Crystal structure of the site-specific recombinase, XerD

Subramanya, Hosahalli; Arciszewska, Lidia K.; Baker, Richard; Bird, Louise E.; Sherratt, David J.; Wigley, Dale B.

doi:10.1093/emboj/16.17.5178

Cited by 199 publications

(170 citation statements)

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“…Since none of these "reference integrases" had been crystallized as a co-complex with its DNA target, we had to deduce the amino acid positions that might be involved in DNA recognition from the x-ray structure of ␥␦ resolvase, which was crystallized bound to its target sequence (24). After the publication of the x-ray structures of Cre (18) and XerD (21), both proteins were included in the alignment of the secondary structures and confirmed the match between x-ray structure and structure prediction. For each protein, we checked to what extent those secondary structure elements, which had been predicted, matched with those secondary structure elements that were deduced from the x-ray structures.…”

Section: Discussionmentioning

confidence: 99%

“…structure with respect to protein function focused on the active sites of the synaptic complex and on the mechanism of Cre-loxP site-specific recombination and less on the target recognition specificity of the protein (18). The crystals of the catalytic cores of HP1 and integrase (19,20), or the crystal of XerD (21), give no final answer to the question of how these proteins specifically recognize their target sequences because these proteins had been crystallized without their target DNA.…”

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confidence: 99%

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Cre Mutants with Altered DNA Binding Properties

Hartung

Kisters‐Woike

1998

Journal of Biological Chemistry

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Cre Mutants with Altered DNA Binding Properties

Hartung

Kisters‐Woike

1998

Journal of Biological Chemistry

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“…Integrative and conjugative elements (ICEs) can in part be identified by the presence of signature proteins associated with core functions of integration into and excision from the host genome (recombinase), replication as an extrachromosomal element (polymerase), and conjugation from the host to recipient cell (conjugation) (Ghinet et al, 2011). Analysis of the Glutamicibacter JB182 RUSTI region revealed homologs of each of these protein classes ( Figure 3A): a recombinase of the site-specific tyrosine recombinase XerD family (Ga0099663_102762) (Subramanya et al, 1997), a hexameric ATPase conjugation protein of the VirD4/TraG/TraD family (Ga0099663_102784) (Hamilton et al, 2000), and a homolog of the bi-functional primase-polymerase DNA replication protein family (Ga0099663_102766). Interestingly, Actinobacterial ICE systems typically use conjugation apparatus belonging to the SpoIIE/FtsK family, which allows transfer of double-stranded DNA (te Poele et al, 2008;Bordeleau et al, 2012).…”

Section: Iron Acquisition Hgtmentioning

confidence: 99%

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

Bonham

Wolfe

Dutton

2016

Preprint

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Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that HGT is prevalent in cheese rind microbiomes, and that identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities.

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“…Two overlapping subsets of this ensemble are used for integrative and excisive recombination (8,14). This complexity facilitates the unique directional control of recombination that is characteristic of Int and related heterobivalent recombinases.Critical insight into the mechanisms of recombination has been provided by crystal and NMR structures of Int family members (15)(16)(17)(18)(19)(20) and each of the individual elements of the intasome. These include x-ray crystal structures of Fis protein (21-23), IHF bound to its cognate DNA site (24), the unliganded catalytic domain of (25), the DNA-liganded carboxyl-terminal domain of (26) and the NMR structures of the amino-terminal domains of Int (27) and Xis (28).…”

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confidence: 99%

Identification of the λ integrase surface that interacts with Xis reveals a residue that is also critical for Int dimer formation

Warren

Sam²,

Manley³

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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Lambda integrase (Int) is a heterobivalent DNA-binding protein that together with the accessory DNA-bending proteins IHF, Fis, and Xis, forms the higher-order protein-DNA complexes that execute integrative and excisive recombination at specific loci on the chromosomes of phage and its Escherichia coli host. The large carboxyl-terminal domain of Int is responsible for binding to core-type DNA sites and catalysis of DNA cleavage and ligation reactions. The small amino-terminal domain (residues 1-70), which specifies binding to arm-type DNA sites distant from the regions of strand exchange, consists of a three-stranded ␤-sheet, proposed to recognize the cognate DNA site, and an ␣-helix. We report here that a site on this ␣-helix is critical for both homomeric interactions between Int protomers and heteromeric interactions with Xis. The mutant E47A, which was identified by alanine-scanning mutagenesis, abolishes interactions between Int and Xis bound at adjacent binding sites and reduces interactions between Int protomers bound at adjacent arm-type sites. Concomitantly, this residue is essential for excisive recombination and contributes to the efficiency of the integrative reaction. NMR titration data with a peptide corresponding to Xis residues 57-69 strongly suggest that the carboxyl-terminal tail of Xis and the ␣-helix of the aminoterminal domain of Int comprise the primary interaction surface for these two proteins. The use of a common site on Int for both homotypic and heterotypic interactions fits well with the complex regulatory patterns associated with this site-specific recombination reaction.T he bacteriophage -encoded integrase (Int) belongs to a subgroup of the tyrosine recombinase family known as the heterobivalent recombinases (1, 2). These recombinases catalyze reactions that are distinguished from other pathways of sitespecific rearrangement and movement of DNA by their directionality. This feature is built on the ability of these recombinases to simultaneously bind and bridge two distinct and well separated DNA-binding sites (3-5). Int binds with high affinity to arm-type DNA sites by means of a small amino-terminal domain (residues 1-70) whereas it binds with lower affinity to core-type sites by means of a larger carboxyl-terminal domain (residues 75-356), which also executes DNA strand cleavage and ligation. Bridging between arm and core sites is facilitated by DNA bends induced by accessory proteins (IHF, Xis, and Fis) bound to DNA sites located between the arm-and core-type sequences (5-9). This ensemble of DNA-bending-and DNA-bridging-proteins forms the large recombinogenic complexes that confer directionality on the recombination reaction. In this article we show that formation of both the Int-Xis and Int-Int complexes, key elements in the structure and function of the higher-order recombinogenic structures, depends on a common site in the amino-terminal domain of Int.The Int recombinase catalyzes the integration and excision of viral DNA into and out of the chromosome of its Escherichia coli...

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Crystal structure of the site-specific recombinase, XerD

Cited by 199 publications

References 58 publications

Cre Mutants with Altered DNA Binding Properties

Cre Mutants with Altered DNA Binding Properties

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

Identification of the λ integrase surface that interacts with Xis reveals a residue that is also critical for Int dimer formation

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