A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi

Miyazono, Ken-ichi; Furuta, Yoshikazu; Watanabe-Matsui, Miki; Miyakawa, Takuya; Ito, Tomoko; Kobayashi, Ichizo

doi:10.1038/ncomms4178

Cited by 27 publications

(61 citation statements)

References 45 publications

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“…Besides ROS1, which recognizes and excises 5mC from the ‘natural’ G:5mC base pair, another enzyme, PabI in Pyrococcus abyssi , initially identified as a restriction enzyme, actually is a sequence-specific adenine DNA glycosylase 56 . The dimeric PabI recognizes a palindromic 5′-GTAC-3′, hydrolyses the N -glycosidic bond between the adenine base and the sugar and produces two opposing AP sites, which are subsequently cleaved by AP endonucleases to introduce a double-strand break.…”

Section: Discussionmentioning

confidence: 99%

The Carboxy-Terminal Domain of ROS1 Is Essential for 5-Methylcytosine DNA Glycosylase Activity

Hong

Hashimoto

Kow

et al. 2014

Journal of Molecular Biology

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Arabidopsis thaliana Repressor of silencing 1 (ROS1) is a multi-domain bifunctional DNA glycosylase/lyase, which excises 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) as well as thymine and 5-hydroxymethyluracil (i.e., the deamination products of 5mC and 5hmC) when paired with a guanine, leaving an apyrimidinic (AP) site that is subsequently incised by the lyase activity. ROS1 is slow in base excision and fast in AP lyase activity, indicating that the recognition of pyrimidine modifications might be a rate-limiting step. In the C-terminal half, the enzyme harbors a Helix-hairpin-Helix DNA glycosylase domain followed by a unique C-terminal domain. We show that the isolated glycosylase domain is inactive for base excision, but retains partial AP lyase activity. Addition of the C-terminal domain restores the base excision activity and increases the AP lyase activity as well. Furthermore, the two domains remain tightly associated and can be co-purified by chromatography. We suggest that the C-terminal domain of ROS1 is indispensable for the 5mC DNA glycosylase activity of ROS1.

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Section: Discussionmentioning

confidence: 99%

The Carboxy-Terminal Domain of ROS1 Is Essential for 5-Methylcytosine DNA Glycosylase Activity

Hong

Hashimoto

Kow

et al. 2014

Journal of Molecular Biology

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“…This work defines the architecture of the HTH_42 family of DNA-binding proteins (33) and an eighth class of DNA glycosylase (29,34). A unique cluster of three tandem WH motifs scaffold a putative DNA-binding channel, with only one WH (WH2) positioned to participate in the canonical helix-major groove recognition used by other WH and HTH motifs (28).…”

Section: Discussionmentioning

confidence: 99%

Structure of a DNA glycosylase that unhooks interstrand cross-links

Mullins

Warren

Bradley

et al. 2017

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

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DNA glycosylases are important editing enzymes that protect genomic stability by excising chemically modified nucleobases that alter normal DNA metabolism. These enzymes have been known only to initiate base excision repair of small adducts by extrusion from the DNA helix. However, recent reports have described both vertebrate and microbial DNA glycosylases capable of unhooking highly toxic interstrand cross-links (ICLs) and bulky minor groove adducts normally recognized by Fanconi anemia and nucleotide excision repair machinery, although the mechanisms of these activities are unknown. Here we report the crystal structure of Streptomyces sahachiroi AlkZ (previously Orf1), a bacterial DNA glycosylase that protects its host by excising ICLs derived from azinomycin B (AZB), a potent antimicrobial and antitumor genotoxin. AlkZ adopts a unique fold in which three tandem winged helix-turn-helix motifs scaffold a positively charged concave surface perfectly shaped for duplex DNA. Through mutational analysis, we identified two glutamine residues and a β-hairpin within this putative DNA-binding cleft that are essential for catalytic activity. Additionally, we present a molecular docking model for how this active site can unhook either or both sides of an AZB ICL, providing a basis for understanding the mechanisms of base excision repair of ICLs. Given the prevalence of this protein fold in pathogenic bacteria, this work also lays the foundation for an emerging role of DNA repair in bacteria-host pathogenesis.

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“…One such enzyme, Pabl, initially identified as a restriction enzyme, actually is a sequence-specific adenine DNA glycosylase, which generates damage. The dimeric Pabl recognises a palindromic 5'-GTAC-3', flips the guanine and adenine out of the DNA helix, hydrolyses the Nglycosidic bond between the adenine base and produces two opposing AP sites (Miyazono et al, 2014; Figure 4), which is subsequently cleaved by AP endonucleases to introduce a double-strand break. PabI DNA glycosylase shares no structural similarity to known DNA glycosylases.…”

Section: Pyrococcus Abyssi Pabi Sequencespecific Dna Glycosylasementioning

confidence: 99%

Base Flipping

Cheng

Roberts

2014

Encyclopedia of Life Sciences

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Base flipping involves rotation of backbone bonds in double‐stranded deoxyribonucleic acid (DNA) to expose an out‐of‐stack base, which can then be a substrate for an enzyme‐catalysed chemical reaction or for a specific protein binding interaction. The phenomenon is fully established for DNA methyltransferases, for several key DNA repair enzymes, and for a few non‐enzymatic DNA binding proteins involved in the DNA methylation and repair pathways, and is likely to prove general for enzymes or proteins that require access to unpaired, mismatched, damaged or modified bases or even undamaged and unmodified bases for specific functions. Although, detailed mechanistic information is emerging, it remains to be proven for each individual system whether base flipping is an active process in which the protein rotates the base out of the helix, or a passive one in which the protein binds to a transiently flipped base. Key Concepts: Base flipping is a key mechanism used by DNA and RNA modifying enzymes including DNA repair enzymes. DNA and RNA methyltransferases use AdoMet as the methyl donor to methylate flipped nucleotides (cytosine or adenine). The family of Fe(II)‐ and α‐ketoglutarate‐dependent dioxygenases includes members of the Tet family and AlkB‐like DNA/RNA repair enzymes. To date, six structural superfamilies of DNA repair glycosylases and newly identified (non‐repair) sequence‐specific DNA glycosylases all use base‐flipping mechanism to access the target base. Eukaryotic SRA domains share structural similarity to that of bacterial modification‐specific endonucleases (MspJI and AbaSI) in recognition of modified bases. Base flipping provides a simple mechanism by which a DNA helix can be opened during the initiation of polymerisation by DNA or RNA polymerases and their associated factors.

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A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi

Cited by 27 publications

References 45 publications

The Carboxy-Terminal Domain of ROS1 Is Essential for 5-Methylcytosine DNA Glycosylase Activity

The Carboxy-Terminal Domain of ROS1 Is Essential for 5-Methylcytosine DNA Glycosylase Activity

Structure of a DNA glycosylase that unhooks interstrand cross-links

Base Flipping

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