DNA restriction-modification enzymes articles within Nature Communications

Featured

• Article
  15 December 2022 | Open Access

  Compact Cas9d and HEARO enzymes for genome editing discovered from uncultivated microbes

  Programmable, RNA-guided nucleases are diverse enzymes that have been repurposed for biotechnological applications. Here, the authors mine an extensive genome-resolved metagenomics database and identified uncharacterized families of RNA-guided, compact nucleases.

  • Daniela S. Aliaga Goltsman
  • , Lisa M. Alexander
  •  & Christopher T. Brown

• Article
  09 November 2022 | Open Access

  Nicking mechanism underlying the DNA phosphorothioate-sensing antiphage defense by SspE

  SspABCD–SspE is a phosphorothioation-sensing bacterial defence system. Here, authors find that SspE exploits DNA phosphorothioation-binding preference to modulate its biochemical activities for the self/nonself discrimination and phage resistance.

  • Haiyan Gao
  • , Xinqi Gong
  •  & Lianrong Wang

• Article
  20 November 2020 | Open Access

  Structural asymmetry governs the assembly and GTPase activity of McrBC restriction complexes

  The bacterial defense system McrBC is a two-component motor-driven nuclease complex that cleaves foreign DNA. Here, the authors present the structures of the GTP-specific AAA + motor protein McrB and two McrBC complexes and discuss the molecular mechanism of how McrC binding stimulates McrB GTP hydrolysis.

  • Yiming Niu
  • , Hiroshi Suzuki
  •  & Joshua S. Chappie

• Article
  29 April 2019 | Open Access

  Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9

  The RNA-guided DNA endonuclease Cas9 from Corynebacterium diphtheriae (CdCas9) recognizes a promiscuous protospacer adjacent motif (PAM). Here the authors provide insights into the CdCas9-mediated PAM recognition mechanism by determining the 2.9 Å crystal structure of CdCas9 in complex with the guide RNA and its target DNA, which is of interest for engineering of CRISPR-Cas9 genome-editor nucleases.

  • Seiichi Hirano
  • , Omar O. Abudayyeh
  •  & Osamu Nureki

• Article
  08 November 2018 | Open Access

  Structural basis for the recognition of sulfur in phosphorothioated DNA

  DNA phosphorothioation (PT-DNA) is a DNA backbone sulfur modification that is recognized by the type-IV restriction endonuclease ScoMcrA. Here the authors provide insights into sulfur recognition by solving the crystal structure of the PT-DNA bound sulfur-binding domain (SBD) from ScoMcrA and they further show that SBD homologs are widely spread among prokaryotes.

  • Guang Liu
  • , Wencheng Fu
  •  & Xinyi He

• Article
  28 April 2017 | Open Access

  Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity

  Cytidine deaminases are evolutionarily conserved enzymes that edit genomes by deaminating cytidine to uridine. Here the authors present the crystal structure of APOBEC3A with a single-stranded DNA substrate bound in the active site to shed light on the mechanism and specificity of substrate recognition.

  • Takahide Kouno
  • , Tania V. Silvas
  •  & Celia A. Schiffer

• Article | 03 May 2011

  Two-dimensional enzyme diffusion in laterally confined DNA monolayers

  Little is known about the effects of molecular crowding and confinement on biomolecule function. Castronovoet al. investigate the reactions of restriction enzymes with DNA confined in bushy matrices and find that the enzymes enter at the side of the matrix before diffusing two-dimensionally.

  • Matteo Castronovo
  • , Agnese Lucesoli
  •  & Giacinto Scoles