DNA manipulators: Caught in the act

Current Opinion in Structural Biology

Volumn 13, Issue 1, 2003, Pages 15-22

  Changela, Anita ^a   Perry, Kay ^a   Taneja, Bhupesh ^a   Mondragón, Alfonso ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA TOPOISOMERASE; DNA TOPOISOMERASE (ATP HYDROLYSING); HELICASE; INTEGRASE; RECOMBINASE; TRANSPOSASE;

CATALYST; DNA RECOMBINATION; DNA STRUCTURE; ENZYME SPECIFICITY; ENZYME STRUCTURE; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; REVIEW;

EID: 0037308997     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(02)00006-4     Document Type: Review

References (40)

1. Sadowski P. Site-specific recombinases: changing partners and doing the twist. J. Bacteriol. 165:1986;341-347.
2. Stark W.M., Boocock M.R., Sherratt D.J. Catalysis by site-specific recombinases. Trends Genet. 8:1992;432-439.
3. Grainge I., Jayaram M. The integrase family of recombinase: organization and function of the active site. Mol. Microbiol. 33:1999;449-456.
4. Pan B., Maciejewski M.W., Marintchev A., Mullen G.P. Solution structure of the catalytic domain of γδ resolvase. Implications for the mechanism of catalysis. J. Mol. Biol. 310:2001;1089-1107.
5. Sarkis G.J., Murley L.L., Leschziner A.E., Boocock M.R., Stark W.M., Grindley N.D. A model for the γδ resolvase synaptic complex. Mol. Cell. 8:2001;623-631.
6. Van Duyne G.D. A structural view of Cre-loxP site-specific recombination. Annu. Rev. Biophys. Biomol. Struct. 30:2001;87-104 A comprehensive review of the site-specific recombination pathway of Cre-loxP.
7. Chen Y., Narendra U., Iype L.E., Cox M.M., Rice P.A. Crystal structure of a Flp recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping. Mol. Cell. 6:2000;885-897.
8. Martin S.S., Pulido E., Chu V.C., Lechner T.S., Baldwin E.P. The order of strand exchanges in Cre-loxP recombination and its basis suggested by the crystal structure of a Cre-loxP Holliday junction complex. J. Mol. Biol. 319:2002;107-127 Recent structure of the Cre-loxP HJ complex that partially resolves issues regarding the order of strand exchange.
9. Woods K.C., Martin S.S., Chu V.C., Baldwin E.P. Quasi-equivalence in site-specific recombinase structure and function: crystal structure and activity of trimeric Cre recombinase bound to a three-way Lox DNA junction. J. Mol. Biol. 313:2001;49-69.
10. Grainge I., Pathania S., Vologodskii A., Harshey R.M., Jayaram M. Symmetric DNA sites are functionally asymmetric within Flp and Cre site-specific DNA recombination synapses. J. Mol. Biol. 320:2002;515-527.
11. Singleton M.R., Wigley D.B. Modularity and specialization in superfamily 1 and 2 helicases. J. Bacteriol. 184:2002;1819-1826.
12. Caruthers J.M., McKay D.B. Helicase structure and mechanism. Curr. Opin. Struct. Biol. 12:2002;123-133.
13. Velankar S.S., Soultanas P., Dillingham M.S., Subramanya H.S., Wigley D.B. Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell. 97:1999;75-84.
14. Dillingham M.S., Wigley D.B., Webb M.R. Demonstration of unidirectional single-stranded DNA translocation by PcrA helicase: measurement of step size and translocation speed. Biochemistry. 39:2000;205-212.
15. Dillingham M.S., Wigley D.B., Webb M.R. Direct measurement of single-stranded DNA translocation by PcrA helicase using the fluorescent base analogue 2-aminopurine. Biochemistry. 41:2002;643-651.
16. Soultanas P., Dillingham M.S., Wiley P., Webb M.R., Wigley D.B. Uncoupling DNA translocation and helicase activity in PcrA: direct evidence for an active mechanism. EMBO J. 19:2000;3799-3810.
17. Singleton M.R., Scaife S., Wigley D.B. Structural analysis of DNA replication fork reversal by RecG. Cell. 107:2001;79-89 The authors report a crystal structure of RecG helicase bound to a three-way DNA junction that is representative of a stalled replication fork. The structure reveals a possible mechanism for fork reversal, and mechanistic differences between RecG and other helicases are highlighted.
18. Ariyoshi M., Nishino T., Iwasaki H., Shinagawa H., Morikawa K. Crystal structure of the Holliday junction DNA in complex with a single RuvA tetramer. Proc. Natl. Acad. Sci. USA. 97:2000;8257-8262.
19. Rice P.A., Baker T.A. Comparative architecture of transposase and integrase complexes. Nat. Struct. Biol. 8:2001;302-307.
20. Davies D.R., Goryshin I.Y., Reznikoff W.S., Rayment I. Three-dimensional structure of the Tn5 synaptic complex transposition intermediate. Science. 289:2000;77-85.
21. Lovell S., Goryshin I.Y., Reznikoff W.R., Rayment I. Two-metal active site binding of a Tn5 transposase synaptic complex. Nat. Struct. Biol. 9:2002;278-281 The authors follow up previous studies [20] by reporting the structure of Tn5 transposase bound to extended transposon DNA ends. This structure reveals a second divalent metal bound at the active site that was not present in the first structure. Comparison between the two Tn5-DNA structures and the locations of the metal ions suggests a possible two-metal-ion model for catalysis.
22. Wang J.Y., Ling H., Yang W., Craigie R. Structure of a two-domain fragment of HIV-1 integrase: implications for domain organization in the intact protein. EMBO J. 20:2001;7333-7343.
23. Champoux J.J. DNA topoisomerases: structure, function, and mechanism. Annu. Rev. Biochem. 70:2001;369-413.
24. Wang J.C. Cellular roles of DNA topoisomerases: a molecular perspective. Nat. Rev. Mol. Cell. Biol. 3:2002;430-440.
25. Sherratt D.J., Wigley D.B. Conserved themes but novel activities in recombinases and topoisomerases. Cell. 93:1998;149-152.
26. Li Z., Mondragon A., DiGate R.J. The mechanism of type IA topoisomerase-mediated DNA topological transformations. Mol. Cell. 7:2001;301-307.
27. Changela A., DiGate R.J., Mondragon A. Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule. Nature. 411:2001;1077-1081 The structure represents the first snapshot of a type IA topoisomerase bound to DNA and highlights an important intermediate in the catalytic cycle of the enzyme.
28. Chen S.J., Wang J.C. Identification of active site residues in Escherichia coli DNA topoisomerase I. J. Biol. Chem. 273:1998;6050-6056.
29. Zhu C.X., Roche C.J., Papanicolaou N., DiPietrantonio A., Tse-Dinh Y.C. Site-directed mutagenesis of conserved aspartates, glutamates and arginines in the active site region of Escherichia coli DNA topoisomerase I. J. Biol. Chem. 273:1998;8783-8789.
30. Dekker N.H., Rybenkov V.V., Duguet M., Crisona N.J., Cozzarelli N.R., Bensimon D., Croquette V. The mechanism of type IA topoisomerases. Proc. Natl. Acad. Sci. USA. 99:2002;12126-12131 The paper reports single molecule studies in real time that further confirms the mechanistic pathway followed by type IA topoisomerases.
31. Crisona N.J., Strick T.R., Bensimon D., Croquette V., Cozzarelli N.R. Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements. Genes Dev. 14:2000;2881-2892.
32. Strick T.R., Croquette V., Bensimon D. Single-molecule analysis of DNA uncoiling by a type II topoisomerase. Nature. 404:2000;901-904.
33. Rodriguez A.C., Stock D. Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA. EMBO J. 21:2002;418-426 This structure reveals the arrangement of topoisomerase and helicase domains in an intact reverse gyrase and the possible interactions between the two domains to positively supercoil DNA.
34. Rodriguez A.C. Studies of a positive supercoiling machine. Nucleotide hydrolysis and a multifunctional "latch" in the mechanism of reverse gyrase. J. Biol. Chem. 277:2002;29865-29873.
35. Guo F., Gopaul D.N., Van Duyne G.D. Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse. Proc. Natl. Acad. Sci. USA. 96:1999;7143-7148.
36. Guo F., Gopaul D.N., van Duyne G.D. Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature. 389:1997;40-46.
37. Gopaul D.N., Guo F., Van Duyne G.D. Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination. EMBO J. 17:1998;4175-4187.
38. Mondragon A., DiGate R. The structure of Escherichia coli DNA topoisomerase III. Struct. Fold Des. 7:1999;1373-1383.
39. Lima C.D., Wang J.C., Mondragon A. Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I. Nature. 367:1994;138-146.
40. Feinberg H., Lima C.D., Mondragon A. Conformational changes in E. coli DNA topoisomerase I. Nat. Struct. Biol. 6:1999;918-922.