Dynamics of phosphodiester synthesis by DNA ligase

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 19, 2008, Pages 6894-6899

  Crut, Aurélien ^a,c   Nair, Pravin A ^b   Koster, Daniel A ^a,d   Shuman, Stewart ^b   Dekker, Nynke H ^a  

^a DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

^b MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^c UNIVERSITÉ LYON 1   (France)

^d WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

DNA ligation; DNA relaxation; Magnetic tweezers

Indexed keywords

ADENOSINE PHOSPHATE; DNA POLYMERASE; DNA TOPOISOMERASE; ESTER; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; CHLORELLA VIRUS DNA LIGASE; DNA DIRECTED DNA POLYMERASE; MUTANT PROTEIN; ORGANOPHOSPHATE; VIRUS PROTEIN;

ARTICLE; CONTROLLED STUDY; DISSOCIATION; DNA DAMAGE; DNA RECOMBINATION; DNA REPLICATION; DNA STRAND BREAKAGE; DNA SUPERCOILING; DNA SYNTHESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; CHEMICAL STRUCTURE; METABOLISM;

ADENOSINE MONOPHOSPHATE; DNA LIGASES; DNA TOPOISOMERASES, TYPE I; DNA, SUPERHELICAL; DNA-DIRECTED DNA POLYMERASE; MODELS, MOLECULAR; MUTANT PROTEINS; PHOSPHORIC ACID ESTERS; VIRAL PROTEINS;

EID: 44349114622     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0800113105     Document Type: Article

References (36)

1. Lehman IR (1974) DNA ligase: Structure, mechanism, and function. Science 186:790-797.
2. Shuman S, Lima CD (2004) The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases. Curr Opin Struct Biol 14:757-764.
3. Tomkinson AE, Vijayakumar S, Pascal JM, Ellenberger T (2006) DNA ligases: Structure, reaction mechanism, and function. Chem Rev 106:687-699.
4. Pascal JM, O'Brien PJ, Tomkinson AE, Ellenberger T (2004) Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 432:473-478.
5. Nandakumar J, Nair PA, Shuman S (2007) Last stop on the road to repair: Structure of E. coli DNA ligase bound to nicked DNA adenylate. Mol Cell 26:257-271.
6. Nair PA, et al. (2007) Structural basis for nick recognition by a minimal pluripotent DNA ligase. Nat Struct Mol Biol 14:770-778.
7. Sriskanda V, Shuman S (1998) Chlorella virus DNA ligase: Nick recognition and mutational analysis. Nucleic Acids Res 26:525-531.
8. Odell M, Shuman S (1999) Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA. J Biol Chem 274:14032-14039.
9. Sriskanda V, Schwer B, Ho CK, Shuman S (1999) Mutational analysis of Escherichia coli DNA ligase identifies amino acids required for nick ligation in vitro and for in vivo complementation of the growth of yeast cells deleted for CDC9 and LIG4. Nucleic Acids Res 27:3953-3963.
10. Odell M, Malinina L, Sriskanda V, Teplova M, Shuman S (2003) Analysis of the DNA joining repertoire of Chlorella virus DNA ligase and a new crystal structure of the ligase-adenylate intermediate. Nucleic Acids Res 31:5090-5100.
11. Sriskanda V, Shuman S (1998) Specificity and fidelity of strand joining by Chlorella virus DNA ligase. Nucleic Acids Res 26:3536-3541.
12. Sriskanda V, Shuman S (1998) Mutational analysis of Chlorella virus DNA ligase: Catalytic roles of domain I and motif VI. Nucleic Acids Res 26:4618-4625.
13. Odell M, Sriskanda V, Shuman S, Nikolov DB (2000) Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining. Mol Cell 6:1183-1193.
14. Sriskanda V, Shuman S (2002) Role of nucleotidyltransferase motifs I, III, and IV in the catalysis of phosphodiester bond formation by Chlorella virus DNA ligase. Nucleic Acids Res 30:903-911.
15. Sriskanda V, Shuman S (2002) Role of nucleotidyl transferase motif V in strand joining by Chlorella virus DNA ligase. J Biol Chem 277:9661-9667.
16. Modrich P, Lehman IR, Wang JC (1972) Enzymatic joining of polynucleotides. XI. Reversal of Escherichia coli deoxyribonucleic acid ligase reaction. J Biol Chem 247:6370-6372.
17. Montecucco A, Ciarrocchi G (1988) AMP-dependent DNA relaxation catalyzed by DNA ligase occurs by a nicking-closing mechanism. Nucleic Acids Res 16:7369-7381.
18. Sekiguchi J, Shuman S (1997) Nick sensing by vaccinia virus DNA ligase requires a 5′ phosphate at the nick and occupancy of the adenylate binding site on the enzyme. J Virol 71:9679-9684.
19. Corbett KD, Berger JM (2004) Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases. Annu Rev Biophys Biomol Struct 33:95-118.
20. Koster DA, Croquette V, Dekker C, Shuman S, Dekker NH (2005) Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB. Nature 434:671-674.
21. Taneja B, Schnurr B, Slesarev A, Marko JF, Mondragon A (2007) Topoisomerase V relaxes supercoiled DNA by a constrained swiveling mechanism. Proc Natl Acad Sci USA 104:14670-14675.
22. Koster DA, Wiggins CH, Dekker NH (2006) Multiple events on single molecules: Unbiased estimation in single-molecule biophysics. Proc Natl Acad Sci USA 103:1750-1755.
23. Gong C, Martins A, Bongiorno P, Glickman M, Shuman S (2004) Biochemical and genetic analysis of the four DNA ligases of mycobacteria. J Biol Chem 279:20594-20606.
24. Zhu H, Shuman S (2007) Characterization of Agrobacterium tumefaciens DNA ligases C and D. Nucleic Acids Res 35:3631-3645.
25. Shuman S (1995) Vaccinia virus DNA ligase: Specificity, fidelity, and inhibition. Biochemistry 34:16138-16147.
26. Cherepanov AV, de Vries S (2003) Kinetics and thermodynamics of nick sealing by T4 DNA ligase. Eur J Biochem 270:4315-4325.
27. Modrich P, Lehman IR (1973) Deoxyribonucleic acid ligase: A steady-state kinetic analysis of the reaction catalyzed by the enzyme from Escherichia coli. J Biol Chem 248:7502-7511.
28. Crut A, Koster DA, Seidel R, Wiggins CH, Dekker NH (2007) Fast dynamics of supercoiled DNA revealed by single-molecule experiments. Proc Natl Acad Sci USA 104:11957-11962.
29. Redinbo MR, Stewart L, Kuhn P, Champoux JJ, Hol WG (1998) Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Science 279:1504-1513.
30. Perry K, Hwang Y, Bushman FD, Van Duyne GD (2006) Structural basis for specificity in the poxvirus topoisomerase. Mol Cell 23:343-354.
31. Mok M, Marians KJ (1987) The Escherichia coli preprimosome and DNA B helicase can form replication forks that move at the same rate. J Biol Chem 262:16644-16654.
32. Ahel I, et al. (2006) The neurodegenerative disease protein aprataxin resolves abortive DNA ligation intermediates. Nature 443:713-716.
33. Charvin G, Vologodskii A, Bensimon D, Croquette V (2005) Braiding DNA: Experiments, simulations, and models. Biophys J 88:4124-4136.
34. Stone MD, et al. (2003) Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases. Proc Natl Acad Sci USA 100:8654-8659.
35. Koster DA, Palle K, Bot ES, Bjornsti MA, Dekker NH (2007) Antitumour drugs impede DNA uncoiling by topoisomerase I. Nature 448:213-217.
36. Kerssemakers JW, et al. (2006) Assembly dynamics of microtubules at molecular resolution. Nature 442:709-712.