Deoxyribose Phosphate Excision by the N-Terminal Domain of the Polymerase β:  The Mechanism Revisited

Crasto, Chiquito J.; Matsumoto, Yoshihiro

doi:10.1021/bi9808619

Cited by 33 publications

(40 citation statements)

References 29 publications

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“…In mammalian cells, most dRp excision is attributable to Polb (Sobol et al, 1996), specifically its amino-terminal 8-kilodalton domain (Matsumoto and Kim, 1995). In this process, lysine-72 performs a nucleophilic attack on the C1-carbonyl carbon of the 5'-terminal AP site, which forms a Schiff base intermediate between the enzyme and the DNA (Feng et al, 1998;Piersen et al, 1996) (Figure 2). belimination breaks the 3' phosphodiester, and the enzyme-deoxyribose complex is hydrolyzed to yield the free abasic-5-phosphate residue.…”

Section: Dual Pathways Of Bermentioning

confidence: 99%

Dynamics and diversions in base excision DNA repair of oxidized abasic lesions

Demple

DeMott

2002

Oncogene

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Section: Dual Pathways Of Bermentioning

confidence: 99%

Dynamics and diversions in base excision DNA repair of oxidized abasic lesions

Demple

DeMott

2002

Oncogene

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“…46). Pol ␤ binds to both the 3Ј and 5Ј termini of short nucleotide gaps as a critical part of its function (34,46,48). At the 3Ј terminus, the highly conserved "fingers," "palm," and "thumb" polymerase subdomains cooperate to bind and catalyze nucleotidyl transfer, with the three universal aspartic acid residues coordinating the incoming Mg 2ϩ -dNTP.…”

Section: Table IImentioning

confidence: 99%

Efficient Processing of DNA Ends during Yeast Nonhomologous End Joining

Wilson¹,

Lieber²

1999

Journal of Biological Chemistry

188

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Repair of DNA double strand breaks by nonhomologous end joining (NHEJ) requires enzymatic processing beyond simple ligation when the terminal bases are damaged or not fully compatible. We transformed yeast with a series of linearized plasmids to examine the role of Pol4 (Pol IV, DNA polymerase ␤) in repair at a variety of end configurations. Mutation of POL4 did not impair DNA polymerase-independent religation of fully compatible ends and led to at most a 2-fold reduction in the frequency of joins that require only DNA polymerization. In contrast, the frequency of joins that also required removal of a 5-or 3-terminal mismatch was markedly reduced in pol4 (but not rev3, exo1, apn1, or rad1) yeast. In a chromosomal double strand break assay, pol4 mutation conferred a marked increase in sensitivity to HO endonuclease in a rad52 background, due primarily to loss of an NHEJ event that anneals with a 3-terminal mismatch. The NHEJ activity of Pol4 was dependent on its nucleotidyl transferase function, as well as its unique amino terminus. Paradoxically, in vitro analyses with oligonucleotide substrates demonstrated that although Pol4 fills gaps with displacement of mismatched but not matched 5 termini, it lacks both 5-and 3-terminal nuclease activities. Pol4 is thus specifically recruited to perform gap-filling in an NHEJ pathway that must also involve as yet unidentified nucleases.

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“…Lys72 is the primary amine responsible for Schiff base formation, although the enzyme retains some lyase activity when this amino acid is mutated. 11–14 Lys84, which is also present in the lyase active site is postulated to substitute for Lys72 in the mutated enzyme, albeit with much lower efficiency. Following Schiff base formation, dRP elimination leaves a single nucleotide gap that contains the appropriate end groups for DNA synthesis (by Pol β) and ligation to complete repair (Scheme 1).…”

Section: Introductionmentioning

confidence: 99%

Irreversible Inhibition of DNA Polymerase β by Small-Molecule Mimics of a DNA Lesion

et al. 2014

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Abasic sites are ubiquitous DNA lesions that are mutagenic and cytotoxic but are removed by the base excision repair pathway. DNA polymerase β carries out two of the four steps during base excision repair, including a lyase reaction that removes the abasic site from DNA following incision of its 5′-phosphate. DNA polymerase β is overexpressed in cancer cells and is a potential anticancer target. Recently, DNA oxidized abasic sites that are produced by potent antitumor agents were shown to inactivate DNA polymerase β. A library of small molecules whose structures were inspired by the oxidized abasic sites was synthesized and screened for their ability to irreversibly inhibit DNA polymerase β. One candidate (3a) was examined more thoroughly and modification of its phosphate backbone led to a molecule that irreversibly inactivates DNA polymerase β in solution (IC50 ~ 16 μM), and inhibits the enzyme’s lyase activity in cell lysates. A bis-acetate analogue is converted in cell lysates to 3a. The bis-acetate is more effective in cell lysates, more cytotoxic in prostate cancer cells than 3a, and potentiates the cytotoxicity of methyl methanesulfonate between 2- and 5-fold. This is the first example of an irreversible inhibitor of the lyase activity of DNA polymerase β that works synergistically with a DNA damaging agent.

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Deoxyribose Phosphate Excision by the N-Terminal Domain of the Polymerase β: The Mechanism Revisited

Cited by 33 publications

References 29 publications

Dynamics and diversions in base excision DNA repair of oxidized abasic lesions

Dynamics and diversions in base excision DNA repair of oxidized abasic lesions

Efficient Processing of DNA Ends during Yeast Nonhomologous End Joining

Irreversible Inhibition of DNA Polymerase β by Small-Molecule Mimics of a DNA Lesion

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