Structural and mechanistic conservation in DNA ligases

Abstract

DNA ligases are enzymes required for the repair, replication and recombination of DNA. DNA ligases catalyse the formation of phosphodiester bonds at single-strand breaks in double-stranded DNA. Despite their occurrence in all organisms, DNA ligases show a wide diversity of amino acid sequences, molecular sizes and properties. The enzymes fall into two groups based on their cofactor specificity, those requiring NAD(+) for activity and those requiring ATP. The eukaryotic, viral and archael bacteria encoded enzymes all require ATP. NAD(+)-requiring DNA ligases have only been found in prokaryotic organisms. Recently, the crystal structures of a number of DNA ligases have been reported. It is the purpose of this review to summarise the current knowledge of the structure and catalytic mechanism of DNA ligases.

Characterization of an ATP-dependent DNA ligase from the acidophilic archaeon “Ferroplasma acidarmanus” Fer1

“…Bioinformatic analysis of the gene sequence suggested that gene 542 (falig) of the F. acidarmanus Fer1 genome would be an ATP-dependent DNA ligase and our in vitro biochemical studies using recombinant protein confirmed this to be the case. The bioinformatic analysis suggests that FaLig is likely to exhibit a modular three-dimensional structure, closely related to those obtained for other DNA ligases (Doherty and Suh 2000;Shuman and Lima 2004;Timson et al 2000;Tomkinson et al 2006). We observed that FaLig favoured Mg 2+ over other divalent cations, though significant activity was retained with Mn 2+ .…”

“…These enzymes are defined by the essential lysine residue situated within motif I, the first of a series of conserved colinear motifs (Doherty and Suh 2000;Shuman and Lima 2004;Tomkinson et al 2006). Closer examination of the sequences within the motifs of FaLig confirmed that it contains all amino acids that are essential for the function of nucleotidyl transferases and all amino acids that are highly conserved in predicted bacterial ATP-dependent DNA ligases (Wilkinson et al 2001) (Fig.…”

“…For the Archaea, the AMP moiety is generally provided by ATP (EC 6.5.1.1), while the essential DNA ligases of bacteria obtain this from NAD + (EC 6.5.1.2) (Wilkinson et al 2001). High resolution structures of several DNA ligases confirm that they exhibit a modular structure, with the common core required for adenylation linked to other domains that bind substrate (Doherty and Suh 2000;Shuman and Lima 2004;Tomkinson et al 2006).…”

“…These enzymes act to join breaks in the backbone of DNA and are essential for all cellular organisms due to the requirement for completion of replication, but they also participate in the repair and recombination of DNA (Doherty and Suh 2000;Shuman and Lima 2004;Tomkinson et al 2006;Wilkinson et al 2001). All nucleotidyl transferases are believed to operate through similar biochemical mechanisms consisting of three separate steps (Doherty and Suh 2000;Lehman 1974;Shuman and Lima 2004;Timson et al 2000;Wilkinson et al 2001). For DNA ligases the first step involves the enzyme attacking the a-phosphate of the nucleotide cosubstrate to form a covalent enzyme-adenylate (AMP) intermediate.…”

Identification of a novel motif in DNA ligases exemplified by DNA ligase IV

“…The DNA ligase IV/Xrcc4 complex is large and its crystal structure has not yet been solved. Structural analysis has relied in part on the use of a range of other ATPdependent DNA ligases as model systems [10][11][12][13][14][15]. The first step of ligation involves the formation of a covalent AMP-enzyme intermediate with AMP being attached to the enzyme via a highly conserved lysine residue.…”