Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities. [PDF]
PLoS Biology, 2016 The creation of restriction enzymes with programmable DNA-binding and -cleavage specificities has long been a goal of modern biology. The recently discovered Type IIL MmeI family of restriction-and-modification (RM) enzymes that possess a shared target ...
Scott J Callahan +6 more
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A pentose, as a cytosine nucleobase modification in Shewanella phage Thanatos genomic DNA, mediates enhanced resistance toward host restriction systems [PDF]
Applied and Environmental MicrobiologyCo-evolution of bacterial defense systems and phage counter-defense mechanisms has resulted in an intricate biological interplay between bacteriophages and their prey.
David Brandt +10 more
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Distinct Phage‐Encoded Enzymes for Substitution of Deoxythymidine by Deoxyuridine in Phage Genomes [PDF]
Advanced ScienceDNA base modification is a common strategy used by bacteriophages to evade host immune detection. A prominent example is dU‐DNA, where thymidine is globally replaced with 2′‐deoxyuridine.
Yating Li +7 more
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Structural insights into DNA sequence recognition by Type ISP restriction-modification enzymes [PDF]
Nucleic Acids Research, 2016 Engineering restriction enzymes with new sequence specificity has been an unaccomplished challenge, presumably because of the complexity of target recognition. Here we report detailed analyses of target recognition by Type ISP restriction-modification enzymes.
Manasi Kulkarni +4 more
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Recycling of protein subunits during DNA translocation and cleavage by Type I restriction-modification enzymes [PDF]
Nucleic Acids Research, 2011 The Type I restriction-modification enzymes comprise three protein subunits; HsdS and HsdM that form a methyltransferase (MTase) and HsdR that associates with the MTase and catalyses Adenosine-5'-triphosphate (ATP)-dependent DNA translocation and cleavage. Here, we examine whether the MTase and HsdR components can 'turnover' in vitro, i.e. whether they
Michelle Simons, Mark D. Szczelkun
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A model for the evolution of prokaryotic DNA restriction-modification systems based upon the structural malleability of Type I restriction-modification enzymes [PDF]
Nucleic Acids Research, 2018 Restriction Modification (RM) systems prevent the invasion of foreign genetic material into bacterial cells by restriction and protect the host's genetic material by methylation. They are therefore important in maintaining the integrity of the host genome.
Edward Kenneth Merrick Bower +6 more
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Dissociation from DNA of Type III Restriction–Modification enzymes during helicase-dependent motion and following endonuclease activity [PDF]
Nucleic Acids Research, 2012 DNA cleavage by the Type III Restriction-Modification (RM) enzymes requires the binding of a pair of RM enzymes at two distant, inversely orientated recognition sequences followed by helicase-catalysed ATP hydrolysis and long-range communication. Here we addressed the dissociation from DNA of these enzymes at two stages: during long-range communication
Julia I. Toth +3 more
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Mapping DNA cleavage by the Type ISP restriction-modification enzymes following long-range communication between DNA sites in different orientations [PDF]
Nucleic Acids Research, 2015 The prokaryotic Type ISP restriction-modification enzymes are single-chain proteins comprising an Mrr-family nuclease, a superfamily 2 helicase-like ATPase, a coupler domain, a methyltransferase, and a DNA-recognition domain. Upon recognising an unmodified DNA target site, the helicase-like domain hydrolyzes ATP to cause site release (remodeling ...
Kara van Aelst +2 more
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The single polypeptide restriction–modification enzyme LlaGI is a self-contained molecular motor that translocates DNA loops [PDF]
Nucleic Acids Research, 2009 To cleave DNA, the single polypeptide restriction-modification enzyme LlaGI must communicate between a pair of indirectly repeated recognition sites. We demonstrate that this communication occurs by a 1-dimensional route, namely unidirectional dsDNA loop translocation rightward of the specific recognition sequence 5'-CTnGAyG-3' as written (where n is ...
Rachel M. Smith +2 more
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Cloning, crystallization and preliminary X-ray diffraction analysis of an intact DNA methyltransferase of a type I restriction–modification enzyme fromVibrio vulnificus [PDF]
Acta Crystallographica Section F Structural Biology Communications, 2014 Independently of the restriction (HsdR) subunit, the specificity (HsdS) and methylation (HsdM) subunits interact with each other, and function as a methyltransferase in type I restriction–modification systems. A single gene that combines the HsdS and HsdM subunits inVibrio vulnificusYJ016 was expressed and purified.
Thi Yen Ly Huynh +2 more
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