Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA : WestminsterResearch

Publication dates
Title	Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA
Authors	Odell, M. and Shuman, S.
Abstract	The 298-amino acid ATP-dependent DNA ligase of Chlorella virus PBCV-1 is the smallest eukaryotic DNA ligase known. The enzyme has intrinsic specificity for binding to nicked duplex DNA. To delineate the ligase-DNA interface, we have footprinted the enzyme binding site on DNA and the DNA binding site on ligase. The size of the exonuclease III footprint of ligase bound a single nick in duplex DNA is 19-21 nucleotides. The footprint is asymmetric, extending 8-9 nucleotides on the 3'-OH side of the nick and 11-12 nucleotides on the 5'-phosphate side. The 5'-phosphate moiety is essential for the binding of Chlorella virus ligase to nicked DNA. Here we show that the 3'-OH moiety is not required for nick recognition. The Chlorella virus ligase binds to a nicked ligand containing 2',3'-dideoxy and 5'-phosphate termini, but cannot catalyze adenylation of the 5'-end. Hence, the 3'-OH is important for step 2 chemistry even though it is not itself chemically transformed during DNA-adenylate formation. A 2'-OH cannot substitute for the essential 3'-OH in adenylation at a nick or even in strand closure at a preadenylated nick. The protein side of the ligase-DNA interface was probed by limited proteolysis of ligase with trypsin and chymotrypsin in the presence and absence of nicked DNA. Protease accessible sites are clustered within a short segment from amino acids 210-225 located distal to conserved motif V. The ligase is protected from proteolysis by nicked DNA. Protease cleavage of the native enzyme prior to DNA addition results in loss of DNA binding. These results suggest a bipartite domain structure in which the interdomain segment either comprises part of the DNA binding site or undergoes a conformational change upon DNA binding. The domain structure of Chlorella virus ligase inferred from the solution experiments is consistent with the structure of T7 DNA ligase determined by x-ray crystallography.
Journal	Journal of Biological Chemistry
Journal citation	274 (20), pp. 14032-14039
ISSN	0021-9258
Year	14 May 1999
Publisher	American Society for Biochemistry and Molecular Biology
Web address (URL)	http://www.jbc.org/cgi/content/abstract/274/20/14032
Published	14 May 1999

Related outputs

Fatty acid metabolism of Mycobacterium tuberculosis: a double-edged sword
Gaspar Quinonez, C., Lee, J.J., Lim, J., Odell, M., Lawson, C.P., Anyogu, A., Raheem, S. and Eoh, H. 2022. Fatty acid metabolism of Mycobacterium tuberculosis: a double-edged sword. mBio. 13 (1) e03559-21. https://doi.org/10.15698/mic2022.05.777

The Role of Fatty Acid Metabolism in Drug Tolerance of Mycobacterium tuberculosis
Gaspar Quinonez, C., Lee, J.J., Lim, J., Odell, M., Lawson, C.P., Anyogu, A., Raheem, S. and Eoh, H. 2022. The Role of Fatty Acid Metabolism in Drug Tolerance of Mycobacterium tuberculosis. mBio. 13 (1), pp. e03559-21. https://doi.org/10.1128/mbio.03559-21

Glutamate mediated metabolic neutralization mitigates propionate toxicity in intracellular Mycobacterium tuberculosis
Lee, J.J., Lim, J., Gao, S., Lawson, C.P., Odell, M., Raheem, S., Woo, J., Kang, S-H., Kang, S-S., Jeon, B-Y. and Eoh, H. 2018. Glutamate mediated metabolic neutralization mitigates propionate toxicity in intracellular Mycobacterium tuberculosis. Scientific Reports. 8 8506. https://doi.org/10.1038/s41598-018-26950-z

Arabidopsis AtPARK13, which confers thermotolerance, targets misfolded proteins
Basak, I., Pal, R., Patil, K.S., Dunne, A., Ho, H.P., Lee, S., Peiris, D., Maple-Grødem, J., Odell, M., Chang, E.J., Larsen, J.P. and Møller, S. 2014. Arabidopsis AtPARK13, which confers thermotolerance, targets misfolded proteins. Journal of Biological Chemistry. 289, pp. 14458-14469. https://doi.org/10.1074/jbc.M114.548156

ROS-mediated DJ-1 monomerization modulates intracellular trafficking involving Karyopherin-2
Bjørkblom, B., Maple-Grødem, J., Puno, M.R., Odell, M., Larsen, J.P. and Møller, S. 2014. ROS-mediated DJ-1 monomerization modulates intracellular trafficking involving Karyopherin-2. Molecular and Cellular Biology. 34 (16), pp. 3024-3040. https://doi.org/10.1128/MCB.00286-14

Proteomics analysis of Bacillus licheniformis in response to oligosaccharides elicitors
Reffatti, P.F., Roy, I., Odell, M. and Keshavarz, T. 2014. Proteomics analysis of Bacillus licheniformis in response to oligosaccharides elicitors. Enzyme Microb Technol. . 61-62, pp. 61-66. https://doi.org/10.1016/j.enzmictec.2014.03.007

Evidence for the involvement of intracellular Ca 2+ ions in the elicitation mechanism of Bacillus Licheniformis
Reffatti, P., Roy, I., Odell, M. and Keshavarz, T. 2013. Evidence for the involvement of intracellular Ca 2+ ions in the elicitation mechanism of Bacillus Licheniformis. Journal of Molecular Microbiology and Biotechnology. OnlineFirst. https://doi.org/10.1159/000351515

The neuroprotective role of catalase overexpression in SH-SY5Y cells against beta-amyloid and H2O2 toxicity
Chilumuri, A., Odell, M. and Milton, N.G.N. 2013. The neuroprotective role of catalase overexpression in SH-SY5Y cells against beta-amyloid and H2O2 toxicity. Alzheimer's & Dementia. 9 (4), p. P361.

Structure of Cu(I)-bound DJ-1 reveals a biscysteinate metal binding site at the homodimer interface: insights into mutational inactivation of DJ-1 in parkinsonism
Puno, M.R., Patel, N.A., Møller, S.G., Robinson, C.V., Moody, P.C.E. and Odell, M. 2013. Structure of Cu(I)-bound DJ-1 reveals a biscysteinate metal binding site at the homodimer interface: insights into mutational inactivation of DJ-1 in parkinsonism. Journal of the American Chemical Society. 135 (43), p. 15974–15977. https://doi.org/10.1021/ja406010m

Benzothiazole aniline-tetra(ethylene glycol) and 3-amino-1,2,4-triazole inhibit neuroprotection against amyloid peptides by catalase overexpression in vitro
Chilumuri, A., Odell, M. and Milton, N.G.N. 2013. Benzothiazole aniline-tetra(ethylene glycol) and 3-amino-1,2,4-triazole inhibit neuroprotection against amyloid peptides by catalase overexpression in vitro. ACS chemical neuroscience. 4 (11), pp. 1501-1512. https://doi.org/10.1021/cn400146a

Is quorum sensing involved in lovastatin production in the filamentous fungus Aspergillus terreus?
Raina, S., De Vizio, D., Palonen, E.K., Odell, M., Brandt, A.M., Soini, J.T. and Keshavarz, T. 2012. Is quorum sensing involved in lovastatin production in the filamentous fungus Aspergillus terreus? Process Biochemistry. 47 (5), pp. 843-852. https://doi.org/10.1016/j.procbio.2012.02.021

Identification, cloning and characterization of two N-acetylgalactosamine binding lectins from the albumen gland of Helix pomatia
Markiv, A., Peiris, D., Curley, G.P., Odell, M. and Dwek, M. 2011. Identification, cloning and characterization of two N-acetylgalactosamine binding lectins from the albumen gland of Helix pomatia. Journal of Biological Chemistry. 286 (23), pp. 20260-20266. https://doi.org/10.1074/jbc.M110.184515

Quorum sensing as a method for improving sclerotiorin production in Penicillium sclerotiorum
Raina, S., Odell, M. and Keshavarz, T. 2010. Quorum sensing as a method for improving sclerotiorin production in Penicillium sclerotiorum. Journal of Biotechnology. 148 (2-3), pp. 91-98. https://doi.org/10.1016/j.jbiotec.2010.04.009

Cancer prognostication using a recombinant form of the lectin from Helix pomatia agglutinin
Dwek, M., Markiv, A. and Odell, M. 2009. Cancer prognostication using a recombinant form of the lectin from Helix pomatia agglutinin. Glycobiology. 19 (11), p. 1318. https://doi.org/10.1093/glycob/cwp135

Microbial quorum sensing: a tool or a target for antimicrobial therapy?
Raina, S., De Vizio, D., Odell, M., Clements, M.O., Vanhulle, S. and Keshavarz, T. 2009. Microbial quorum sensing: a tool or a target for antimicrobial therapy? Biotechnology and Applied Biochemistry. 54 (2), pp. 65-84. https://doi.org/10.1042/BA20090072

Polyhydroxyalkanoate synthase in Bacillus cereus SPV, a class IV PHA synthase
Philip, S.E., Odell, M., Keshavarz, T. and Roy, I. 2008. Polyhydroxyalkanoate synthase in Bacillus cereus SPV, a class IV PHA synthase. 11th International Symposium on Biodegradable Polyesters. Massey University in Auckland, New Zealand 23 - 26 Nov 2008

Structural basis for nick recognition by a minimal pluripotent DNA ligase
Nair, P.A., Nandakumar, J., Smith, P., Odell, M., Lima, C.D. and Shuman, S. 2007. Structural basis for nick recognition by a minimal pluripotent DNA ligase. Nature Structural and Molecular Biology. 14 (8), pp. 770-778. https://doi.org/10.1038/nsmb1266

Polyhydroxy-alkanoates - the biodegradable polymers
Philip, S.E., Odell, M., Keshavarz, T. and Roy, I. 2007. Polyhydroxy-alkanoates - the biodegradable polymers. International Conference on Biodegradable Polymers: their production, characterisation and application. SCI, London 10 Dec 2007

Circadian orchestration of the hepatic proteome
Reddy, A.B., Karp, N.A., Maywood, E.S., Sage, E.A., Deery, M., O'Neill, J.S., Wong, G.K.Y., Chesham, J., Odell, M., Lilley, K.S., Kyriacou, C.P. and Hastings, M.H. 2006. Circadian orchestration of the hepatic proteome. Current Biology. 16 (11), pp. 1107-1115. https://doi.org/10.1016/j.cub.2006.04.026

Polyhydroxyalkanoate synthases: the enzymes involved in biodegradable polymer synthesis
Valappil, S.P., Philip, S.E., Odell, M., Keshavarz, T. and Roy, I. 2005. Polyhydroxyalkanoate synthases: the enzymes involved in biodegradable polymer synthesis. Proceedings of Frontiers in Chemical Biology: Mechanistic Enzymology and Biocatalysis. Exeter, UK 31 Aug - 02 Sep 2005

DNA Ligases: Stuctures
Odell, M. 2004. DNA Ligases: Stuctures. in: Lennarz, W.J. and Lane, M.D. (ed.) Encyclopedia of biological chemistry Amsterdam, Netherlands Elsevier.

No ARM in it? (reply to Kippert and Gerloff)
Kyriacou, C.P. and Odell, M. 2004. No ARM in it? (reply to Kippert and Gerloff). Current Biology. 14 (16), pp. R652-R653. https://doi.org/10.1016/j.cub.2004.08.009

Analysis of the DNA joining repertoire of Chlorella virus DNA ligase and a new crystal structure of the ligase-adenylate intermediate
Odell, M., Malinina, L., Sriskanda, V., Teplova, M. and 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 Research. 31 (17), pp. 5090-5100. https://doi.org/10.1093/nar/gkg665

Structure-based experimental confirmation of biochemical function to a methyltransferase, MJ0882, from hyperthermophile Methanococcus jannaschii
Huang, L., Hung, L., Odell, M., Yokota, H., Kim, R. and Kim, S.H. 2002. Structure-based experimental confirmation of biochemical function to a methyltransferase, MJ0882, from hyperthermophile Methanococcus jannaschii. Journal of Structural and Functional Genomics. 2 (3), pp. 121-127. https://doi.org/10.1023/A:1021279113558

The Drosophila clock protein Timeless is a member of the Arm/HEAT family
Vodovar, N., Clayton, J., Costa, R., Odell, M. and Kyriacou, C.P. 2002. The Drosophila clock protein Timeless is a member of the Arm/HEAT family. Current Biology. 12 (18), pp. R610-R611. https://doi.org/10.1016/S0960-9822(02)01130-2

Crystal structure of eukaryotic DNA ligase–adenylate illuminates the mechanism of nick sensing and strand joining
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. Molecular Cell. 6 (5), pp. 1183-1193.

Permalink - https://westminsterresearch.westminster.ac.uk/item/94537/footprinting-of-chlorella-virus-dna-ligase-bound-at-a-nick-in-duplex-dna

Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA

Related outputs

Share this

Usage statistics

Export as