Similarities and differences among 105 members of the Int family of site-specific recombinases

Abstract

Alignments of 105 site-specific recombinases belonging to the Int family of proteins identified extended areas of similarity and three types of structural differences. In addition to the previously recognized conservation of the tetrad R-H-R-Y, located in boxes I and II, several newly identified sequence patches include charged amino acids that are highly conserved and a specific pattern of buried residues contributing to the overall protein fold. With some notable exceptions, unconserved regions correspond to loops in the crystal structures of the catalytic domains of lambda Int (Int c170) and HP1 Int (HPC) and of the recombinases XerD and Cre. Two structured regions also harbor some pronounced differences. The first comprises beta-sheets 4 and 5, alpha-helix D and the adjacent loop connecting it to alpha-helix E: two Ints of phages infecting thermophilic bacteria are missing this region altogether; the crystal structures of HPC, XerD and Cre reveal a lack of beta-sheets 4 and 5; Cre displays two additional beta-sheets following alpha-helix D; five recombinases carry large insertions. The second involves the catalytic tyrosine and is seen in a comparison of the four crystal structures. The yeast recombinases can theoretically be fitted to the Int fold, but the overall differences, involving changes in spacing as well as in motif structure, are more substantial than seen in most other proteins. The phenotypes of mutations compiled from several proteins are correlated with the available structural information and structure-function relationships are discussed. In addition, a few prokaryotic and eukaryotic enzymes with partial homology with the Int family of recombinases may be distantly related, either through divergent or convergent evolution. These include a restriction enzyme and a subgroup of eukaryotic RNA helicases (D-E-A-D proteins).

Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome

“…S7B). Notably, as in the case of the Cre and Flp recombinases, ACV ORF33 possesses an active-site tryptophan instead of the histidine residue found in the active sites of the vast majority of tyrosine recombinases (27,28). The closest homolog of ORF33 (with the same domain organization) is encoded in the genome of the ammonia-oxidizing soil thaumarchaeon Candidatus Nitrosopumilus koreensis, whereas weak hits to proteins from other organisms are confined to the catalytic domain.…”

Analysis of Insertion into Secondary Attachment Sites by Phage λ and by int Mutants with Altered Recombination Specificity

“…2,4 Replacement of E319 by any of several amino acids (including glycine), whose only common element is loss of a negative charge, increases recombination of HK022 sites. 22 These considerations suggest that E319 does not directly contact core site DNA, but instead affects site recognition indirectly, perhaps through interaction with residues that themselves contact DNA.…”

“…Family members are characterized by an invariant tyrosine residue that becomes transiently joined to the DNA backbone during strand cleavage and by several other highly conserved amino acids that activate strand cleavage, exchange, and rejoining. 2 Comparison of the three-dimensional structures of four widely diverged family members reveals considerable conservation of structure around the catalytic center. 3 -6 Phage l Int (Int-l) recognizes two distinct sequence motifs, the arm-type and the core-type binding sites (Figure 1).…”

Interstrain transfer of the large pathogenicity island (PAPI-1) of Pseudomonas aeruginosa

“…1 A). This integrase belongs to the tyrosine recombinase family that catalyzes a sitespecific recombination between a chromosomal site (attB) and a similar or identical sequence (attP) found on mobile genetic elements including bacteriophages, insertion sequences, and transposons (15,16). To explore the biological functions of PAPI-1 int, we generated an int deletion mutant of strain PA14 (PA14⌬int) and examined the excision of PAPI-1 in this mutant strain.…”