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. 1997 Apr 1;25(7):1369–1374. doi: 10.1093/nar/25.7.1369

Characterization of an ATP-dependent DNA ligase encoded by Haemophilus influenzae.

C Cheng 1, S Shuman 1
PMCID: PMC146593  PMID: 9060431

Abstract

We report that Haemophilus influenzae encodes a 268 amino acid ATP-dependent DNA ligase. The specificity of Haemophilus DNA ligase was investigated using recombinant protein produced in Escherichia coli. The enzyme catalyzed efficient strand joining on a singly nicked DNA in the presence of magnesium and ATP (Km = 0.2 microM). Other nucleoside triphosphates or deoxynucleoside triphosphates could not substitute for ATP. Haemophilus ligase reacted with ATP in the absence of DNA substrate to form a covalent ligase-adenylate intermediate. This nucleotidyl transferase reaction required a divalent cation and was specific for ATP. The Haemophilus enzyme is the first example of an ATP-dependent DNA ligase encoded by a eubacterial genome. It is also the smallest member of the covalent nucleotidyl transferase superfamily, which includes the bacteriophage and eukaryotic ATP-dependent polynucleotide ligases and the GTP-dependent RNA capping enzymes.

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Selected References

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  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. Fleischmann R. D., Adams M. D., White O., Clayton R. A., Kirkness E. F., Kerlavage A. R., Bult C. J., Tomb J. F., Dougherty B. A., Merrick J. M. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995 Jul 28;269(5223):496–512. doi: 10.1126/science.7542800. [DOI] [PubMed] [Google Scholar]
  6. Fresco L. D., Buratowski S. Active site of the mRNA-capping enzyme guanylyltransferase from Saccharomyces cerevisiae: similarity to the nucleotidyl attachment motif of DNA and RNA ligases. Proc Natl Acad Sci U S A. 1994 Jul 5;91(14):6624–6628. doi: 10.1073/pnas.91.14.6624. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hammond J. M., Kerr S. M., Smith G. L., Dixon L. K. An African swine fever virus gene with homology to DNA ligases. Nucleic Acids Res. 1992 Jun 11;20(11):2667–2671. doi: 10.1093/nar/20.11.2667. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Ho C. K., Van Etten J. L., Shuman S. Characterization of an ATP-dependent DNA ligase encoded by Chlorella virus PBCV-1. J Virol. 1997 Mar;71(3):1931–1937. doi: 10.1128/jvi.71.3.1931-1937.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Ho C. K., Van Etten J. L., Shuman S. Expression and characterization of an RNA capping enzyme encoded by Chlorella virus PBCV-1. J Virol. 1996 Oct;70(10):6658–6664. doi: 10.1128/jvi.70.10.6658-6664.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. 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]
  11. 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]
  12. 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]
  13. 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]
  14. Montecucco A., Lestingi M., Pedrali-Noy G., Spadari S., Ciarrocchi G. Use of ATP, dATP and their alpha-thio derivatives to study DNA ligase adenylation. Biochem J. 1990 Oct 1;271(1):265–268. doi: 10.1042/bj2710265. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Niles E. G., Christen L. Identification of the vaccinia virus mRNA guanyltransferase active site lysine. J Biol Chem. 1993 Nov 25;268(33):24986–24989. [PubMed] [Google Scholar]
  16. Preston A., Maskell D., Johnson A., Moxon E. R. Altered lipopolysaccharide characteristic of the I69 phenotype in Haemophilus influenzae results from mutations in a novel gene, isn. J Bacteriol. 1996 Jan;178(2):396–402. doi: 10.1128/jb.178.2.396-402.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. 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]
  18. Shuman S., Golder M., Moss B. Characterization of vaccinia virus DNA topoisomerase I expressed in Escherichia coli. J Biol Chem. 1988 Nov 5;263(31):16401–16407. [PubMed] [Google Scholar]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. Tatusov R. L., Mushegian A. R., Bork P., Brown N. P., Hayes W. S., Borodovsky M., Rudd K. E., Koonin E. V. Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli. Curr Biol. 1996 Mar 1;6(3):279–291. doi: 10.1016/s0960-9822(02)00478-5. [DOI] [PubMed] [Google Scholar]
  26. Teraoka H., Sumikawa T., Tsukada K. Purification of DNA ligase II from calf thymus and preparation of rabbit antibody against calf thymus DNA ligase II. J Biol Chem. 1986 May 25;261(15):6888–6892. [PubMed] [Google Scholar]
  27. 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]
  28. Tomkinson A. E., Totty N. F., Ginsburg M., Lindahl T. Location of the active site for enzyme-adenylate formation in DNA ligases. Proc Natl Acad Sci U S A. 1991 Jan 15;88(2):400–404. doi: 10.1073/pnas.88.2.400. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Wang Y. C., Burkhart W. A., Mackey Z. B., Moyer M. B., Ramos W., Husain I., Chen J., Besterman J. M., Tomkinson A. E. Mammalian DNA ligase II is highly homologous with vaccinia DNA ligase. Identification of the DNA ligase II active site for enzyme-adenylate formation. J Biol Chem. 1994 Dec 16;269(50):31923–31928. [PubMed] [Google Scholar]
  30. 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]

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