrimidine Lesions on DNA
    Marc Greenberg; Fiscal Year: 2006
    ..abstract_text> ..
  4. Combined Substrate Polymerase Inhibitors
    MICHAEL DOUGHTY; Fiscal Year: 2007
    ..These targets include DNA polymerase, reverse transcriptases, viral RNA dependent DNA polymerases, and inosine monophosphate dehydrogenase, a control enzyme in the cell synthesis of GMP. [unreadable] [unreadable] [unreadable]..
  5. Non-natural Nucleoside Inhibitors of DNA Polymerases
    Anthony Berdis; Fiscal Year: 2009
    ..This knowledge will facilitate the development of new drugs as the repertoire of targets becomes more differentiated. ..
  6. Regulation of DNA Replication and Repair
    Mark Sutton; Fiscal Year: 2008
    ..abstract_text> ..
  7. MOUSE MODELS OF DNA REPAIR - DEFECTIVE HUMAN DISEASES
    Errol Friedberg; Fiscal Year: 2011
    ..abstract_text> ..