The integrase family of recombinases: organization and function of the active site

Abstract

SummaryThe integrase family of site-speci®c recombinases (also called the tyrosine recombinases) mediate a wide range of biological outcomes by the sequential exchange of two pairs of DNA strands at de®ned phosphodiester positions.Thereactionproducesarecombinantarrangement of the DNA sequences¯anking the cross-over region. The crystal structures of four integrase family members have revealed very similar three-dimensional protein folds that belie the large diversity in amino acid sequences among them. The active sites are similar in organization to those seen in structures of eukaryotic type IB topoisomerases, and conservation of catalytic mechanism is expected. The crystal structures, combined with previous biochemical knowledge, allow the re®nement of models for recombination and the assignment of catalytic function to the active site residues. However, each system has its own peculiarities, and the exact sequence of events that allows the reaction to proceed from the ®rst exchange reaction to the second is still unclear for at least some family members.

MicroPET imaging of Cre–loxP-mediated conditional activation of a herpes simplex virus type 1 thymidine kinase reporter gene

“…This is usually achieved by the use of site-specific recombinases. 1,2 Site-specific recombinases are useful reagents for genomic manipulations that allow for tissue-specific or developmental stage-specific modulation of gene expression in knockout and transgenic mice. 3 The four members of the family of site-specific recombinases (Cre, XerD, HP1 and Flp) recognize a relatively short, unique nucleic acid sequence, which serves for both recognition and recombination.…”

“…3 The four members of the family of site-specific recombinases (Cre, XerD, HP1 and Flp) recognize a relatively short, unique nucleic acid sequence, which serves for both recognition and recombination. 1,2,4 One of the most widely used site-specific recombinases is the enzyme Cre recombinase, from the bacteriophage P1. Cre recombinase recognizes DNA at a 34 bp sequence called loxP, which consists of two 13 bp palindromic sequences flanking an 8 bp core sequence.…”

Predicting Knot or Catenane Type of Site-Specific Recombination Products

“…The DNA-protein complex then proceeds through an intermediary structure (a Holliday junction) before repeating the process with the other two DNA backbones. 17,49 Most tyrosine recombinases, including Flp, λ Int and Cre, tolerate varying number of supercoils outside of the recombinase complex. However, there are exceptions, most notably XerCD, which trap a fixed number of supercoils using accessory proteins before initiating cleavage.…”

Comparison of the structure–activity relationships of the integron-associated recombination sites attI3 and attI1 reveals common features

“…Members of the tyrosine recombinase or integrase superfamily use a tyrosine residue as the nucleophile in their strand exchange reactions and share similarities in a large C-terminal domain of~180 aa which contains six conserved residues that are part of the catalytic site (NunesDüby et al, 1998;Grindley, 1997;Yang & Mizuuchi, 1997;Grainge & Jayaram, 1999). A few members of the tyrosine 3Present address:…”

“…Some of these integrons are part of the mobile gene pool (Stokes & Hall, 1989;Arakawa et al, 1995;Recchia & Hall, 1995; Hochhut et al, 2001), some are a feature of a bacterial chromosome (Rowe-Magnus et al, 2001;Drouin et al, 2002) and the location of others has not been established (Nield et al, 2001;Vaisvila et al, 2001). Known members of the IntI family share as little as 35 % sequence identity (see Collis et al, 2002b for a compilation), indicating a long evolutionary history for this natural gene cloning system.Members of the tyrosine recombinase or integrase superfamily use a tyrosine residue as the nucleophile in their strand exchange reactions and share similarities in a large C-terminal domain of~180 aa which contains six conserved residues that are part of the catalytic site (NunesDüby et al, 1998;Grindley, 1997;Yang & Mizuuchi, 1997;Grainge & Jayaram, 1999). A few members of the tyrosine 3Present address:…”