Type I restriction endonucleases are true catalytic enzymes

Bianco, Piero R.; Xu, Cuiling; Chi, Min

doi:10.1093/nar/gkp195

Cited by 13 publications

(33 citation statements)

References 38 publications

(111 reference statements)

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“…In a typical reaction, approximately 80 data points were fit to a linear curve. The rate of ATP hydrolysis at each ATP concentration was calculated by multiplying the slope of the line by 159 (the change in absorbance of NADH per unit time) [49]. In the optimization experiments (Fig.…”

Section: Methodsmentioning

confidence: 99%

ATP binding and hydrolysis by Saccharomyces cerevisiae Msh2–Msh3 are differentially modulated by mismatch and double-strand break repair DNA substrates

et al. 2014

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In Saccharomyces cerevisiae, Msh2-Msh3-mediated mismatch repair (MMR) recognizes and targets insertion/deletion loops for repair. Msh2-Msh3 is also required for 3′ non-homologous tail removal (3′NHTR) in double-strand break repair. In both pathways, Msh2-Msh3 binds double-strand/single-strand junctions and initiates repair in an ATP-dependent manner. However, we recently demonstrated that the two pathways have distinct requirements with respect to Msh2-Msh3 activities. We identified a set of aromatic residues in the nucleotide binding pocket (FLY motif) of Msh3 that, when mutated, disrupted MMR, but left 3′ NHTR largely intact. One of these mutations, msh3Y942A, was predicted to disrupt the nucleotide sandwich and allow altered positioning of ATP within the pocket. To develop a mechanistic understanding of the differential requirements for ATP binding and/or hydrolysis in the two pathways, we characterized Msh2-Msh3 and Msh2-msh3Y942A ATP binding and hydrolysis activities in the presence of MMR and 3′ NHTR DNA substrates. We observed distinct, substrate-dependent ATP hydrolysis and nucleotide turnover by Msh2-Msh3, indicating that the MMR and 3′ NHTR DNA substrates differentially modify the ATP binding/hydrolysis activities of Msh2-Msh3. Msh2-msh3Y942A retained the ability to bind DNA and ATP but exhibited altered ATP hydrolysis and nucleotide turnover. We propose that both ATP and structure-specific repair substrates cooperate to direct Msh2-Msh3-mediated repair and suggest an explanation for the msh3Y942A separation-of-function phenotype.

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Section: Methodsmentioning

confidence: 99%

ATP binding and hydrolysis by Saccharomyces cerevisiae Msh2–Msh3 are differentially modulated by mismatch and double-strand break repair DNA substrates

et al. 2014

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“…All SF2 helicases are capable of binding nucleic acids and have nucleic acid stimulated NTPase activity (3). However, some families, such as type I restriction enzymes and RIG-I do not perform the canonical helicase reaction of unwinding duplex NA (132)). DEAD-box family members unwind RNA, but without translocation (34).…”

Section: Discussionmentioning

confidence: 99%

“…Type I restriction enzymes or endonucleases (T1RE) are part of the restriction-modification system in bacteria (131, 132). They protect the bacterial genome against cleavage by methylating target sequences and restriction of foreign DNA.…”

Section: Familiesmentioning

confidence: 99%

“…They are encoded by the Host Specificity for DNA ( hsdS, hsdM , and hsdR genes (136). A dimer of two R 2 M 2 S holoenzymes, with each bound to a target sequence, is the active form of the enzyme for restriction of the DNA (132). …”

Section: Familiesmentioning

confidence: 99%

“…HsdM and HsdS are sufficient for methylation (136). When the target sequence is unmethylated, HsdR restricts the foreign DNA (132). …”

Section: Familiesmentioning

confidence: 99%

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Superfamily 2 helicases

Byrd

Raney²

2012

Front Biosci

115

118

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Superfamily 2 helicases are involved in all aspects of RNA metabolism, and many steps in DNA metabolism. This review focuses on the basic mechanistic, structural and biological properties of each of the families of helicases within superfamily 2. There are ten separate families of helicases within superfamily 2, each playing specific roles in nucleic acid metabolism. The mechanisms of action are diverse, as well as the effect on the nucleic acid. Some families translocate on single-stranded nucleic acid and unwind duplexes, some unwind double-stranded nucleic acids without translocation, and some translocate on double-stranded or single-stranded nucleic acids without unwinding.

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Restriction–Modification Systems as a Barrier for Genetic Manipulation of Staphylococcus aureus

Sadykov

2014

Methods in Molecular Biology

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Genetic manipulation is a powerful approach to study fundamental aspects of bacterial physiology, metabolism, and pathogenesis. Most Staphylococcus aureus strains are remarkably difficult to genetically manipulate as they possess strong host defense mechanisms that protect bacteria from cellular invasion by foreign DNA. In S. aureus these bacterial "immunity" mechanisms against invading genomes are mainly associated with restriction-modification systems. To date, prokaryotic restriction-modification systems are classified into four different types (Type I-IV), all of which have been found in the sequenced S. aureus genomes. This chapter describes the roles, classification, mechanisms of action of different types of restriction-modification systems and the recent advances in the biology of restriction and modification in S. aureus.

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Type I restriction endonucleases are true catalytic enzymes

Cited by 13 publications

References 38 publications

ATP binding and hydrolysis by Saccharomyces cerevisiae Msh2–Msh3 are differentially modulated by mismatch and double-strand break repair DNA substrates

ATP binding and hydrolysis by Saccharomyces cerevisiae Msh2–Msh3 are differentially modulated by mismatch and double-strand break repair DNA substrates

Superfamily 2 helicases

Restriction–Modification Systems as a Barrier for Genetic Manipulation of Staphylococcus aureus

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