DNA Ligases

Abstract

DNA ligases are essential enzymes that catalyse the formation of a phosphodiester bond at a discontinuity in the deoxyribose phosphate backbone of duplex DNA.

Keywords: DNA ligase; polynucleotide ligase; RNA capping enzymes; phosphodiester bond formation; NAD+; NMN; ATP; DNA; nicked

Figure 1.

Pathways leading to the formation of the substrate of DNA ligase. The horizontal lines represent DNA strands associated by hydrogen‐bonded base pairs, which are represented by the short vertical lines. (a) The red asterisk and lines represent a damaged base that is removed to leave a gap in the duplex. A DNA polymerase fills (green line) the gap to leave a nicked DNA. (b). The red coloured portion of the upper strand is the RNA primer of an Okazaki fragment that is also removed and the gap filled to produce a nicked molecule. DNA ligase eradicates the discontinuity by synthesizing a phosphodiester bond. Reprinted from Subramanya et al. (1996). Cell85: 607–615. Copyright © 1996 with permission from Elsevier Science.

Figure 2.

The mechanism of an ATP‐dependent DNA ligase reaction. Step 1, the amino group of the active site lysine attacks the α‐phosphate of ATP, where A represents adenosine, to form a phosphoamide‐linked AMP with the elimination of PPi. Step 2, the 5′‐phosphate at the nick attacks the activated phosphoryl group of the AMP to form an adenylated DNA. Step 3, the nonadenylated enzyme catalyses the attack of the 3′‐OH of the DNA at the nick upon the activated 5′‐phosphate to form the phosphodiester bond and release AMP. The reaction of an NAD+‐dependent enzyme is analogous except that NAD+ provides the adenyl group and NMN is released rather than PPi.

Figure 3.

Motif alignments for DNA ligases and RNA capping enzymes. The ligases are grouped in the top section, capping enzymes in the bottom section. Enzymes are from human (Hu), vaccinia virus (vac), Desulfurolobus ambivalens (Dam), Methanococcus jannaschii (Mja), Saccharomyces cerevisiae (Sce), Schizosaccharomyces pombe (Spo), African swine fever virus (asf), mouse (Mus), and Chlorella virus (ChV). Interactions of conserved side‐chains with moieties on the nucleotide (revealed by crystal structures of T7 ligase and Chlorella virus capping enzyme) are denoted by arrows at the bottom. The dashes before motif I indicate that N‐terminal amino acids precede it. The numbers between hyphens indicate the number of amino acids between motifs.

Figure 4.

Structure of bacteriophage T7 DNA ligase•ATP complex (Subramanya et al., ). The crystallographic coordinates for the structure are available from the Brookhaven Protein Data Bank (Accession Code 1A0I). A ribbon structure is shown for the protein and the ATP is coloured orange. The conserved motifs (see text and Figure ) are coloured yellow (motif I), green (motif III), light blue (motif IIIa), red–orange (motif IV), magenta (motif V), and dark blue (motif VI).

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References

Cheng C and Shuman S (1997) Characterization of an ATP‐dependent DNA ligase encoded by Haemophilus influenzae. Nucleic Acids Research 25: 1369–1375.

Hakansson K, Doherty AJ, Shuman S and Wigley DB (1997) X‐ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes. Cell 89: 545–553.

Lehman IR (1974) DNA ligase: structure, mechanism, and function. Science 186: 790–797.

Luo J, Bergstrom DE and Barany F (1996) Improving the fidelity of Thermus thermophilus DNA ligase. Nucleic Acids Research 24: 3071–3078.

Sekiguchi J and Shuman S (1997) Nick sensing by DNA ligase requires a 5′ phosphate at the nick and occupancy of the adenylate binding site on the enzyme. Journal of Virology 71: 9679–9684.

Shuman S and Schwer B (1995) RNA capping enzyme and DNA ligase: a superfamily of covalent nucleotidyl transferases. Molecular Microbiology 17: 405–410.

Singleton MR, Hakansson K, Timson DJ and Wigley DB (1999) Structure of the adenylation domain of an NAD+‐dependent DNA ligase. Structure 7: 35–42.

Sriskanda V and Shuman S (1998a) Specificity and fidelity of strand joining by Chorella virus DNA ligase. Nucleic Acids Research 26: 3536–3541.

Sriskanda V and Shuman S (1998b) Chlorella virus DNA ligase: nick recognition and mutational analysis. Nucleic Acids Research 26: 525–531.

Subramanya HS, Doherty AJ, Ashford SR and Wigley DB (1996) Crystal structure of an ATP‐dependent DNA ligase from bacteriophage T7. Cell 85: 607–615.

Tomkinson AE and Mackey ZB (1998) Structure and function of mammalian DNA ligases. Mutation Research 407: 1–9.

Further Reading

Gumport RI and Lehman IR (1971) Structure of the DNA ligase–adenylate intermediate: lysine (ε‐amino‐linked) adenosine monophosphoramidate. Proceedings of the National Academy of Sciences of the USA 68: 2559–2563.

Harvey CL, Gabriel TF, Wilt EM and Richardson CC (1971) Enzymatic breakage and joining of deoxyribonucleic acid, IX. Synthesis and properties of the deoxyribonucleic acid adenylate in the phage T4 ligase reaction. Journal of Biological Chemistry 246: 4523–4530.

Modrich P and Lehman IR (1973) Deoxyribonucleic acid ligase: a steady state kinetic analysis of the enzyme from Escherichia coli. Journal of Biological Chemistry 248: 7502–7511.

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How to Cite close
Shuman, Stewart, and Gumport, Richard I(Jan 2002) DNA Ligases. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0001057]