Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: DNA polymerase I, 5' --> 3' polymerase, 5' --> 3' and 3' --> 5' exonuclease



Gene: polA Accession Numbers: EG10746 (EcoCyc), b3863, ECK3855

Synonyms: resA

Regulation Summary Diagram: ?

Summary:
DNA Polymerase I (Pol I) is a multifunctional enzyme that combines a DNA polymerase activity, a 5' to 3' exonuclease activity and a 3' to 5' proofreading exonuclease activity. It is required for several types of DNA repair and appears to be the primary enzyme responsible for stripping RNA primers from newly-synthesized DNA and replacing them with DNA.

Pol I is involved in several DNA repair pathways. It is required for excision repair, displacing the UvrABC nuclease and patching the gap it leaves behind [Sharon75, Sung03, Glickman75, Heyneker75, Orren92, Husain85, Matson81]. Pol I is also required in MutHLS-mediated very short patch repair [Dzidic89]. Pol I can excise and replace pyrimidine dimers directly [Dorson78]. It also cleaves the faulty nucleotide from abasic lesion sites following nicking by endonuclease III [Mosbaugh82]. Finally, Pol I is generally involved in postreplication repair of DNA gaps and double-strand breaks [Sharma87]. Participation of fluorescently labeled Pol I in the base excision repair (BER) of single nucleotide gaps generated in live E. coli cells has been visualised and quantified [Uphoff13]

Pol I primer removal and subsequent DNA gap filling has been shown directly in phiX174 phage DNA synthesis [Shlomai81]. A similar role for Pol I in E. coli is supported by the observations that Pol I can initiate synthesis at a DNA nick, that Okazaki fragment joining is only 10% of normal in mutants lacking polA and that normal replication depends on Pol I [Kelly70, Okazaki71, Olivera74].

Pol I consists of two domains. The larger domain, commonly known as the Klenow fragment when it is proteolytically separated, contains the polymerase and 3' to 5' exonuclease activities [Setlow72]. The smaller domain contains the 5' to 3' exonuclease activity [Setlow72a]. The Klenow domain itself has a large and a small subdomain, with its carboxy-terminal large domain containing the polymerase but not the 3' to 5' exonuclease function [Freemont86]. The Klenow domain also contains a "thumb" structure that is required for DNA binding, processivity and frameshifts and a J-helix region that regulates both the polymerase and 3' to 5' exonuclease functions [Minnick96, Tuske00, Singh05]. The Klenow portion undergoes conformational changes on binding template, then again on the subsequent binding of dNTPs [Dzantiev00].

Pol I and its subdomains have been crystallized several times. The initial crystallization was to 3.5 Å resolution [Steitz83]. Crystal structures have been determined for Klenow fragment bound to dNTP, pyrophosphate, ssDNA and dsDNA [Beese93, Freemont88]. Crystal structures of Pol I bound to dNMP and ssDNA have been determined to 2.6 Å and 3.1 Å resolution, respectively [Beese91].

Pol I binds DNA via hydrogen bonding between the minor groove an a hydrogen-bonding track on the protein [Spratt01, Singh03, Meyer04, Freemont88]. Pol I binds only one oligonucleotide at a time and only binds dsDNA at nicks or strand ends [Englund69]. It has a higher affinity for primers containing template mismatches or hairpin-like elements, and has a separate binding site for the 3'-hydroxyl end of substrates [Ljach92, Huberman70]. The binding of DNA by the Pol I 5' to 3' exonuclease function has been examined in detail [Xu01].

Polymerization by Pol I is processive, typically covering stretches of 20-40 nucleotides but potentially going up to hundreds of nucleotides [Bambara78, Uyemura75]. The kinetics of polymerization have been extensively evaluated [Travaglini75, McClure75, Mizrahi85, elDeiry88, Dahlberg91]. The nucleotide-dependence of polymerization termination has also been examined [Abbotts88].

Pol I polymerization is also specific; though error rates in vitro of 1 in 8,000-80,000 have been measured, the estimated rate on natural DNA is between 1 in 680,000 and 1 in 6.3 million [Agarwal79, Kunkel80]. The mechanisms behind specificity have been examined, as well as the role of differing metal cofactors in specificity [Astatke98, Astatke98a, Sirover79, Hillebrand84].

The two exonuclease activities of Pol I have also been evaluated. The 5' to 3' exonuclease activity requires a free 5' end at an ssDNA-dsDNA junction and is slower than the 3' to 5' exonuclease activity [Xu97, Deutscher69]. The 3' to 5' exonuclease, which is responsible for proofreading, does not identify base-pair mismatches. Instead, Pol I lingers when a mismatch occurs, allowing more time for the exonuclease to act on the mismatch [Kuchta88, Bailly84]. The transfer of DNA from the polymerase to the 3' to 5' exonuclease active site can occur either intra- or intermolecularly, with mismatches favoring the latter [Joyce89].

polA mutants are more vulnerable to UV and X-rays and experience more deletions, duplications and frameshifts [Billen85, Nagata02, Barfknecht78]. polA mutU4 double mutants are inviable [Siegel73].

Citations: [Bailey04]

Locations: cytosol

Map Position: [4,044,989 -> 4,047,775] (87.18 centisomes)
Length: 2787 bp / 928 aa

Molecular Weight of Polypeptide: 103.12 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0012618 , CGSC:375 , DIP:DIP-10524N , EchoBASE:EB0739 , EcoGene:EG10746 , EcoliWiki:b3863 , Mint:MINT-1225247 , ModBase:P00582 , OU-Microarray:b3863 , PortEco:polA , PR:PRO_000023565 , Pride:P00582 , Protein Model Portal:P00582 , RefSeq:NP_418300 , RegulonDB:EG10746 , SMR:P00582 , String:511145.b3863 , UniProt:P00582

Relationship Links: InterPro:IN-FAMILY:IPR001098 , InterPro:IN-FAMILY:IPR002298 , InterPro:IN-FAMILY:IPR002421 , InterPro:IN-FAMILY:IPR002562 , InterPro:IN-FAMILY:IPR003583 , InterPro:IN-FAMILY:IPR008918 , InterPro:IN-FAMILY:IPR012337 , InterPro:IN-FAMILY:IPR018320 , InterPro:IN-FAMILY:IPR019760 , InterPro:IN-FAMILY:IPR020045 , InterPro:IN-FAMILY:IPR020046 , PDB:Structure:1D8Y , PDB:Structure:1D9D , PDB:Structure:1D9F , PDB:Structure:1DPI , PDB:Structure:1KFD , PDB:Structure:1KFS , PDB:Structure:1KLN , PDB:Structure:1KRP , PDB:Structure:1KSP , PDB:Structure:1QSL , PDB:Structure:2KFN , PDB:Structure:2KFZ , PDB:Structure:2KZM , PDB:Structure:2KZZ , Pfam:IN-FAMILY:PF00476 , Pfam:IN-FAMILY:PF01367 , Pfam:IN-FAMILY:PF01612 , Pfam:IN-FAMILY:PF02739 , Prints:IN-FAMILY:PR00868 , Prosite:IN-FAMILY:PS00447 , Smart:IN-FAMILY:SM00278 , Smart:IN-FAMILY:SM00279 , Smart:IN-FAMILY:SM00474 , Smart:IN-FAMILY:SM00475 , Smart:IN-FAMILY:SM00482

In Paralogous Gene Group: 459 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006260 - DNA replication Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Setlow72]
GO:0006261 - DNA-dependent DNA replication Inferred from experiment Inferred by computational analysis [GOA01, Shlomai81]
GO:0006281 - DNA repair Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Sharon75]
GO:0006284 - base-excision repair Inferred from experiment [Uphoff13]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis Inferred from experiment [Deutscher69, Setlow72a, Setlow72, UniProtGOA11, GOA01]
GO:0006974 - cellular response to DNA damage stimulus Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Englund69]
GO:0003887 - DNA-directed DNA polymerase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01a, GOA01, Rhodes79, Lehman58]
GO:0008408 - 3'-5' exonuclease activity Inferred from experiment Inferred by computational analysis [GOA01, Deutscher69, Setlow72]
GO:0008409 - 5'-3' exonuclease activity Inferred from experiment [Deutscher69, Setlow72a]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11]
GO:0004527 - exonuclease activity Inferred by computational analysis [UniProtGOA11]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016779 - nucleotidyltransferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Lasserre06]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: information transfer DNA related DNA replication

Essentiality data for polA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox No 37 Aerobic 7   No [Baba06, Yamamoto09]

Enzymatic reaction of: 5' to 3' exonuclease (DNA polymerase I, 5' --> 3' polymerase, 5' --> 3' and 3' --> 5' exonuclease)

EC Number: 3.1.11.-

a double stranded DNA + H2O <=> a single stranded DNA + a 5'-phosphomononucleotide

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.


Enzymatic reaction of: 3' to 5' proofreading exonuclease (DNA polymerase I, 5' --> 3' polymerase, 5' --> 3' and 3' --> 5' exonuclease)

EC Number: 3.1.11.-

DNAn + n H2O <=> n a nucleoside 5'-monophosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Cofactors or Prosthetic Groups: Mn2+ [Mullen90]


Enzymatic reaction of: DNA polymerase

EC Number: 2.7.7.7

a deoxyribonucleoside triphosphate + (deoxynucleotides)(n) <=> (deoxynucleotides)(n+1) + diphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

Citations: [Bessman58]

Cofactors or Prosthetic Groups: Mg2+ [Lehman58]


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 1 -> 323
[UniProt09]
UniProt: 5'-3' exonuclease;
Protein-Segment 324 -> 928
[UniProt10]
UniProt: Klenow fragment; Sequence Annotation Type: region of interest;
Conserved-Region 324 -> 517
[UniProt09]
UniProt: 3'-5' exonuclease;
Active-Site 355, 357, 361, 424, 473, 497, 501
[Derbyshire91]
The active site for the 3' to 5' exonuclease activity of Pol I contains two divalent metal ions anchored by three Asp residues (355, 424, 501). Three other resides, Leu-361, Phe-473 and Tyr-497, bind substrate.
Protein-Segment 521 -> 928
[UniProt10]
UniProt: Polymerase; Sequence Annotation Type: region of interest;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b3863 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10746; confirmed by SwissProt match.


References

Abbotts88: Abbotts J, SenGupta DN, Zon G, Wilson SH (1988). "Studies on the mechanism of Escherichia coli DNA polymerase I large fragment. Effect of template sequence and substrate variation on termination of synthesis." J Biol Chem 263(29);15094-103. PMID: 2971662

Agarwal79: Agarwal SS, Dube DK, Loeb LA (1979). "On the fidelity of DNA replication. Accuracy of Escherichia coli DNA polymerase I." J Biol Chem 254(1);101-6. PMID: 363714

Astatke98: Astatke M, Grindley ND, Joyce CM (1998). "How E. coli DNA polymerase I (Klenow fragment) distinguishes between deoxy- and dideoxynucleotides." J Mol Biol 278(1);147-65. PMID: 9571040

Astatke98a: Astatke M, Ng K, Grindley ND, Joyce CM (1998). "A single side chain prevents Escherichia coli DNA polymerase I (Klenow fragment) from incorporating ribonucleotides." Proc Natl Acad Sci U S A 95(7);3402-7. PMID: 9520378

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bailey04: Bailey MF, van der Schans EJ, Millar DP (2004). "Thermodynamic dissection of the polymerizing and editing modes of a DNA polymerase." J Mol Biol 336(3);673-93. PMID: 15095980

Bailly84: Bailly V, Verly WG (1984). "The excision of AP sites by the 3'-5' exonuclease activity of the Klenow fragment of Escherichia coli DNA polymerase I." FEBS Lett 178(2);223-7. PMID: 6391956

Bambara78: Bambara RA, Uyemura D, Choi T (1978). "On the processive mechanism of Escherichia coli DNA polymerase I. Quantitative assessment of processivity." J Biol Chem 253(2);413-23. PMID: 338607

Barfknecht78: Barfknecht TR, Smith KC (1978). "The involvement of DNA polymerase I in the postreplication repair of ultraviolet radiation-induced damage in Escherichia coli K-12." Mol Gen Genet 167(1);37-41. PMID: 368586

Beese91: Beese LS, Steitz TA (1991). "Structural basis for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism." EMBO J 10(1);25-33. PMID: 1989886

Beese93: Beese LS, Friedman JM, Steitz TA (1993). "Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate." Biochemistry 32(51);14095-101. PMID: 8260491

Bessman58: Bessman MJ, Lehman IR, Simms ES, Kornberg A (1958). "Enzymatic synthesis of deoxyribonucleic acid. II. General properties of the reaction." J Biol Chem 233(1);171-7. PMID: 13563463

Billen85: Billen D (1985). "DNA polymerase I is crucial for the repair of potentially lethal damage caused by the indirect effects of X irradiation in Escherichia coli." Radiat Res 103(1);163-9. PMID: 2999864

Dahlberg91: Dahlberg ME, Benkovic SJ (1991). "Kinetic mechanism of DNA polymerase I (Klenow fragment): identification of a second conformational change and evaluation of the internal equilibrium constant." Biochemistry 30(20);4835-43. PMID: 1645180

Derbyshire91: Derbyshire V, Grindley ND, Joyce CM (1991). "The 3'-5' exonuclease of DNA polymerase I of Escherichia coli: contribution of each amino acid at the active site to the reaction." EMBO J 10(1);17-24. PMID: 1989882

Deutscher69: Deutscher MP, Kornberg A (1969). "Enzymatic synthesis of deoxyribonucleic acid. XXIX. Hydrolysis of deoxyribonucleic acid from the 5' terminus by an exonuclease function of deoxyribonucleic acid polymerase." J Biol Chem 244(11);3029-37. PMID: 4890763

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Dorson78: Dorson JW, Deutsch WA, Moses RE (1978). "Role of DNA polymerases in excision repair in Escherichia coli." J Biol Chem 253(3);660-4. PMID: 340455

Dzantiev00: Dzantiev L, Romano LJ (2000). "A conformational change in E. coli DNA polymerase I (Klenow fragment) is induced in the presence of a dNTP complementary to the template base in the active site." Biochemistry 39(2);356-61. PMID: 10630996

Dzidic89: Dzidic S, Radman M (1989). "Genetic requirements for hyper-recombination by very short patch mismatch repair: involvement of Escherichia coli DNA polymerase I." Mol Gen Genet 217(2-3);254-6. PMID: 2671653

elDeiry88: el-Deiry WS, So AG, Downey KM (1988). "Mechanisms of error discrimination by Escherichia coli DNA polymerase I." Biochemistry 27(2);546-53. PMID: 3280024

Englund69: Englund PT, Kelly RB, Kornberg A (1969). "Enzymatic synthesis of deoxyribonucleic acid. XXXI. Binding of deoxyribonucleic acid to deoxyribonucleic acid polymerase." J Biol Chem 244(11);3045-52. PMID: 4890764

Freemont86: Freemont PS, Ollis DL, Steitz TA, Joyce CM (1986). "A domain of the Klenow fragment of Escherichia coli DNA polymerase I has polymerase but no exonuclease activity." Proteins 1(1);66-73. PMID: 3329725

Freemont88: Freemont PS, Friedman JM, Beese LS, Sanderson MR, Steitz TA (1988). "Cocrystal structure of an editing complex of Klenow fragment with DNA." Proc Natl Acad Sci U S A 85(23);8924-8. PMID: 3194400

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

Glickman75: Glickman BW (1975). "The role of DNA polymerase I in excision-repair." Basic Life Sci 5A;213-8. PMID: 1103827

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Heyneker75: Heyneker HL, Klenow H (1975). "Involvement of Escherichia coli DNA polymerase-I-associated 5' in equilibrium 3' exonuclease in excision-repair of UV-damaged DNA." Basic Life Sci 5A;219-23. PMID: 1103828

Hillebrand84: Hillebrand GG, Beattie KL (1984). "Template-dependent variation in the relative fidelity of DNA polymerase I of Escherichia coli in the presence of Mg2+ versus Mn2+." Nucleic Acids Res 12(7);3173-83. PMID: 6371712

Huberman70: Huberman JA, Kornberg A (1970). "Enzymatic synthesis of deoxyribonucleic acid. XXXV. A 3'-hydroxylribonucleotide binding site of Escherichia coli deoxyribonucleic acid polymerase." J Biol Chem 245(20);5326-34. PMID: 4918843

Husain85: Husain I, Van Houten B, Thomas DC, Abdel-Monem M, Sancar A (1985). "Effect of DNA polymerase I and DNA helicase II on the turnover rate of UvrABC excision nuclease." Proc Natl Acad Sci U S A 82(20);6774-8. PMID: 2931721

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Joyce89: Joyce CM (1989). "How DNA travels between the separate polymerase and 3'-5'-exonuclease sites of DNA polymerase I (Klenow fragment)." J Biol Chem 264(18);10858-66. PMID: 2659595

Kelly70: Kelly RB, Cozzarelli NR, Deutscher MP, Lehman IR, Kornberg A (1970). "Enzymatic synthesis of deoxyribonucleic acid. XXXII. Replication of duplex deoxyribonucleic acid by polymerase at a single strand break." J Biol Chem 245(1);39-45. PMID: 4904090

Kuchta88: Kuchta RD, Benkovic P, Benkovic SJ (1988). "Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity." Biochemistry 27(18);6716-25. PMID: 3058205

Kunkel80: Kunkel TA, Loeb LA (1980). "On the fidelity of DNA replication. The accuracy of Escherichia coli DNA polymerase I in copying natural DNA in vitro." J Biol Chem 255(20);9961-6. PMID: 6448843

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Lehman58: Lehman IR, Bessman MJ, Simms ES, Kornberg A (1958). "Enzymatic synthesis of deoxyribonucleic acid. I. Preparation of substrates and partial purification of an enzyme from Escherichia coli." J Biol Chem 233(1);163-70. PMID: 13563462

Ljach92: Ljach MV, Kolocheva TI, Gorn VV, Levina AS, Nevinsky GA (1992). "The affinity of the Klenow fragment of E. coli DNA-polymerase 1 to primers containing bases noncomplementary to the template and hairpin-like elements." FEBS Lett 300(1);18-20. PMID: 1547884

Matson81: Matson SW, Bambara RA (1981). "Short deoxyribonucleic acid repair patch length in Escherichia coli is determined by the processive mechanism of deoxyribonucleic acid polymerase I." J Bacteriol 146(1);275-84. PMID: 7012116

McClure75: McClure WR, Jovin TM (1975). "The steady state kinetic parameters and non-processivity of Escherichia coli deoxyribonucleic acid polymerase I." J Biol Chem 250(11);4073-80. PMID: 1092683

Meyer04: Meyer AS, Blandino M, Spratt TE (2004). "Escherichia coli DNA polymerase I (Klenow fragment) uses a hydrogen-bonding fork from Arg668 to the primer terminus and incoming deoxynucleotide triphosphate to catalyze DNA replication." J Biol Chem 279(32);33043-6. PMID: 15210707

Minnick96: Minnick DT, Astatke M, Joyce CM, Kunkel TA (1996). "A thumb subdomain mutant of the large fragment of Escherichia coli DNA polymerase I with reduced DNA binding affinity, processivity, and frameshift fidelity." J Biol Chem 271(40);24954-61. PMID: 8798775

Mizrahi85: Mizrahi V, Henrie RN, Marlier JF, Johnson KA, Benkovic SJ (1985). "Rate-limiting steps in the DNA polymerase I reaction pathway." Biochemistry 24(15);4010-8. PMID: 3902078

Mosbaugh82: Mosbaugh DW, Linn S (1982). "Characterization of the action of Escherichia coli DNA polymerase I at incisions produced by repair endodeoxyribonucleases." J Biol Chem 257(1);575-83. PMID: 6273443

Mullen90: Mullen GP, Serpersu EH, Ferrin LJ, Loeb LA, Mildvan AS (1990). "Metal binding to DNA polymerase I, its large fragment, and two 3',5'-exonuclease mutants of the large fragment." J Biol Chem 265(24);14327-34. PMID: 2201684

Nagata02: Nagata Y, Mashimo K, Kawata M, Yamamoto K (2002). "The roles of Klenow processing and flap processing activities of DNA polymerase I in chromosome instability in Escherichia coli K12 strains." Genetics 160(1);13-23. PMID: 11805041

Okazaki71: Okazaki R, Arisawa M, Sugino A (1971). "Slow joining of newly replicated DNA chains in DNA polymerase I-deficient Escherichia coli mutants." Proc Natl Acad Sci U S A 68(12);2954-7. PMID: 4943548

Olivera74: Olivera RM, Bonhoeffer E (1974). "Replication of Escherichia coli requires DNA polymerase I." Nature 250(5466);513-4. PMID: 4620020

Orren92: Orren DK, Selby CP, Hearst JE, Sancar A (1992). "Post-incision steps of nucleotide excision repair in Escherichia coli. Disassembly of the UvrBC-DNA complex by helicase II and DNA polymerase I." J Biol Chem 267(2);780-8. PMID: 1530937

Rhodes79: Rhodes G, Jentsch KD, Jovin TM (1979). "A simple and rapid purification method for Escherichia coli DNA polymerase I." J Biol Chem 254(16);7465-7. PMID: 381283

Setlow72: Setlow P, Brutlag D, Kornberg A (1972). "Deoxyribonucleic acid polymerase: two distinct enzymes in one polypeptide. I. A proteolytic fragment containing the polymerase and 3' leads to 5' exonuclease functions." J Biol Chem 247(1);224-31. PMID: 4552924

Setlow72a: Setlow P, Kornberg A (1972). "Deoxyribonucleic acid polymerase: two distinct enzymes in one polypeptide. II. A proteolytic fragment containing the 5' leads to 3' exonuclease function. Restoration of intact enzyme functions from the two proteolytic fragments." J Biol Chem 247(1);232-40. PMID: 4552925

Sharma87: Sharma RC, Smith KC (1987). "Role of DNA polymerase I in postreplication repair: a reexamination with Escherichia coli delta polA." J Bacteriol 169(10);4559-64. PMID: 3308845

Sharon75: Sharon R, Miller C, Ben-Ishai R (1975). "Two modes of excision repair in toluene-treated Escherichia coli." J Bacteriol 123(3);1107-14. PMID: 169227

Shlomai81: Shlomai J, Polder L, Arai K, Kornberg A (1981). "Replication of phi X174 dna with purified enzymes. I. Conversion of viral DNA to a supercoiled, biologically active duplex." J Biol Chem 256(10);5233-8. PMID: 6262323

Siegel73: Siegel EC (1973). "Ultraviolet-sensitive mutator mutU4 of Escherichia coli inviable with polA." J Bacteriol 113(1);161-6. PMID: 4347245

Singh03: Singh K, Modak MJ (2003). "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." J Biol Chem 278(13);11289-302. PMID: 12522214

Singh05: Singh K, Modak MJ (2005). "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." Biochemistry 44(22);8101-10. PMID: 15924429

Sirover79: Sirover MA, Dube DK, Loeb LA (1979). "On the fidelity of DNA replication. Metal activation of Escherichia coli DNA polymerase I." J Biol Chem 254(1);107-11. PMID: 363715

Spratt01: Spratt TE (2001). "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." Biochemistry 40(9);2647-52. PMID: 11258875

Steitz83: Steitz TA, Weber IT, Ollis D, Brick P (1983). "Crystallographic studies of protein-nucleic acid interaction: catabolite gene activator protein and the large fragment of DNA polymerase I." J Biomol Struct Dyn 1(4);1023-37. PMID: 6101086

Sung03: Sung JS, Mosbaugh DW (2003). "Escherichia coli uracil- and ethenocytosine-initiated base excision DNA repair: rate-limiting step and patch size distribution." Biochemistry 42(16);4613-25. PMID: 12705824

Travaglini75: Travaglini EC, Mildvan AS, Loeb LA (1975). "Kinetic analysis of Escherichia coli deoxyribonucleic acid polymerase I." J Biol Chem 250(22);8647-56. PMID: 1102540

Tuske00: Tuske S, Singh K, Kaushik N, Modak MJ (2000). "The J-helix of Escherichia coli DNA polymerase I (Klenow fragment) regulates polymerase and 3'- 5'-exonuclease functions." J Biol Chem 275(31);23759-68. PMID: 10818095

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Uphoff13: Uphoff S, Reyes-Lamothe R, Garza de Leon F, Sherratt DJ, Kapanidis AN (2013). "Single-molecule DNA repair in live bacteria." Proc Natl Acad Sci U S A 110(20);8063-8. PMID: 23630273

Uyemura75: Uyemura D, Bambara R, Lehman IR (1975). "On the processive mechanism of Escherichia coli DNA polymerase I." J Biol Chem 250(22);8577-84. PMID: 1102539

Xu01: Xu Y, Potapova O, Leschziner AE, Grindley ND, Joyce CM (2001). "Contacts between the 5' nuclease of DNA polymerase I and its DNA substrate." J Biol Chem 276(32);30167-77. PMID: 11349126

Xu97: Xu Y, Derbyshire V, Ng K, Sun XC, Grindley ND, Joyce CM (1997). "Biochemical and mutational studies of the 5'-3' exonuclease of DNA polymerase I of Escherichia coli." J Mol Biol 268(2);284-302. PMID: 9159471

Yamamoto09: Yamamoto N, Nakahigashi K, Nakamichi T, Yoshino M, Takai Y, Touda Y, Furubayashi A, Kinjyo S, Dose H, Hasegawa M, Datsenko KA, Nakayashiki T, Tomita M, Wanner BL, Mori H (2009). "Update on the Keio collection of Escherichia coli single-gene deletion mutants." Mol Syst Biol 5;335. PMID: 20029369

Other References Related to Gene Regulation

Quinones97: Quinones A, Wandt G, Kleinstauber S, Messer W (1997). "DnaA protein stimulates polA gene expression in Escherichia coli." Mol Microbiol 1997;23(6);1193-202. PMID: 9106210


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Thu Dec 18, 2014, BIOCYC14B.