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TitleMechanisms of Cre recombinase synaptic complex assembly and activation illuminated by Cryo-EM.
Journal, issue, pagesNucleic Acids Res, Vol. 50, Issue 3, Page 1753-1769, Year 2022
Publish dateFeb 22, 2022
AuthorsKye Stachowski / Andrew S Norris / Devante Potter / Vicki H Wysocki / Mark P Foster /
PubMed AbstractCre recombinase selectively recognizes DNA and prevents non-specific DNA cleavage through an orchestrated series of assembly intermediates. Cre recombines two loxP DNA sequences featuring a pair of ...Cre recombinase selectively recognizes DNA and prevents non-specific DNA cleavage through an orchestrated series of assembly intermediates. Cre recombines two loxP DNA sequences featuring a pair of palindromic recombinase binding elements and an asymmetric spacer region, by assembly of a tetrameric synaptic complex, cleavage of an opposing pair of strands, and formation of a Holliday junction intermediate. We used Cre and loxP variants to isolate the monomeric Cre-loxP (54 kDa), dimeric Cre2-loxP (110 kDa), and tetrameric Cre4-loxP2 assembly intermediates, and determined their structures using cryo-EM to resolutions of 3.9, 4.5 and 3.2 Å, respectively. Progressive and asymmetric bending of the spacer region along the assembly pathway enables formation of increasingly intimate interfaces between Cre protomers and illuminates the structural bases of biased loxP strand cleavage order and half-the-sites activity. Application of 3D variability analysis to the tetramer data reveals constrained conformational sampling along the pathway between protomer activation and Holliday junction isomerization. These findings underscore the importance of protein and DNA flexibility in Cre-mediated site selection, controlled activation of alternating protomers, the basis for biased strand cleavage order, and recombination efficiency. Such considerations may advance development of site-specific recombinases for use in gene editing applications.
External linksNucleic Acids Res / PubMed:35104890 / PubMed Central
MethodsEM (single particle)
Resolution3.23 - 4.48 Å
Structure data

24470

7rhx

EMDB-24470, PDB-7rhx:
Cryo-EM structure of precleavage Cre tetrameric complex
Method: EM (single particle) / Resolution: 3.23 Å

24471

7rhy

EMDB-24471, PDB-7rhy:
Cre recombinase mutant (D33A/A36V/R192A) in complex with loxA DNA hairpin
Method: EM (single particle) / Resolution: 3.91 Å

24472

7rhz

EMDB-24472, PDB-7rhz:
Heterodimer of Cre recombinase mutants D33A/A36V/R192A and R72E/L115D/R119D in complex with loxP DNA.
Method: EM (single particle) / Resolution: 4.48 Å

Source
  • escherichia phage p1 (virus)
KeywordsRECOMBINATION/DNA / Cre / recombinase / tetramer / loxP / RECOMBINATION-DNA complex / monomer / hairpin / dimer

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