Purification and characterization of a novel deoxyinosine-specific enzyme, deoxyinosine 3' endonuclease, from Escherichia coli.

Yao, Min; Hatahet, Zafer; Melamede, Robert J.; Kow, Yoke W.

doi:10.1016/s0021-9258(17)34002-4

Cited by 112 publications

(50 citation statements)

References 31 publications

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“…Endonuclease V (endo V) was initially discovered in E.coli as a DNA repair enzyme because it nicked DNA that was treated with acid, exposed to osmium tetroxide or irradiated with ultraviolet light (16,17). A series of biochemical analyses reveals that endo V is active toward several deaminated DNA bases; including uridine, inosine and xanthine (18)(19)(20)(21)(22)(23). The cleavage site generated by endo V is at the second phosphodiester bond 3 0 to a lesion (18,23).…”

Section: Introductionmentioning

confidence: 99%

“…A series of biochemical analyses reveals that endo V is active toward several deaminated DNA bases; including uridine, inosine and xanthine (18)(19)(20)(21)(22)(23). The cleavage site generated by endo V is at the second phosphodiester bond 3 0 to a lesion (18,23). Endo V is also active toward AP and urea sites (18,23), base pair mismatches (23,24), Flap and pseudo Y structures (25) and small insertions/deletions (25,26).…”

Section: Introductionmentioning

confidence: 99%

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Cleavage of deoxyoxanosine-containing oligodeoxyribonucleotides by bacterial endonuclease V

Hitchcock¹

2004

Nucleic Acids Research

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Oxanine (O) is a deamination product derived from guanine with the nitrogen at the N1 position substituted by oxygen. Cytosine, thymine, adenine, guanine as well as oxanine itself can be incorporated by Klenow Fragment to pair with oxanine in a DNA template with similar efficiency, indicating that oxanine in DNA may cause various mutations. As a nucleotide, deoxyoxanosine may substitute for deoxyguanosine to complete a primer extension reaction. Endonuclease V, an enzyme known for its enzymatic activity on uridine-, inosine- and xanthosine-containing DNA, can cleave oxanosine-containing DNA at the second phosphodiester bond 3' to the lesion. Mg2+ or Mn2+, and to a small extent Co2+ or Ni2+, support the oxanosine-containing DNA cleavage activity. All four oxanosine-containing base pairs (A/O, T/O, C/O and G/O) were cleaved with similar efficiency. The cleavage of double-stranded oxanosine-containing DNA was approximately 6-fold less efficient than that of double-stranded inosine-containing DNA. Single-stranded oxanosine-containing DNA was cleaved with a lower efficiency as compared with double-stranded oxanosine-containing DNA. A metal ion enhances the binding of endonuclease V to double-stranded and single-stranded oxanosine-containing DNA 6- and 4-fold, respectively. Hypothetic models of oxanine-containing base pairs and deaminated base recognition mechanism are presented.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Cleavage of deoxyoxanosine-containing oligodeoxyribonucleotides by bacterial endonuclease V

Hitchcock¹

2004

Nucleic Acids Research

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“…Endonuclease V (Nfi/EndoV) is another enzyme performing the cleavage of lesion-containing DNA. Nfi was originally isolated from E. coli in 1977 [ 197 ] and characterized as a Hx-specific enzyme in 1994 [ 198 ]. Nfi homologs are present in all domains of life and show activity towards DNA and RNA substrates.…”

Section: Alternative Excision Repair Pathway: An Unusual Variation On the Endonuclease Themementioning

confidence: 99%

“…Further steps of the Nfi-mediated repair remain unclear, since the extension of the 3′-OH terminus will not lead to damage removal. The purified E. coli Nfi protein exhibits activities towards U, Hx, Xan, urea [ 198 ] and towards regular DNA containing mismatched bases, flap and pseudo-Y structures [ 199 , 200 ]. The Nfi-catalyzed activity towards Hx is ~20-fold higher than with any other DNA substrate [ 200 ].…”

Section: Alternative Excision Repair Pathway: An Unusual Variation On the Endonuclease Themementioning

confidence: 99%

Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases

Prorok

Grin

Matkarimov

et al. 2021

Cells

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It was proposed that the last universal common ancestor (LUCA) evolved under high temperatures in an oxygen-free environment, similar to those found in deep-sea vents and on volcanic slopes. Therefore, spontaneous DNA decay, such as base loss and cytosine deamination, was the major factor affecting LUCA’s genome integrity. Cosmic radiation due to Earth’s weak magnetic field and alkylating metabolic radicals added to these threats. Here, we propose that ancient forms of life had only two distinct repair mechanisms: versatile apurinic/apyrimidinic (AP) endonucleases to cope with both AP sites and deaminated residues, and enzymes catalyzing the direct reversal of UV and alkylation damage. The absence of uracil–DNA N-glycosylases in some Archaea, together with the presence of an AP endonuclease, which can cleave uracil-containing DNA, suggests that the AP endonuclease-initiated nucleotide incision repair (NIR) pathway evolved independently from DNA glycosylase-mediated base excision repair. NIR may be a relic that appeared in an early thermophilic ancestor to counteract spontaneous DNA damage. We hypothesize that a rise in the oxygen level in the Earth’s atmosphere ~2 Ga triggered the narrow specialization of AP endonucleases and DNA glycosylases to cope efficiently with a widened array of oxidative base damage and complex DNA lesions.

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“…In eukaryotes, U:G mismatches generated as a result of cytosine deamination are also repaired by the mismatch repair pathway (21). In prokaryotes, endonuclease V (EndoV) cleaves the second phosphodiester bond on the 3′ side of deoxyinosine (dI: 2′-deoxynucleotide form of Hx) in double-stranded DNA, which has been proposed to initiate an alternative excision repair pathway for deaminated purine bases (22)(23)(24).…”

mentioning

confidence: 99%

Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q

Shi

Moeller

Banerjee

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Spontaneous deamination of DNA cytosine and adenine into uracil and hypoxanthine, respectively, causes C to T and A to G transition mutations if left unrepaired. Endonuclease Q (EndoQ) initiates the repair of these premutagenic DNA lesions in prokaryotes by cleaving the phosphodiester backbone 5′ of either uracil or hypoxanthine bases or an apurinic/apyrimidinic (AP) lesion generated by the excision of these damaged bases. To understand how EndoQ achieves selectivity toward these structurally diverse substrates without cleaving undamaged DNA, we determined the crystal structures of Pyrococcus furiosus EndoQ bound to DNA substrates containing uracil, hypoxanthine, or an AP lesion. The structures show that substrate engagement by EndoQ depends both on a highly distorted conformation of the DNA backbone, in which the target nucleotide is extruded out of the helix, and direct hydrogen bonds with the deaminated bases. A concerted swing motion of the zinc-binding and C-terminal helical domains of EndoQ toward its catalytic domain allows the enzyme to clamp down on a sharply bent DNA substrate, shaping a deep active-site pocket that accommodates the extruded deaminated base. Within this pocket, uracil and hypoxanthine bases interact with distinct sets of amino acid residues, with positioning mediated by an essential magnesium ion. The EndoQ–DNA complex structures reveal a unique mode of damaged DNA recognition and provide mechanistic insights into the initial step of DNA damage repair by the alternative excision repair pathway. Furthermore, we demonstrate that the unique activity of EndoQ is useful for studying DNA deamination and repair in mammalian systems.

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Purification and characterization of a novel deoxyinosine-specific enzyme, deoxyinosine 3' endonuclease, from Escherichia coli.

Cited by 112 publications

References 31 publications

Cleavage of deoxyoxanosine-containing oligodeoxyribonucleotides by bacterial endonuclease V

Cleavage of deoxyoxanosine-containing oligodeoxyribonucleotides by bacterial endonuclease V

Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases

Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q

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