Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1997 Feb 15;25(4):727–734. doi: 10.1093/nar/25.4.727

Domain structure of vaccinia DNA ligase.

J Sekiguchi 1, S Shuman 1
PMCID: PMC146513  PMID: 9016621

Abstract

The 552 amino acid vaccinia virus DNA ligase consists of three structural domains defined by partial proteolysis: (i) an amino-terminal 175 amino acid segment that is susceptible to digestion with chymotrypsin and trypsin; (ii) a protease-resistant central domain that contains the active site of nucleotidyl transfer (Lys-231); (iii) a protease-resistant carboxyl domain. The two protease-resistant domains are separated by a protease-sensitive interdomain bridge from positions 296 to 307. Adenylyltransferase and DNA ligation activities are preserved when the N-terminal 200 amino acids are deleted. However, the truncated form of vaccinia ligase has a reduced catalytic rate in strand joining and a lower affinity for DNA than does the full-sized enzyme. The 350 amino acid catalytic core of the vaccinia ligase is similar in size and protease-sensitivity to the full-length bacteriophage T7 DNA ligase.

Full Text

The Full Text of this article is available as a PDF (150.3 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Barnes D. E., Johnston L. H., Kodama K., Tomkinson A. E., Lasko D. D., Lindahl T. Human DNA ligase I cDNA: cloning and functional expression in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1990 Sep;87(17):6679–6683. doi: 10.1073/pnas.87.17.6679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Chen J., Tomkinson A. E., Ramos W., Mackey Z. B., Danehower S., Walter C. A., Schultz R. A., Besterman J. M., Husain I. Mammalian DNA ligase III: molecular cloning, chromosomal localization, and expression in spermatocytes undergoing meiotic recombination. Mol Cell Biol. 1995 Oct;15(10):5412–5422. doi: 10.1128/mcb.15.10.5412. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cong P., Shuman S. Covalent catalysis in nucleotidyl transfer. A KTDG motif essential for enzyme-GMP complex formation by mRNA capping enzyme is conserved at the active sites of RNA and DNA ligases. J Biol Chem. 1993 Apr 5;268(10):7256–7260. [PubMed] [Google Scholar]
  4. Cong P., Shuman S. Mutational analysis of mRNA capping enzyme identifies amino acids involved in GTP binding, enzyme-guanylate formation, and GMP transfer to RNA. Mol Cell Biol. 1995 Nov;15(11):6222–6231. doi: 10.1128/mcb.15.11.6222. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Doherty A. J., Ashford S. R., Wigley D. B. Characterization of proteolytic fragments of bacteriophage T7 DNA ligase. Nucleic Acids Res. 1996 Jun 15;24(12):2281–2287. doi: 10.1093/nar/24.12.2281. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Husain I., Tomkinson A. E., Burkhart W. A., Moyer M. B., Ramos W., Mackey Z. B., Besterman J. M., Chen J. Purification and characterization of DNA ligase III from bovine testes. Homology with DNA ligase II and vaccinia DNA ligase. J Biol Chem. 1995 Apr 21;270(16):9683–9690. doi: 10.1074/jbc.270.16.9683. [DOI] [PubMed] [Google Scholar]
  7. Kerr S. M., Johnston L. H., Odell M., Duncan S. A., Law K. M., Smith G. L. Vaccinia DNA ligase complements Saccharomyces cerevisiae cdc9, localizes in cytoplasmic factories and affects virulence and virus sensitivity to DNA damaging agents. EMBO J. 1991 Dec;10(13):4343–4350. doi: 10.1002/j.1460-2075.1991.tb05012.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Kletzin A. Molecular characterisation of a DNA ligase gene of the extremely thermophilic archaeon Desulfurolobus ambivalens shows close phylogenetic relationship to eukaryotic ligases. Nucleic Acids Res. 1992 Oct 25;20(20):5389–5396. doi: 10.1093/nar/20.20.5389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Kodama K., Barnes D. E., Lindahl T. In vitro mutagenesis and functional expression in Escherichia coli of a cDNA encoding the catalytic domain of human DNA ligase I. Nucleic Acids Res. 1991 Nov 25;19(22):6093–6099. doi: 10.1093/nar/19.22.6093. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Lehman I. R. DNA ligase: structure, mechanism, and function. Science. 1974 Nov 29;186(4166):790–797. doi: 10.1126/science.186.4166.790. [DOI] [PubMed] [Google Scholar]
  11. Lindahl T., Barnes D. E. Mammalian DNA ligases. Annu Rev Biochem. 1992;61:251–281. doi: 10.1146/annurev.bi.61.070192.001343. [DOI] [PubMed] [Google Scholar]
  12. Montecucco A., Savini E., Weighardt F., Rossi R., Ciarrocchi G., Villa A., Biamonti G. The N-terminal domain of human DNA ligase I contains the nuclear localization signal and directs the enzyme to sites of DNA replication. EMBO J. 1995 Nov 1;14(21):5379–5386. doi: 10.1002/j.1460-2075.1995.tb00222.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Odell M., Kerr S. M., Smith G. L. Ligation of double-stranded and single-stranded [oligo(dT)] DNA by vaccinia virus DNA ligase. Virology. 1996 Jul 1;221(1):120–129. doi: 10.1006/viro.1996.0358. [DOI] [PubMed] [Google Scholar]
  14. Riggs A. D., Suzuki H., Bourgeois S. Lac repressor-operator interaction. I. Equilibrium studies. J Mol Biol. 1970 Feb 28;48(1):67–83. doi: 10.1016/0022-2836(70)90219-6. [DOI] [PubMed] [Google Scholar]
  15. Schwer B., Shuman S. Mutational analysis of yeast mRNA capping enzyme. Proc Natl Acad Sci U S A. 1994 May 10;91(10):4328–4332. doi: 10.1073/pnas.91.10.4328. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Shuman S., Liu Y., Schwer B. Covalent catalysis in nucleotidyl transfer reactions: essential motifs in Saccharomyces cerevisiae RNA capping enzyme are conserved in Schizosaccharomyces pombe and viral capping enzymes and among polynucleotide ligases. Proc Natl Acad Sci U S A. 1994 Dec 6;91(25):12046–12050. doi: 10.1073/pnas.91.25.12046. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Shuman S., Ru X. M. Mutational analysis of vaccinia DNA ligase defines residues essential for covalent catalysis. Virology. 1995 Aug 1;211(1):73–83. doi: 10.1006/viro.1995.1380. [DOI] [PubMed] [Google Scholar]
  18. Shuman S., Schwer B. RNA capping enzyme and DNA ligase: a superfamily of covalent nucleotidyl transferases. Mol Microbiol. 1995 Aug;17(3):405–410. doi: 10.1111/j.1365-2958.1995.mmi_17030405.x. [DOI] [PubMed] [Google Scholar]
  19. Shuman S. Vaccinia virus DNA ligase: specificity, fidelity, and inhibition. Biochemistry. 1995 Dec 12;34(49):16138–16147. doi: 10.1021/bi00049a029. [DOI] [PubMed] [Google Scholar]
  20. Smith G. L., Chan Y. S., Kerr S. M. Transcriptional mapping and nucleotide sequence of a vaccinia virus gene encoding a polypeptide with extensive homology to DNA ligases. Nucleic Acids Res. 1989 Nov 25;17(22):9051–9062. doi: 10.1093/nar/17.22.9051. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Subramanya H. S., Doherty A. J., Ashford S. R., Wigley D. B. Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7. Cell. 1996 May 17;85(4):607–615. doi: 10.1016/s0092-8674(00)81260-x. [DOI] [PubMed] [Google Scholar]
  22. Tomkinson A. E., Tappe N. J., Friedberg E. C. DNA ligase I from Saccharomyces cerevisiae: physical and biochemical characterization of the CDC9 gene product. Biochemistry. 1992 Dec 1;31(47):11762–11771. doi: 10.1021/bi00162a013. [DOI] [PubMed] [Google Scholar]
  23. Wei Y. F., Robins P., Carter K., Caldecott K., Pappin D. J., Yu G. L., Wang R. P., Shell B. K., Nash R. A., Schär P. Molecular cloning and expression of human cDNAs encoding a novel DNA ligase IV and DNA ligase III, an enzyme active in DNA repair and recombination. Mol Cell Biol. 1995 Jun;15(6):3206–3216. doi: 10.1128/mcb.15.6.3206. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES