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Chapter 6 : A Structural View of Tyrosine Recombinase Site-Specific Recombination

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Abstract:

The DNA recombination sequences where recombinase binding and strand exchange take place are referred to as the core recombination sites. These sites are composed of two recombinase binding elements (RBEs) arranged as inverted repeats surrounding a central strand exchange or crossover region. A parallel alignment of sites is defined as one in which the DNA helical axes of the crossover regions form an angle less than 90° with respect to the crossover sequence directions. The helices, which carry the tyrosine nucleophiles, are provided into the neighboring subunits, where they participate in the formation of shared active sites between pairs of adjacent subunits. The mechanistic implications of this alternative arrangement are discussed in this chapter. The author summarizes what one has learned from the crystal structures of recombinase-HJ intermediates and then relates the structural models to recent experimental data in the tyrosine recombinase family. A study by Arciszewska et al. demonstrated using permanganate oxidation sensitivity of thymine bases that the recombinase-bound form of the junction is clearly distinct from the stacked-X conformation. Voziyanov et al. presented a thorough geometric treatment of the tyrosine recombinase reaction pathway model that focuses on the relative rotation and positioning of the reaction components as the reaction proceeds. The current understanding of the tyrosine recombinase site-specific recombination pathway in the three-dimensional sense has been guided primarily by structures of reaction intermediates in the Cre-P system.

Citation: Van Duyne G. 2002. A Structural View of Tyrosine Recombinase Site-Specific Recombination, p 93-117. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch6

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Figures

Image of Figure 1.
Figure 1.

Organization of the recombination sites. (a) The simplest sites, such as those found in the Cre-system ( ), are composed of two 11- to 13-bp RBEs arranged as inverted repeats around a central crossover region. Cleavage of the sites occurs at the borders between the crossover region and the RBEs. (b) Resolution of ColE1 plasmid multimers by XerC and XerD recombinases occurs at sites. Nearly 200 bp of accessory sequences located adjacent to the core site are bound by the ArgR and PepA proteins when two sites are arranged in direct repeat on a supercoiled substrate ( ). (c) The integration reaction of bacteriophage λ integrase requires a complex phage site () composed of a core site and flanking accessory arms and a bacterial site () composed of only the core site. The P and P′ arms of contain binding sites for the armbinding domains of integrase protein, for IHF, and for two other accessory proteins (Xis and Fis) which stimulate the excision reaction ( ).

Citation: Van Duyne G. 2002. A Structural View of Tyrosine Recombinase Site-Specific Recombination, p 93-117. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch6
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Image of Figure 2.
Figure 2.

The branch migration model for integrase family site-specific recombination ( ). Two recombinase-bound sites associate to form a recombination synapse (top left panel). Two subunits cleave the top strands of the substrates with conserved tyrosine side chains to form 3′-phosphotyrosine linkages and release free 5′-hydroxyl groups (middle left panel). The 5′- hydroxyl groups undergo intermolecular attack of the partner phosphotyrosine to complete the exchange of one pair of DNA strands between the two substrates and form an H-J intermediate (bottom left panel). The branch point of the junction starts at the site of initial strand exchange and then migrates through the crossover region to the second set of cleavage sites. The second pair of subunits are then activated and/or positioned for cleavage of the bottom substrate strands, which are exchanged to form recombinant products. Heterology between crossover sequences could block efficient branch migration and prevent the reaction from proceeding to the second strand exchange. For simplicity, the DNA sites are shown associating in a parallel orientation in this figure. For a schematic representation of the same reaction in an antiparallel alignment, see reference 5.

Citation: Van Duyne G. 2002. A Structural View of Tyrosine Recombinase Site-Specific Recombination, p 93-117. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch6
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Image of Figure 3.
Figure 3.

Domain structure of the tyrosine recombinases. (a) The tyrosine recombinases and the eukaryotic topoisomerase Ib family (represented here by the vaccinia virus enzyme) share conserved C-terminal catalytic domains but have more-divergent N-terminal domains. The arrangement of conserved catalytic residues in the C-terminal domains is indicated (see definitions in Table 2 ). V.v. topo-IB, vaccinia virus topoisomerase Ib. (b) Folding pattern of Cre recombinase. Helices A to E comprise the N-terminal domain and the remainder makes up the catalytic domain. A similar fold has been observed for the catalytic domains of λ integrase, HP1 integrase, and XerD recombinase, and this fold forms a subset of the eukaryotic topoisomerase Ib and the yeast (Flp) recombinase catalytic domains (see Table 1 ). The locations of conserved catalytic residues are indicated. (c) Ribbon-cylinder representation of a Cre recombinase subunit in the DNA-bound form, with the DNA removed from the drawing. Helices are labeled as in panel b, and active-site residues are drawn as black sticks. The location of Lys201 (Lys-β) is indicated. (d) Structure of the Cre recombinase catalytic domain, viewed from the amino-terminal domain (from the top as drawn in panel c). Active-site residues are indicated by arrows. Ribbon-cylinder illustrations in this chapter were produced with the program RIBBONS ( ).

Citation: Van Duyne G. 2002. A Structural View of Tyrosine Recombinase Site-Specific Recombination, p 93-117. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch6
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Image of Figure 4.
Figure 4.

Schematic representation of the tyrosine recombinase active site. See Table 2 for the residue identities in each of the wellstudied systems. The RBE flanks the 3′ side of the scissile phosphate and the central crossover strand flanks the 5′ side.

Citation: Van Duyne G. 2002. A Structural View of Tyrosine Recombinase Site-Specific Recombination, p 93-117. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch6
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Image of Figure 5.
Figure 5.

Exchange of DNA strands by strand swapping. (a) DNA structure in the covalent Cre-DNA intermediate ( ). 5′- Cytidine residues were cleaved and allowed to diffuse away in order to trap this intermediate ( ). These residues are shown modeled into the structure, with the direction of nucleophilic attack indicated by arrows. (b) DNA structure in the Cre-HJ intermediate ( ). The formation of 3 bp with the partner substrates as a result of strand exchange is indicated by arrows. Only the phosphodiester backbone of the exchanged bases needs to move in order to form the HJ intermediate.

Citation: Van Duyne G. 2002. A Structural View of Tyrosine Recombinase Site-Specific Recombination, p 93-117. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch6
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Image of Figure 6.
Figure 6.

Isomerization model for the HJ intermediate in Cre-site-specific recombination. The conformer on the left differs from that on the right by an exchange in the interarm angles and an exchange in the positions of the branch point phosphates. The stereochemical identities of the dark (crossing) strands on the left are identical to those of the light (crossing) strands on the right. Likewise, the light strands (continuous) on the left are equivalent to the dark (continuous) strands on the right. The strands labeled “crossing” are activated for cleavage and exchange in the two conformers.

Citation: Van Duyne G. 2002. A Structural View of Tyrosine Recombinase Site-Specific Recombination, p 93-117. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch6
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Image of Figure 7.
Figure 7.

A cleavage mechanism for tyrosine recombinases. The general base responsible for accepting a proton from the tyrosine nucleophile during cleavage (indicated by “Base:”) has not been clearly identified biochemically, but could be His/ Lys-II. The general acid responsible for protonating the 5′-OH leaving group has been identified as Lys-β in the eukaryotic topoisomerases and is therefore likely to play the same role in the tyrosine recombinases as shown here ( ). The ligation reaction is simply the reverse of that shown above, beginning with nucleophilic attack of the 3′-phosphotyrosine intermediate by a crossing strand 5′-hydroxyl group.

Citation: Van Duyne G. 2002. A Structural View of Tyrosine Recombinase Site-Specific Recombination, p 93-117. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch6
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Image of Figure 8.
Figure 8.

Strand-swapping model of Cre-site-specific recombination. Dark gray subunits are active for cleavage in the top half of the pathway, and light gray subunits are active for cleavage in the bottom half of the pathway. The DNA substrates lie nearly in the same plane and undergo only a subtle scissoring motion at the HJ isomerization step of the reaction, which serves to switch the roles of the protein subunits and switch which strands are activated for exchange. The mechanism does not involve branch migration of the HJ intermediate. I and II refer to the type I and type II interfaces formed between protein subunits in the tetrameric recombination synapse, and curved gray arrows indicate the directionality of the interface (see text). The two circled interfaces are the ones illustrated in Color Plate 13

Citation: Van Duyne G. 2002. A Structural View of Tyrosine Recombinase Site-Specific Recombination, p 93-117. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch6
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Tables

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Table 1.

Structural models in the tyrosine recombinase and topoisomerase Ib families

Citation: Van Duyne G. 2002. A Structural View of Tyrosine Recombinase Site-Specific Recombination, p 93-117. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch6
Generic image for table
Table 2.

Catalytic residues in the tyrosine recombinases and topoisomerases Ib

Citation: Van Duyne G. 2002. A Structural View of Tyrosine Recombinase Site-Specific Recombination, p 93-117. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch6

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