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TitleStructures, activity and mechanism of the Type IIS restriction endonuclease PaqCI.
Journal, issue, pagesNucleic Acids Res, Vol. 51, Issue 9, Page 4467-4487, Year 2023
Publish dateMay 22, 2023
AuthorsMadison A Kennedy / Christopher J Hosford / Caleigh M Azumaya / Yvette A Luyten / Minyong Chen / Richard D Morgan / Barry L Stoddard /
PubMed AbstractType IIS restriction endonucleases contain separate DNA recognition and catalytic domains and cleave their substrates at well-defined distances outside their target sequences. They are employed in ...Type IIS restriction endonucleases contain separate DNA recognition and catalytic domains and cleave their substrates at well-defined distances outside their target sequences. They are employed in biotechnology for a variety of purposes, including the creation of gene-targeting zinc finger and TAL effector nucleases and DNA synthesis applications such as Golden Gate assembly. The most thoroughly studied Type IIS enzyme, FokI, has been shown to require multimerization and engagement with multiple DNA targets for optimal cleavage activity; however, details of how it or similar enzymes forms a DNA-bound reaction complex have not been described at atomic resolution. Here we describe biochemical analyses of DNA cleavage by the Type IIS PaqCI restriction endonuclease and a series of molecular structures in the presence and absence of multiple bound DNA targets. The enzyme displays a similar tetrameric organization of target recognition domains in the absence or presence of bound substrate, with a significant repositioning of endonuclease domains in a trapped DNA-bound complex that is poised to deliver the first of a series of double-strand breaks. PaqCI and FokI share similar structural mechanisms of DNA cleavage, but considerable differences in their domain organization and quaternary architecture, facilitating comparisons between distinct Type IIS enzymes.
External linksNucleic Acids Res / PubMed:36987874 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.5 - 3.15 Å
Structure data

28534

8epx

EMDB-28534, PDB-8epx:
Type IIS Restriction Endonuclease PaqCI, DNA bound
Method: EM (single particle) / Resolution: 3.15 Å

PDB-8em1:
Type IIS Restriction Endonuclease PaqCI, DNA Unbound
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

Chemicals

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-HOH:
WATER

ChemComp-CA:
Unknown entry

Source
  • paucibacter aquatile (bacteria)
  • dna molecule (others)
KeywordsDNA BINDING PROTEIN / homotetramer / restriction endonuclease / DNA binding / DNA cleavage

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