1zr4 Citations

Structure of a synaptic gammadelta resolvase tetramer covalently linked to two cleaved DNAs.

Science 309 1210-5 (2005)
Cited: 79 times
EuropePMC logo PMID: 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.

Reviews - 1zr4 mentioned but not cited (2)

  1. Topoisomerases and site-specific recombinases: similarities in structure and mechanism. Yang W. Crit Rev Biochem Mol Biol 45 520-534 (2010)
  2. Serine Resolvases. Rice PA. Microbiol Spectr 3 MDNA3-0045-2014 (2015)

Articles - 1zr4 mentioned but not cited (19)

  1. Implications of structures of synaptic tetramers of gamma delta resolvase for the mechanism of recombination. Kamtekar S, Ho RS, Cocco MJ, Li W, Wenwieser SV, Boocock MR, Grindley ND, Steitz TA. Proc Natl Acad Sci U S A 103 10642-10647 (2006)
  2. Attachment site recognition and regulation of directionality by the serine integrases. Rutherford K, Yuan P, Perry K, Sharp R, Van Duyne GD. Nucleic Acids Res 41 8341-8356 (2013)
  3. Structural basis for catalytic activation of a serine recombinase. Keenholtz RA, Rowland SJ, Boocock MR, Stark WM, Rice PA. Structure 19 799-809 (2011)
  4. Synapsis and catalysis by activated Tn3 resolvase mutants. Olorunniji FJ, He J, Wenwieser SV, Boocock MR, Stark WM. Nucleic Acids Res 36 7181-7191 (2008)
  5. A proposed mechanism for IS607-family serine transposases. Boocock MR, Rice PA. Mob DNA 4 24 (2013)
  6. Regulatory mutations in Sin recombinase support a structure-based model of the synaptosome. Rowland SJ, Boocock MR, McPherson AL, Mouw KW, Rice PA, Stark WM. Mol Microbiol 74 282-298 (2009)
  7. Crystal structure of an intermediate of rotating dimers within the synaptic tetramer of the G-segment invertase. Ritacco CJ, Kamtekar S, Wang J, Steitz TA. Nucleic Acids Res 41 2673-2682 (2013)
  8. The Hin recombinase assembles a tetrameric protein swivel that exchanges DNA strands. Dhar G, McLean MM, Heiss JK, Johnson RC. Nucleic Acids Res 37 4743-4756 (2009)
  9. Zinc-finger recombinase activities in vitro. Prorocic MM, Wenlong D, Olorunniji FJ, Akopian A, Schloetel JG, Hannigan A, McPherson AL, Stark WM. Nucleic Acids Res 39 9316-9328 (2011)
  10. The catalytic residues of Tn3 resolvase. Olorunniji FJ, Stark WM. Nucleic Acids Res 37 7590-7602 (2009)
  11. Multiple interfaces between a serine recombinase and an enhancer control site-specific DNA inversion. McLean MM, Chang Y, Dhar G, Heiss JK, Johnson RC. Elife 2 e01211 (2013)
  12. Redesigning Recombinase Specificity for Safe Harbor Sites in the Human Genome. Wallen MC, Gaj T, Barbas CF. PLoS One 10 e0139123 (2015)
  13. Intrasubunit and intersubunit interactions controlling assembly of active synaptic complexes during Hin-catalyzed DNA recombination. Heiss JK, Sanders ER, Johnson RC. J Mol Biol 411 744-764 (2011)
  14. Site-specific DNA Inversion by Serine Recombinases. Johnson RC. Microbiol Spectr 3 1-36 (2015)
  15. Controlling tetramer formation, subunit rotation and DNA ligation during Hin-catalyzed DNA inversion. Chang Y, Johnson RC. Nucleic Acids Res 43 6459-6472 (2015)
  16. Controlled rotation mechanism of DNA strand exchange by the Hin serine recombinase. Xiao B, McLean MM, Lei X, Marko JF, Johnson RC. Sci Rep 6 23697 (2016)
  17. In Silico Discovery of Anticancer Peptides from Sanghuang. Liu M, Lv J, Chen L, Li W, Han W. Int J Mol Sci 23 13682 (2022)
  18. Retraction: Site‐specific recombination of nitrogen‐fixation genes in cyanobacteria by XisF–XisH–XisI complex: Structures and models, William C. Hwang, James W. Golden, Jaime Pascual, Dong Xu, Anton Cheltsov, Adam Godzik Proteins 86 268 (2018)
  19. Structural basis for topological regulation of Tn3 resolvase. Montaño SP, Rowland SJ, Fuller JR, Burke ME, MacDonald AI, Boocock MR, Stark WM, Rice PA. Nucleic Acids Res 51 1001-1018 (2023)


Reviews citing this publication (13)

  1. Mechanisms of site-specific recombination. Grindley ND, Whiteson KL, Rice PA. Annu Rev Biochem 75 567-605 (2006)
  2. Nucleases: diversity of structure, function and mechanism. Yang W. Q Rev Biophys 44 1-93 (2011)
  3. New applications for phage integrases. Fogg PC, Colloms S, Rosser S, Stark M, Smith MC. J Mol Biol 426 2703-2716 (2014)
  4. Mechanisms of DNA Transposition. Hickman AB, Dyda F. Microbiol Spectr 3 MDNA3-0034-2014 (2015)
  5. Site-specific recombinases as tools for heterologous gene integration. Hirano N, Muroi T, Takahashi H, Haruki M. Appl Microbiol Biotechnol 92 227-239 (2011)
  6. The ins and outs of serine integrase site-specific recombination. Rutherford K, Van Duyne GD. Curr Opin Struct Biol 24 125-131 (2014)
  7. The mu transpososome through a topological lens. Harshey RM, Jayaram M. Crit Rev Biochem Mol Biol 41 387-405 (2006)
  8. The bacterial chromosome. Saier MH. Crit Rev Biochem Mol Biol 43 89-134 (2008)
  9. Orchestrating serine resolvases. Rice PA, Mouw KW, Montaño SP, Boocock MR, Rowland SJ, Stark WM. Biochem Soc Trans 38 384-387 (2010)
  10. Intermediates in serine recombinase-mediated site-specific recombination. Marshall Stark W, Boocock MR, Olorunniji FJ, Rowland SJ. Biochem Soc Trans 39 617-622 (2011)
  11. The molecular underpinnings of genetic phenomena. Lehman N. Heredity (Edinb) 100 6-12 (2008)
  12. The Impact of Space and Time on the Functional Output of the Genome. Nollmann M, Bennabi I, Götz M, Gregor T. Cold Spring Harb Perspect Biol 14 a040378 (2022)
  13. Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes. Wang J, Arantes PR, Ahsan M, Sinha S, Kyro GW, Maschietto F, Allen B, Skeens E, Lisi GP, Batista VS, Palermo G. Front Mol Biosci 9 1072733 (2022)

Articles citing this publication (45)

  1. Permanent genetic memory with >1-byte capacity. Yang L, Nielsen AA, Fernandez-Rodriguez J, McClune CJ, Laub MT, Lu TK, Voigt CA. Nat Methods 11 1261-1266 (2014)
  2. PR65, the HEAT-repeat scaffold of phosphatase PP2A, is an elastic connector that links force and catalysis. Grinthal A, Adamovic I, Weiner B, Karplus M, Kleckner N. Proc Natl Acad Sci U S A 107 2467-2472 (2010)
  3. A motif in the C-terminal domain of phiC31 integrase controls the directionality of recombination. Rowley PA, Smith MC, Younger E, Smith MC. Nucleic Acids Res 36 3879-3891 (2008)
  4. Structure-guided reprogramming of serine recombinase DNA sequence specificity. Gaj T, Mercer AC, Gersbach CA, Gordley RM, Barbas CF. Proc Natl Acad Sci U S A 108 498-503 (2011)
  5. Single-molecule analysis reveals the molecular bearing mechanism of DNA strand exchange by a serine recombinase. Bai H, Sun M, Ghosh P, Hatfull GF, Grindley ND, Marko JF. Proc Natl Acad Sci U S A 108 7419-7424 (2011)
  6. Evolution of programmable zinc finger-recombinases with activity in human cells. Gordley RM, Smith JD, Gräslund T, Barbas CF. J Mol Biol 367 802-813 (2007)
  7. Tetrameric structure of a serine integrase catalytic domain. Yuan P, Gupta K, Van Duyne GD. Structure 16 1275-1286 (2008)
  8. Architecture of a serine recombinase-DNA regulatory complex. Mouw KW, Rowland SJ, Gajjar MM, Boocock MR, Stark WM, Rice PA. Mol Cell 30 145-155 (2008)
  9. Sequences in attB that affect the ability of phiC31 integrase to synapse and to activate DNA cleavage. Gupta M, Till R, Smith MC. Nucleic Acids Res 35 3407-3419 (2007)
  10. A comprehensive approach to zinc-finger recombinase customization enables genomic targeting in human cells. Gaj T, Mercer AC, Sirk SJ, Smith HL, Barbas CF. Nucleic Acids Res 41 3937-3946 (2013)
  11. Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments. Laganeckas M, Margelevicius M, Venclovas C. Nucleic Acids Res 39 1187-1196 (2011)
  12. Mechanical constraints on Hin subunit rotation imposed by the Fis/enhancer system and DNA supercoiling during site-specific recombination. Dhar G, Heiss JK, Johnson RC. Mol Cell 34 746-759 (2009)
  13. Rearranging the centromere of the human Y chromosome with phiC31 integrase. Malla S, Dafhnis-Calas F, Brookfield JF, Smith MC, Brown WR. Nucleic Acids Res 33 6101-6113 (2005)
  14. Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis. Yu Q, Qu K, Modis Y. Mol Cell 72 999-1012.e6 (2018)
  15. Gated rotation mechanism of site-specific recombination by ϕC31 integrase. Olorunniji FJ, Buck DE, Colloms SD, McEwan AR, Smith MC, Stark WM, Rosser SJ. Proc Natl Acad Sci U S A 109 19661-19666 (2012)
  16. The site-specific integration reaction of Listeria phage A118 integrase, a serine recombinase. Mandali S, Dhar G, Avliyakulov NK, Haykinson MJ, Johnson RC. Mob DNA 4 2 (2013)
  17. A switch in the mechanism of communication between the two DNA-binding sites in the SfiI restriction endonuclease. Bellamy SR, Milsom SE, Kovacheva YS, Sessions RB, Halford SE. J Mol Biol 373 1169-1183 (2007)
  18. Control of directionality in Streptomyces phage φBT1 integrase-mediated site-specific recombination. Zhang L, Zhu B, Dai R, Zhao G, Ding X. PLoS One 8 e80434 (2013)
  19. Arginine as a general acid catalyst in serine recombinase-mediated DNA cleavage. Keenholtz RA, Mouw KW, Boocock MR, Li NS, Piccirilli JA, Rice PA. J Biol Chem 288 29206-29214 (2013)
  20. Zinc finger recombinases with adaptable DNA sequence specificity. Proudfoot C, McPherson AL, Kolb AF, Stark WM. PLoS One 6 e19537 (2011)
  21. A novel site-specific recombination system derived from bacteriophage phiMR11. Rashel M, Uchiyama J, Ujihara T, Takemura I, Hoshiba H, Matsuzaki S. Biochem Biophys Res Commun 368 192-198 (2008)
  22. Role of the N-terminal domain of phiC31 integrase in attB-attP synapsis. Rowley PA, Smith MC. J Bacteriol 190 6918-6921 (2008)
  23. Mutational analysis of highly conserved residues in the phage phiC31 integrase reveals key amino acids necessary for the DNA recombination. Liu S, Ma J, Wang W, Zhang M, Xin Q, Peng S, Li R, Zhu H. PLoS One 5 e8863 (2010)
  24. Sin resolvase catalytic activity and oligomerization state are tightly coupled. Mouw KW, Steiner AM, Ghirlando R, Li NS, Rowland SJ, Boocock MR, Stark WM, Piccirilli JA, Rice PA. J Mol Biol 404 16-33 (2010)
  25. DNA bending in the Sin recombination synapse: functional replacement of HU by IHF. Rowland SJ, Boocock MR, Stark WM. Mol Microbiol 59 1730-1743 (2006)
  26. Fluorescence resonance energy transfer analysis of recombination signal sequence configuration in the RAG1/2 synaptic complex. Ciubotaru M, Kriatchko AN, Swanson PC, Bright FV, Schatz DG. Mol Cell Biol 27 4745-4758 (2007)
  27. Organization of DNA partners and strand exchange mechanisms during Flp site-specific recombination analyzed by difference topology, single molecule FRET and single molecule TPM. Ma CH, Liu YT, Savva CG, Rowley PA, Cannon B, Fan HF, Russell R, Holzenburg A, Jayaram M. J Mol Biol 426 793-815 (2014)
  28. Predicting knot or catenane type of site-specific recombination products. Buck D, Flapan E. J Mol Biol 374 1186-1199 (2007)
  29. Coiled-coil interactions mediate serine integrase directionality. Gupta K, Sharp R, Yuan JB, Li H, Van Duyne GD. Nucleic Acids Res 45 7339-7353 (2017)
  30. Determinants of product topology in a hybrid Cre-Tn3 resolvase site-specific recombination system. Kilbride EA, Burke ME, Boocock MR, Stark WM. J Mol Biol 355 185-195 (2006)
  31. Site-specific recombination system based on actinophage TG1 integrase for gene integration into bacterial genomes. Hirano N, Muroi T, Kihara Y, Kobayashi R, Takahashi H, Haruki M. Appl Microbiol Biotechnol 89 1877-1884 (2011)
  32. Crossover-site sequence and DNA torsional stress control strand interchanges by the Bxb1 site-specific serine recombinase. Keenholtz RA, Grindley ND, Hatfull GF, Marko JF. Nucleic Acids Res 44 8921-8932 (2016)
  33. Recombination directionality factor gp3 binds ϕC31 integrase via the zinc domain, potentially affecting the trajectory of the coiled-coil motif. Fogg PCM, Younger E, Fernando BD, Khaleel T, Stark WM, Smith MCM. Nucleic Acids Res 46 1308-1320 (2018)
  34. RNA-Guided Recombinase-Cas9 Fusion Targets Genomic DNA Deletion and Integration. Standage-Beier K, Brookhouser N, Balachandran P, Zhang Q, Brafman DA, Wang X. CRISPR J 2 209-222 (2019)
  35. An algebraic view of bacterial genome evolution. Francis AR. J Math Biol 69 1693-1718 (2014)
  36. Comment Assembly of a tightly interwound DNA recombination complex poised for deletion. Johnson RC, Heiss JK. Structure 16 653-655 (2008)
  37. Recombining DNA by protein swivels. Johnson RC, McLean MM. Structure 19 751-753 (2011)
  38. Wavelet Analysis of Protein Motion. Benson NC, Daggett V. Int J Wavelets Multiresolut Inf Process 10 (2012)
  39. Nicked-site substrates for a serine recombinase reveal enzyme-DNA communications and an essential tethering role of covalent enzyme-DNA linkages. Olorunniji FJ, McPherson AL, Pavlou HJ, McIlwraith MJ, Brazier JA, Cosstick R, Stark WM. Nucleic Acids Res 43 6134-6143 (2015)
  40. Snapshots of a molecular swivel in action. Trejo CS, Rock RS, Stark WM, Boocock MR, Rice PA. Nucleic Acids Res 46 5286-5296 (2018)
  41. Conformation and stability of the Streptococcus pyogenes pSM19035-encoded site-specific beta recombinase, and identification of a folding intermediate. Bhardwaj A, Welfle K, Misselwitz R, Ayora S, Alonso JC, Welfle H. Biol Chem 387 525-533 (2006)
  42. Control of the Serine Integrase Reaction: Roles of the Coiled-Coil and Helix E Regions in DNA Site Synapsis and Recombination. Mandali S, Johnson RC. J Bacteriol 203 e0070320 (2021)
  43. Multiple serine transposase dimers assemble the transposon-end synaptic complex during IS607-family transposition. Chen W, Chen W, Mandali S, Hancock SP, Kumar P, Collazo M, Cascio D, Johnson RC. Elife 7 (2018)
  44. Solution structure and DNA binding of the catalytic domain of the large serine resolvase TnpX. Headey SJ, Sivakumaran A, Adams V, Lyras D, Rood JI, Scanlon MJ, Wilce MC. J Mol Recognit 28 316-324 (2015)
  45. Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination. Rowley PA, Kachroo AH, Ma CH, Maciaszek AD, Guga P, Jayaram M. Nucleic Acids Res 43 6023-6037 (2015)