title: Single molecule TPM analysis of the catalytic pentad mutants of Cre and Flp site-specific recombinases: contributions of the pentad residues to the pre-chemical steps of recombination.
abstract: Cre and Flp site-specific recombinase variants harboring point mutations at their conserved catalytic pentad positions were characterized using single molecule tethered particle motion (TPM) analysis. The findings reveal contributions of these amino acids to the pre-chemical steps of recombination. They suggest functional differences between positionally conserved residues in how they influence recombinase-target site association and formation of 'non-productive', 'pre-synaptic' and 'synaptic' complexes. The most striking difference between the two systems is noted for the single conserved lysine. The pentad residues in Cre enhance commitment to recombination by kinetically favoring the formation of pre-synaptic complexes. These residues in Flp serve a similar function by promoting Flp binding to target sites, reducing non-productive binding and/or enhancing the rate of assembly of synaptic complexes. Kinetic comparisons between Cre and Flp, and between their derivatives lacking the tyrosine nucleophile, are consistent with a stronger commitment to recombination in the Flp system. The effect of target site orientation (head-to-head or head-to-tail) on the TPM behavior of synapsed DNA molecules supports the selection of anti-parallel target site alignment prior to the chemical steps. The integrity of the synapse, whose establishment/stability is fostered by strand cleavage in the case of Flp but not Cre, appears to be compromised by the pentad mutations.
authors.affiliation: Department of Life Sciences and Institute of Genome Sciences, National Yang Ming University, Taipei 112, Taiwan hffan2@ym.edu.tw.
authors.forename: Hsiu-Fang
authors.initials: HF
authors.lastname: Fan
authors.affiliation: Department of Life Sciences and Institute of Genome Sciences, National Yang Ming University, Taipei 112, Taiwan.
authors.forename: Yong-Song
authors.initials: YS
authors.lastname: Cheng
authors.affiliation: Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
authors.forename: Chien-Hui
authors.initials: CH
authors.lastname: Ma
authors.affiliation: Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA hffan2@ym.edu.tw.
authors.forename: Makkuni
authors.initials: M
authors.lastname: Jayaram
mesh_terms: D019943:Amino Acid Substitution; D002384:Catalysis; D020134:Catalytic Domain / Q000235:genetics; D004254:DNA Nucleotidyltransferases / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D019426:Integrases / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D007700:Kinetics; D008958:Models, Molecular; D017354:Point Mutation; D011995:Recombination, Genetic; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D029701:Saccharomyces cerevisiae Proteins; C045073:Cre recombinase; D004254:DNA Nucleotidyltransferases; C045119:FLP recombinase; D019426:Integrases