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Escherichia coli K-12 substr. MG1655 Enzyme: DNA polymerase II



Gene: polB Accession Numbers: EG10747 (EcoCyc), b0060, ECK0061

Synonyms: dinA

Regulation Summary Diagram: ?

Summary:
DNA polymerase II (Pol II) is a combined polymerase and exonuclease involved in replication restart following UV exposure, translesion synthesis and nucleotide excision repair.

Pol II catalyzes both a DNA polymerase activity and a 3' to 5' exonuclease activity [Kornberg71, Ishino92]. Pol II is also required for rapid restart of DNA replication following UV irradiation [Rangarajan02a, Rangarajan99]. In addition to its role in translesion bypass, discussed below, Pol II is required for a nucleotide excision repair pathway that fixes DNA crosslinks [Berardini99]. Pol II also plays a role in surviving thymine dimers and avoiding the mutagenic effects of agents such as peroxide [Sedliakova01, Escarceller94].

Pol II tends to make more errors in replication of AT-rich sequences, which differs from the behavior of most other DNA polymerases [Wang02b].

Pol II allows replication to bypass some kinds of DNA lesions. Under certain conditions Pol II is required for bypass of abasic lesions [Tessman94, PazElizur96a]. This bypass increases when Pol II exonuclease activity is disabled [PazElizur96a]. Pol II can also bypass 3,N(4)-ethenocytosine lesions and carries out mutagenic bypass of 2-acetylaminofluorene-induced lesions, the latter resulting in -2 frameshifts [Al06, Napolitano00, Fuchs01]. Pol II and Pol V appear to compete directly to bypass AAF lesion sites [Becherel01]. Pol II has also been implicated in bypass of crosslinking lesions [Kanuri05].

The exonuclease function of Pol II appears to be located in its amino-terminal region [Ishino94]. A crystal structure of all of Pol II has been determined to 3 Å resolution [Anderson94a].

In vitro, the DNA polymerase III gamma clamp loader complex and beta clamp stimulate Pol II activity on ssDNA template, increasing its processivity several hundred fold [Hughes91, Bonner92].

In mutants lacking Pol II exonuclease activity, mutation increases, including adaptive mutation [Rangarajan97, Foster95]. These exonuclease-deficient strains especially experience mutations in the lagging strand and suffer a synergestic increase in mutation in strains with mutator versions of DNA polymerase III [BanachOrlowska05]. In mutants lacking the DNA polymerase III gamma complex, the presence of Pol II is lethal [Viguera03].

Pol II is regulated by the SOS response and is induced by the SOS-inducing agents nalidixic acid, peroxide and ethanol [Iwasaki90, Oh99]. Pol II fidelity may also increase during induction of the SOS response [Kanuri05].

Citations: [Moses74, Cai95a, Qiu97]

Locations: cytosol

Map Position: [63,429 <- 65,780] (1.37 centisomes)
Length: 2352 bp / 783 aa

Molecular Weight of Polypeptide: 90.052 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0000202 , CGSC:374 , EchoBASE:EB0740 , EcoGene:EG10747 , EcoliWiki:b0060 , ModBase:P21189 , OU-Microarray:b0060 , PortEco:polB , PR:PRO_000023566 , Pride:P21189 , Protein Model Portal:P21189 , RefSeq:NP_414602 , RegulonDB:EG10747 , SMR:P21189 , String:511145.b0060 , UniProt:P21189

Relationship Links: InterPro:IN-FAMILY:IPR006133 , InterPro:IN-FAMILY:IPR006134 , InterPro:IN-FAMILY:IPR006172 , InterPro:IN-FAMILY:IPR012337 , InterPro:IN-FAMILY:IPR017964 , InterPro:IN-FAMILY:IPR023211 , PDB:Structure:1Q8I , PDB:Structure:3K57 , PDB:Structure:3K58 , PDB:Structure:3K59 , PDB:Structure:3K5L , PDB:Structure:3K5M , PDB:Structure:3K5N , PDB:Structure:3K5O , PDB:Structure:3MAQ , Pfam:IN-FAMILY:PF00136 , Pfam:IN-FAMILY:PF03104 , Prints:IN-FAMILY:PR00106 , Prosite:IN-FAMILY:PS00116 , Smart:IN-FAMILY:SM00486

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0000738 - DNA catabolic process, exonucleolytic Inferred from experiment [Kornberg71]
GO:0006261 - DNA-dependent DNA replication Inferred from experiment [Rangarajan99]
GO:0009432 - SOS response Inferred from experiment Inferred by computational analysis [UniProtGOA11, Iwasaki90]
GO:0045004 - DNA replication proofreading Inferred from experiment [Ishino92]
GO:0006139 - nucleobase-containing compound metabolic process Inferred by computational analysis [GOA01]
GO:0006260 - DNA replication Inferred by computational analysis [GOA01]
GO:0006281 - DNA repair Inferred by computational analysis [UniProtGOA11]
GO:0006297 - nucleotide-excision repair, DNA gap filling Inferred by computational analysis [Gaudet10]
GO:0006974 - cellular response to DNA damage stimulus Inferred by computational analysis [UniProtGOA11]
GO:0019985 - translesion synthesis Inferred by computational analysis [Gaudet10]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis [Gaudet10]
Molecular Function: GO:0003887 - DNA-directed DNA polymerase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01a, GOA01, Gaudet10, Chen89]
GO:0008296 - 3'-5'-exodeoxyribonuclease activity Inferred from experiment [Kornberg71]
GO:0000166 - nucleotide binding Inferred by computational analysis [GOA01]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0008408 - 3'-5' exonuclease activity Inferred by computational analysis [Gaudet10]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016779 - nucleotidyltransferase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005694 - chromosome Inferred by computational analysis [Gaudet10]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes protection radiation
cell processes SOS response
information transfer DNA related DNA repair
information transfer DNA related DNA replication

Essentiality data for polB 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 Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Enzymatic reaction of: DNA polymerase

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.

Citations: [Ishino92]


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.

Cofactors or Prosthetic Groups: Mg2+ [Kornberg71]

Inhibitors (Competitive): aphidicolin [Ishino92, Chen90b]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Bonner90a, Iwasaki91a, UniProt11a]
UniProt: Removed.
Chain 2 -> 783
[UniProt09]
UniProt: DNA polymerase II;
Sequence-Conflict 172
[Chen90c, UniProt10]
Alternate sequence: G → A; UniProt: (in Ref. 2; AAA24406/AAA24407);
Sequence-Conflict 257 -> 258
[Bonner90a, UniProt10]
Alternate sequence: EH → DD; UniProt: (in Ref. 6; AAA63764/AAA23684);
Sequence-Conflict 272
[Bonner90a, UniProt10]
Alternate sequence: R → G; UniProt: (in Ref. 6; AAA63764/AAA23684);
Extrinsic-Sequence-Variant 401
[UniProt10]
Alternate sequence: G → D; UniProt: (in allele POLB100);
Sequence-Conflict 735
[Chen90c, UniProt10]
Alternate sequence: N → T; UniProt: (in Ref. 2; AAA24406/AAA24407);
Sequence-Conflict 740 -> 783
[Chen90c, UniProt10]
Alternate sequence: LDYQRSPLDYEHYLTRQLQPVAEGILPFIEDNFATLMTGQLGLF → PGLPTFTTGLRTLSDPPATTRGGGNTPFY; UniProt: (in Ref. 2);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b0060 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10747; confirmed by SwissProt match.


References

Al06: Al Mamun AA, Humayun MZ (2006). "Escherichia coli DNA polymerase II can efficiently bypass 3,N(4)-ethenocytosine lesions in vitro and in vivo." Mutat Res 593(1-2):164-76. PMID: 16171831

Anderson94a: Anderson WF, Prince DB, Yu H, McEntee K, Goodman MF (1994). "Crystallization of DNA polymerase II from Escherichia coli." J Mol Biol 238(1);120-2. PMID: 8145251

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

BanachOrlowska05: Banach-Orlowska M, Fijalkowska IJ, Schaaper RM, Jonczyk P (2005). "DNA polymerase II as a fidelity factor in chromosomal DNA synthesis in Escherichia coli." Mol Microbiol 58(1);61-70. PMID: 16164549

Becherel01: Becherel OJ, Fuchs RP (2001). "Mechanism of DNA polymerase II-mediated frameshift mutagenesis." Proc Natl Acad Sci U S A 98(15);8566-71. PMID: 11447256

Berardini99: Berardini M, Foster PL, Loechler EL (1999). "DNA polymerase II (polB) is involved in a new DNA repair pathway for DNA interstrand cross-links in Escherichia coli." J Bacteriol 181(9);2878-82. PMID: 10217781

Bonner90a: Bonner CA, Hays S, McEntee K, Goodman MF (1990). "DNA polymerase II is encoded by the DNA damage-inducible dinA gene of Escherichia coli." Proc Natl Acad Sci U S A 87(19);7663-7. PMID: 2217198

Bonner92: Bonner CA, Stukenberg PT, Rajagopalan M, Eritja R, O'Donnell M, McEntee K, Echols H, Goodman MF (1992). "Processive DNA synthesis by DNA polymerase II mediated by DNA polymerase III accessory proteins." J Biol Chem 267(16);11431-8. PMID: 1534562

Cai95a: Cai H, Yu H, McEntee K, Goodman MF (1995). "Purification and properties of DNA polymerase II from Escherichia coli." Methods Enzymol 262;13-21. PMID: 8594343

Chen89: Chen H, Bryan SK, Moses RE (1989). "Cloning the polB gene of Escherichia coli and identification of its product." J Biol Chem 264(34);20591-5. PMID: 2684981

Chen90b: Chen H, Lawrence CB, Bryan SK, Moses RE (1990). "Aphidicolin inhibits DNA polymerase II of Escherichia coli, an alpha-like DNA polymerase." Nucleic Acids Res 18(23);7185-6. PMID: 2124684

Chen90c: Chen H, Sun Y, Stark T, Beattie W, Moses RE (1990). "Nucleotide sequence and deletion analysis of the polB gene of Escherichia coli." DNA Cell Biol 9(9);631-5. PMID: 2261080

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

Escarceller94: Escarceller M, Hicks J, Gudmundsson G, Trump G, Touati D, Lovett S, Foster PL, McEntee K, Goodman MF (1994). "Involvement of Escherichia coli DNA polymerase II in response to oxidative damage and adaptive mutation." J Bacteriol 176(20);6221-8. PMID: 7928992

Foster95: Foster PL, Gudmundsson G, Trimarchi JM, Cai H, Goodman MF (1995). "Proofreading-defective DNA polymerase II increases adaptive mutation in Escherichia coli." Proc Natl Acad Sci U S A 92(17);7951-5. PMID: 7644519

Fuchs01: Fuchs RP, Koffel-Schwartz N, Pelet S, Janel-Bintz R, Napolitano R, Becherel OJ, Broschard TH, Burnouf DY, Wagner J (2001). "DNA polymerases II and V mediate respectively mutagenic (-2 frameshift) and error-free bypass of a single N-2-acetylaminofluorene adduct." Biochem Soc Trans 29(Pt 2);191-5. PMID: 11356152

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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

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.

Hughes91: Hughes AJ, Bryan SK, Chen H, Moses RE, McHenry CS (1991). "Escherichia coli DNA polymerase II is stimulated by DNA polymerase III holoenzyme auxiliary subunits." J Biol Chem 266(7);4568-73. PMID: 1999435

Ishino92: Ishino Y, Iwasaki H, Fukui H, Mineno J, Kato I, Shinagawa H (1992). "Aphidicolin inhibits DNA polymerizing activity but not nucleolytic activity of Escherichia coli DNA polymerase II." Biochimie 74(2);131-6. PMID: 1581388

Ishino94: Ishino Y, Iwasaki H, Kato I, Shinagawa H (1994). "Amino acid sequence motifs essential to 3'-->5' exonuclease activity of Escherichia coli DNA polymerase II." J Biol Chem 269(20);14655-60. PMID: 8182073

Iwasaki90: Iwasaki H, Nakata A, Walker GC, Shinagawa H (1990). "The Escherichia coli polB gene, which encodes DNA polymerase II, is regulated by the SOS system." J Bacteriol 172(11);6268-73. PMID: 2228959

Iwasaki91a: Iwasaki H, Ishino Y, Toh H, Nakata A, Shinagawa H (1991). "Escherichia coli DNA polymerase II is homologous to alpha-like DNA polymerases." Mol Gen Genet 226(1-2);24-33. PMID: 2034216

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kanuri05: Kanuri M, Nechev LV, Kiehna SE, Tamura PJ, Harris CM, Harris TM, Lloyd RS (2005). "Evidence for Escherichia coli polymerase II mutagenic bypass of intrastrand DNA crosslinks." DNA Repair (Amst) 4(12);1374-80. PMID: 16257273

Kornberg71: Kornberg T, Gefter ML (1971). "Purification and DNA synthesis in cell-free extracts: properties of DNA polymerase II." Proc Natl Acad Sci U S A 68(4);761-4. PMID: 4927672

Moses74: Moses RE (1974). "The isolation and properties of DNA polymerase II from Escherichia coli." Methods Enzymol 29(0);13-22. PMID: 4605284

Napolitano00: Napolitano R, Janel-Bintz R, Wagner J, Fuchs RP (2000). "All three SOS-inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis." EMBO J 19(22);6259-65. PMID: 11080171

Oh99: Oh TJ, Lee CW, Kim IG (1999). "The damage-inducible (din) genes of Escherichia coli are induced by various genotoxins in a different way." Microbiol Res 154(2);179-83. PMID: 10522385

PazElizur96a: Paz-Elizur T, Takeshita M, Goodman M, O'Donnell M, Livneh Z (1996). "Mechanism of translesion DNA synthesis by DNA polymerase II. Comparison to DNA polymerases I and III core." J Biol Chem 271(40);24662-9. PMID: 8798733

Qiu97: Qiu Z, Goodman MF (1997). "The Escherichia coli polB locus is identical to dinA, the structural gene for DNA polymerase II. Characterization of Pol II purified from a polB mutant." J Biol Chem 272(13);8611-7. PMID: 9079692

Rangarajan02a: Rangarajan S, Woodgate R, Goodman MF (2002). "Replication restart in UV-irradiated Escherichia coli involving pols II, III, V, PriA, RecA and RecFOR proteins." Mol Microbiol 43(3);617-28. PMID: 11929519

Rangarajan97: Rangarajan S, Gudmundsson G, Qiu Z, Foster PL, Goodman MF (1997). "Escherichia coli DNA polymerase II catalyzes chromosomal and episomal DNA synthesis in vivo." Proc Natl Acad Sci U S A 94(3);946-51. PMID: 9023362

Rangarajan99: Rangarajan S, Woodgate R, Goodman MF (1999). "A phenotype for enigmatic DNA polymerase II: a pivotal role for pol II in replication restart in UV-irradiated Escherichia coli." Proc Natl Acad Sci U S A 96(16);9224-9. PMID: 10430924

Sedliakova01: Sedliakova M, Slezarikova V, Masek F, Vizvaryova M, Pirsel M (2001). "Role of DNA polymerase II in the tolerance of thymine dimers remaining unexcised in UV-irradiated Escherichia coli exposed to pre-UV nutritional stress." J Photochem Photobiol B 65(2-3);145-50. PMID: 11809372

Tessman94: Tessman I, Kennedy MA (1994). "DNA polymerase II of Escherichia coli in the bypass of abasic sites in vivo." Genetics 136(2);439-48. PMID: 7908652

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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

Viguera03: Viguera E, Petranovic M, Zahradka D, Germain K, Ehrlich DS, Michel B (2003). "Lethality of bypass polymerases in Escherichia coli cells with a defective clamp loader complex of DNA polymerase III." Mol Microbiol 50(1);193-204. PMID: 14507374

Wang02b: Wang Z, Lazarov E, O'Donnell M, Goodman MF (2002). "Resolving a fidelity paradox: why Escherichia coli DNA polymerase II makes more base substitution errors in AT- compared with GC-rich DNA." J Biol Chem 277(6);4446-54. PMID: 11733526

Other References Related to Gene Regulation

Lewis92: Lewis LK, Jenkins ME, Mount DW (1992). "Isolation of DNA damage-inducible promoters in Escherichia coli: regulation of polB (dinA), dinG, and dinH by LexA repressor." J Bacteriol 174(10);3377-85. PMID: 1577702

Lewis94: Lewis LK, Harlow GR, Gregg-Jolly LA, Mount DW (1994). "Identification of high affinity binding sites for LexA which define new DNA damage-inducible genes in Escherichia coli." J Mol Biol 241(4);507-23. PMID: 8057377

Stringer14: Stringer AM, Currenti S, Bonocora RP, Baranowski C, Petrone BL, Palumbo MJ, Reilly AA, Zhang Z, Erill I, Wade JT (2014). "Genome-scale analyses of Escherichia coli and Salmonella enterica AraC reveal noncanonical targets and an expanded core regulon." J Bacteriol 196(3);660-71. PMID: 24272778


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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 Nov 27, 2014, BIOCYC13A.