ATP-dependent DNA ligase fromThermococcussp. 1519 displays a new arrangement of the OB-fold domain

Abstract

DNA ligases join single-strand breaks in double-stranded DNA by catalyzing the formation of a phosphodiester bond between adjacent 5 0-phosphate and 3 0-hydroxyl termini. Their function is essential for maintaining genome integrity in the replication, recombination and repair of DNA. High flexibility is important for the function of DNA ligase molecules. Two types of overall conformations of archaeal DNA ligase that depend on the relative position of the OB-fold domain have previously been revealed: closed and open extended conformations. The structure of ATP-dependent DNA ligase from Thermococcus sp. 1519 (LigTh1519) in the crystalline state determined at a resolution of 3.02 Å shows a new relative arrangement of the OB-fold domain which is intermediate between the positions of this domain in the closed and the open extended conformations of previously determined archaeal DNA ligases. However, small-angle X-ray scattering (SAXS) measurements indicate that in solution the LigTh1519 molecule adopts either an open extended conformation or both an intermediate and an open extended conformation with the open extended conformation being dominant.

Structure of the Catalytic Region of DNA Ligase IV in Complex with an Artemis Fragment Sheds Light on Double-Strand Break Repair

“…In the crystals, the structure of LigIV 1–609 is captured in an open conformation and probably stabilized by burying a surface of area 1,104 Å 2 between OBD and NTD. This differs from other open conformations of archaeal DNA ligases available in the Protein Data Bank (PDB) (Pascal et al., 2006; Petrova et al., 2012), the buried areas of which are 337 and 80 Å 2 , respectively. Given that the archaeal structures have much smaller buried areas, they are likely to be more flexible than human LigIV and the observed conformers may be stabilized by crystallographic contacts.…”

From Structure-Function Analyses to Protein Engineering for Practical Applications of DNA Ligase

“…In contrast, three crystal structures of large ATP-dependent DNA ligases, which mainly ligate the nicks between Okazaki fragment in DNA replication in Eukarya and Archaea, with an additional N-terminal DNA-binding domain (DBD), have been reported ( Figure 9(a) , bottom) [ 9 – 11 , 82 , 83 ]. This extra domain is not essential for hLigI activity in vitro [ 84 , 85 ] but is considered to be crucial for detecting a singly nicked dsDNA [ 9 ].…”

Archaeal Nucleic Acid Ligases and Their Potential in Biotechnology

“…To date, the structures of six archaeal DNA ligases have been solved, from Archaeoglobus fulgidus [ 25 ], Pyrococcus furiosus [ 26 , 27 ], Sulfolobus solfataricus [ 28 ], S. zilligii [ 29 ], Thermococcus sibiricus [ 30 ], and Thermococcus sp. 1519 [ 31 ]. Each enzyme comprises three domains: the adenylation domain (AdD), the oligonucleotide-binding domain (OBD), and the N-terminal DNA-binding domain (DBD).…”