Analysis of the DNA joining repertoire of Chlorella virus DNA ligase and a new crystal structure of the ligase-adenylate intermediate

Nucleic Acids Research

Volumn 31, Issue 17, 2003, Pages 5090-5100

  Odell, Mark ^a   Malinina, Lucy ^a   Sriskanda, Verl ^a   Teplova, Marianna ^a   Shuman, Stewart ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE PHOSPHATE; CELL ENZYME; ENZYME PRECURSOR; HYDROXIDE; PHOSPHATE; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; SULFATE; VIRUS DNA; VIRUS ENZYME;

ARTICLE; CELL COMPARTMENTALIZATION; CELL GROWTH; CHLORELLA VIRUS; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA BINDING; DNA DETERMINATION; DNA FOOTPRINTING; DNA STRAND; ENZYME ACTIVITY; ENZYME STRUCTURE; EUKARYOTIC CELL; GENE DUPLICATION; IN VIVO STUDY; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; YEAST CELL;

ADENOSINE MONOPHOSPHATE; BASE SEQUENCE; BINDING SITES; CATALYSIS; CRYSTALLOGRAPHY, X-RAY; DNA; DNA LIGASES; DNA REPAIR; PHOSPHATES; PLASMIDS; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; VIRAL PROTEINS;

CHLORELLA VIRUS; DNA VIRUSES; EUKARYOTA;

EID: 0345306347     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg665     Document Type: Article

References (44)

1. Doherty, A.J. and Suh, S.W. (2000) Structural and mechanistic conservation in DNA ligases. Nucleic Acids Res., 28, 4051-4058.
2. Little, J.W., Zimmerman, S.B., Oshinsky, C.K. and Gellert, M. (1967) Enzymatic joining of DNA strands: an enzyme-adenylate intermediate in the DPN-dependent DNA ligase reaction. Proc. Natl Acad. Sci. USA, 59, 2004-2011.
3. Weiss, B., Thompson, A. and Richardson, C.C. (1968) Enzymatic breakage and rejoining of deoxyribonucleic acid: properties of the enzyme-adenylate intermediate in the polynucleotide ligase reaction. J. Biol. Chem., 246, 4523-4530.
4. Gumport, R.I. and Lehman, I.R. (1971) Structure of the DNA ligase-adenylate intermediate: lysine (epsilon-amino)-linked adenosine monophosphoramidate. Proc. Natl Acad. Sci. USA, 68, 2559-2563.
5. Tomkinson, A.E., Totty, N.F., Ginsburg, M. and Lindahl, T. (1991) Location of the active site for enzyme-adenylate formation in DNA ligases. Proc. Natl Acad. Sci. USA, 88, 400-404.
6. Kodama, K., Barnes, D.E. and Lindahl, T. (1991) In vitro mutagenesis and functional expression in Escherichia coli of a cDNA encoding the catalytic domain of human DNA ligase I. Nucleic Acids Res., 19, 6093-6099.
7. Olivera, B.M., Hall, Z.W. and Lehman, I.R. (1968) Enzymatic joining of polynucleotides: a DNA-adenylate intermediate in the polynucleotide joining reaction. Proc. Natl Acad. Sci. USA, 61, 237-244.
8. Harvey, C.L., Gabriel, T.F., Wilt, E.M. and Richardson, C.C. (1971) Enzymatic breakage and rejoining of deoxyribonucleic acid: synthesis and properties of the deoxyribonucleic acid adenylate in the phage T4 ligase reaction. J. Biol. Chem., 246, 4523-4530.
9. Subramanya, H.S., Doherty, A.J., Ashford, S.R. and Wigley, D.B. (1996) Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7. Cell, 85, 607-615.
10. Odell, M., Sriskanda, V., Shuman, S. and Nikolov, D.B. (2000) Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining. Mol. Cell, 6, 1183-1193.
11. Shuman, S. and Schwer, B. (1995) RNA capping enzyme and DNA ligase - a superfamily of covalent nucleotidyl transferases. Mol. Microbiol., 17, 405-410.
12. Håkansson, K., Doherty, A.J., Shuman, S. and Wigley, D.B. (1997). X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes. Cell, 89, 545-553.
13. Shuman, S. (2001) The mRNA capping apparatus as drug target and guide to eukaryotic phylogeny. Cold Spring Harbor Symp. Quant. Biol., 66, 301-312.
14. +-dependent DNA ligase: modular architecture and functional implications. EMBO J., 19, 1119-1129.
15. Fabrega, C., Shen, V., Shuman, S. and Lima, C.D. (2003) Structure of an mRNA capping enzyme bound to the phosphorylated carboxyl-terminal domain of RNA polymerase II. Mol. Cell, 11, 1549-1561.
16. Yin, S., Ho, C.K. and Shuman, S. (2003) Structure-function analysis of T4 RNA ligase 2. J. Biol. Chem., 278, 17601-17608.
17. Sriskanda, V. and Shuman, S. (1998) Chlorella virus DNA ligase: nick recognition and mutational analysis. Nucleic Acids Res., 26, 525-531.
18. Sriskanda, V. and Shuman, S. (2002) Role of nucleotidyl transferase motifs I, III and IV in the catalysis of phosphodiester bond formation by Chlorella virus DNA ligase. Nucleic Acids Res., 30, 903-911.
19. Sriskanda, V. and Shuman, S. (2002) Role of nucleotidyl transferase motif V in strand joining by Chlorella virus DNA ligase. J. Biol. Chem., 277, 9661-9667.
20. Sriskanda, V. and Shuman, S. (1998) Mutational analysis of Chlorella virus DNA ligase: catalytic role, of domain I and motif VI. Nucleic Acids Res., 26, 4618-4625.
21. Ho, C.K., Van Etten, J.L. and Shuman, S. (1997) Characterization of an ATP-dependent DNA ligase encoded by Chlorella virus PBCV-1. J. Virol., 71, 1931-1937.
22. Tomkinson, A.E. and Mackey, Z.B. (1998) Structure and function of mammalian DNA ligases. Mutat. Res., 407, 1-9.
23. Sriskanda, V., Schwer, B., Ho, C.K. and 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.
24. Odell, M. and Shuman, S. (1999) Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA. J. Biol. Chem., 274, 14032-14039.
25. Otwinowsky, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326.
26. Navaza, J. (1994) AMoRe: an automated package for molecular replacement. Acta Crystallogr. A, 50, 157-163.
27. Murshudov, G.N., Vagin, A.A. and Dodson, E.J. (1977) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D, 53, 240-255.
28. Winn, M.D., Isupov, M.N. and Murshudov, G.N. (2001) Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D, 57, 122-133.
29. Johnston, L.H. (1983) The cdc9 ligase joins completed replicons in baker's yeast. Mol. Gen. Genet., 190, 315-317.
30. Tomkinson, A.E., Tappe, N.J. and Friedberg, E.C. (1992) DNA ligase I from Saccharomyces cerevisiae: physical and biochemical characterization of the CDC9 gene product. Biochemistry, 31, 11762-11771.
31. Wu, X., Braithwaite, E. and Wang, Z. (1999) DNA ligation during excision repair in yeast cell-free extracts is specifically catalyzed by the CDC9 gene product. Biochemistry, 38, 2628-2635.
32. Wilson, T.E., Grawunder, U. and Lieber, M.R. (1997) Yeast DNA ligase IV mediates non-homologous DNA end joining. Nature, 388, 495-498.
33. Teo, S.H. and Jackson, S.P. (1997) Identification of Saccharomyces cerevisiae DNA ligase IV: involvement in DNA double-strand break repair. EMBO J., 16, 4788-4795.
34. Schär, P., Herrmann, G., Daly, G. and Lindahl, T. (1997) A newly identified DNA ligase of Saccharomyces cerevisiae involved in RAD52-independent repair of DNA double strand breaks. Genes Dev., 11, 1912-1924.
35. Lane, M.J., Paner, T., Kishin, I., Faldasz, B.D., Li, B., Gallo, F.J. and Benight, A.S. (1997) The thermodynamic advantage of DNA oligonucleotide 'stacking hybridization' reactions: energetic of a DNA nick. Nucleic Acids Res., 25, 611-616.
36. Nakatani, M., Ezaki, S., Atomi, H. and Imanaka, T. (2002) Substrate recognition and fidelity of strand joining by an archaeal DNA ligase. Eur. J. Biochem., 269, 650-656.
37. Pritchard, C.E. and Southern, E.M. (1997) Effects of base mismatches on joining of short oligodeoxynucleotides by DNA ligases. Nucleic Acids Res., 25, 3403-3407.
38. Hermann, G., Lindahl, T. and Schär, P. (1998) Saccharomyces cerevisiae LIF1: a function involved in DNA double-strand break repair related to mammalian XRCC4. EMBO J., 17, 4188-4198.
39. Teo, S.H. and Jackson, S.P. (2000) Lif1p targets the DNA ligase Lig4p to sites of DNA double-strand breaks. Curr. Biol., 10, 165-168.
40. Willer, M., Rainey, M., Pullen, T. and Stirling, C.J. (1999) The yeast CDC9 gene encodes both a nuclear and a mitochondrial form of DNA ligase I. Curr. Biol., 9, 1085-1094.
41. Donahue, S.L., Corner, B.E., Bordone, L. and Campbell, C. (2001) Mitochondrial DNA ligase function in Saccharomyces cerevisiae. Nucleic Acids Res., 29, 1582-1589.
42. Sweasy, J.B. and Loeb, L.A. (1992) Mammalian DNA polymerase β can substitute for DNA polymerase I during DNA replication in Escherichia coli. J. Biol. Chem., 267, 1407-1410.
43. Sweasy, J.B. and Loeb, L.A. (1993) Detection and characterization of mammalian DNA polymerase P mutants by functional complementation in Escherichia coli. Proc. Natl Acad. Sci. USA, 90, 4626-4630.
44. Sweasy, J.B., Chen, M. and Loeb, L.A. (1995) DNA polymerase β can substitute for DNA polymerase I in the initiation of plasmid DNA replication. J. Bacteriol., 177, 2923-2925.