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[[File:Classification_of_site-specific_recombinases_according_to_mechanism.png|thumb|755x755px|'''Tyr- and Ser-SSRs from prokaryotes''' (phages; grey) '''and eukaryotes''' (yeasts; brown); a comprehensive overview (including references) can be found in.<ref name="turan">{{cite journal|last2=Bode|first2=J.|year=2011|title=Site-specific recombinases: From tag-and-target- to tag-and-exchange-based genomic modifications|journal=The FASEB Journal|volume=25|issue=12|pages=4088–107|doi=10.1096/fj.11-186940|pmid=21891781|last1=Turan|first1=S.|doi-access=free |s2cid=7075677}}</ref>]]
The founding member of the YR family is the [[lambda integrase]], encoded by [[Bacteriophage| bacteriophage λ]], enabling the integration of phage DNA into the bacterial genome. A common feature of this class is a conserved tyrosine nucleophile attacking the scissile DNA-phosphate to form a 3'-phosphotyrosine linkage. Early members of the SR family are closely related [[wiktionary:resolvase|resolvase]] / [[DNA invertase]]s from the bacterial [[transposons]] Tn3 and γδ, which rely on a catalytic serine responsible for attacking the scissile phosphate to form a 5'-phosphoserine linkage. These undisputed facts, however, were compromised by a good deal of confusion at the time other members entered the scene, for instance the YR recombinases [[Cre recombinase|Cre]] and [[FLP-FRT recombination|Flp]] (capable of integration, excision/resolution as well as inversion), which were nevertheless welcomed as new members of the "integrase family". The converse examples are PhiC31 and related SRs, which were originally introduced as resolvase/invertases although, in the absence of auxiliary factors, integration is their only function. Nowadays the standard activity of each enzyme determines its classification reserving the general term "recombinase" for family members which, per se, comprise all three routes, INT, RES and INV:
Our table extends the selection of the conventional SSR systems and groups these according to their performance. All of these enzymes recombine two target sites, which are either identical (subfamily A1) or distinct (phage-derived enzymes in A2, B1 and B2).<ref name="turan" /> Whereas for A1 these sites have individual designations ("''FRT''" in case of Flp-recombinase, [[Cre-Lox recombination#''loxP'' site|''loxP'']] for Cre-recombinase), the terms "''att''P" and "''att''B" (attachment sites on the phage and bacterial part, respectively) are valid in the other cases. In case of subfamily A1 we have to deal with short (usually 34 bp-) sites consisting of two (near-)identical 13 bp arms (arrows) flanking an 8 bp spacer (the crossover region, indicated by red line doublets).<ref>{{cite journal |doi=10.1515/BC.2000.103 |title=The Transgeneticists Toolbox: Novel Methods for the Targeted Modification of Eukaryotic Genomes |year=2000 |last1=Bode |first1=Jürgen |last2=Schlake |first2=Thomas |last3=Iber |first3=Michaela |last4=Schübeler |first4=Dirk |last5=Seibler |first5=Jost |last6=Snezhkov |first6=Evgeney |last7=Nikolaev |first7=Lev |journal=Biological Chemistry |volume=381 |issue=9–10 |pmid=11076013 |pages=801–13|s2cid=36479502 }}</ref> Note that for Flp there is an alternative, 48 bp site available with three arms, each accommodating a Flp unit (a so-called "protomer"). ''att''P- and ''att''B-sites follow similar architectural rules, but here the arms show only partial identity (indicated by the broken lines) and differ in both cases. These features account for relevant differences:
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