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PDBsum entry 1zr4

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Top Page protein dna_rna Protein-protein interface(s) links
Recombination/DNA PDB id
1zr4
Jmol
Contents
Protein chains
183 a.a.
DNA/RNA

References listed in PDB file
Key reference
Title Structure of a synaptic gammadelta resolvase tetramer covalently linked to two cleaved dnas.
Authors W.Li, S.Kamtekar, Y.Xiong, G.J.Sarkis, N.D.Grindley, T.A.Steitz.
Ref. Science, 2005, 309, 1210-1215. [DOI no: 10.1126/science.1112064]
PubMed id 15994378
Abstract
The structure of a synaptic intermediate of the site-specific recombinase gammadelta resolvase covalently linked through Ser10 to two cleaved duplex DNAs has been determined at 3.4 angstrom resolution. This resolvase, activated for recombination by mutations, forms a tetramer whose structure is substantially changed from that of a presynaptic complex between dimeric resolvase and the cleavage site DNA. Because the two cleaved DNA duplexes that are to be recombined lie on opposite sides of the core tetramer, large movements of both protein and DNA are required to achieve strand exchange. The two dimers linked to the DNAs that are to be recombined are held together by a flat interface. This may allow a 180 degrees rotation of one dimer relative to the other in order to reposition the DNA duplexes for strand exchange.
Figure 1.
Fig. 1. Site-specific recombination by resolvase. (A) Two res sites in negatively supercoiled, closed circular DNA bind wild-type resolvase as a dimer (blue and red spheres) at site I in the presynaptic state (dashed-line box). The synaptosome consists of the two res sites, each containing three resolvase dimers bound to sites I, II, and III (left) associating to form an assembly (right). During strand exchange, a synaptic complex at site I (yellow box) is formed by a resolvase tetramer that becomes covalently linked (black line) to four cleaved half sites (red and green arrows). (B) A tetramer of resolvase (left) recombines two site I DNAs [same as in (A)]. Two models of resolvase strand exchange (right) are domain swap (top) and subunit rotation (bottom). The interfaces formed by E helices (blue and red sticks) are intact in the domain swap model but rotate relative to each other in the subunit rotation model. (C) (Top) resolvase requires three sites to form the synaptic complex but performs recombination exclusively on site I. The length and spacing of these sites are shown. (Bottom) The sequence of the symmetrized site I analog used, with the bases of the original sequence of site I shown in italics above and below the mutated bases. The double-strand cleavage sites are shown in black arrows. Thymidines substituted by 5-bromo-2'-deoxyuridine in oligonucleotide derivatives are shown shaded in yellow. Nicks in the crystallographic substrates are opposite the dashes.
Figure 3.
Fig. 3. The structure of the mutant -resolvase tetramer covalently linked to cleaved DNA. (A) The two site I DNAs (light and dark green, yellow, and orange coils) are cleaved into half sites labeled L, R, L', and R'. S10 (blue and red spheres) in each subunit is covalently linked to the 5' phosphate of adenine 20 (Ade20, green stick). The subunits of the resolvase tetramer (blue, green, red, and magenta) can be divided into two dimers containing antiparallel E helices (L-L' and R-R') or two site I dimers bound to L-R DNA or L'-R' DNA. The D and E helices form a four-helix bundle within the antiparallel dimer. The two antiparallel E helix dimers interact through a flat interface, and the V114 C114 (21) mutation in the E helix crosslinks across the flat interface. The position of the missing phosphates resulting from the use of symmetrized oligos is marked by an orange sphere; its absence does not distort the DNA. (B) The active site at the covalent, cleaved DNA intermediate. A phosphoserine bond formed between Ade20 and S10. R8, D67, R68, and the two nonbridging oxygens of the phosphoserine form a hydrogen-bonding network (blue dashed lines). In the religation step, the free 3'-hydroxyl attacks of the DNA to be exchanged (black arrow) is presumably in line with the phosphoserine bond. (C) A view of the tetramer rotated by 90° from the orientation in (A) shows the packing of four E helices and preceding loops and ß strands.
The above figures are reprinted by permission from the AAAs: Science (2005, 309, 1210-1215) copyright 2005.
PROCHECK
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