Structural basis for nick recognition by a minimal pluripotent DNA ligase.

Publication Type:

Journal Article

Authors:

Nair, Pravin A; Nandakumar, Jayakrishnan; Smith, Paul; Odell, Mark; Lima, Christopher D; Shuman, Stewart

Source:

Nat Struct Mol Biol, Volume 14, Issue 8, p.770-8 (2007)

Keywords:

Binding Sites, Crystallography, X-Ray, DNA Breaks, Single-Stranded, DNA Ligases, Models, Molecular, Nucleotides, Protein Structure, Tertiary, Structure-Activity Relationship, Viral Proteins

Abstract:

<p>Chlorella virus DNA ligase, the smallest eukaryotic ligase known, has pluripotent biological activity and an intrinsic nick-sensing function, despite having none of the accessory domains found in cellular ligases. A 2.3-A crystal structure of the Chlorella virus ligase-AMP intermediate bound to duplex DNA containing a 3'-OH-5'-PO4 nick reveals a new mode of DNA envelopment, in which a short surface loop emanating from the OB domain forms a beta-hairpin 'latch' that inserts into the DNA major groove flanking the nick. A network of interactions with the 3'-OH and 5'-PO4 termini in the active site illuminates the DNA adenylylation mechanism and the crucial roles of AMP in nick sensing and catalysis. Addition of a divalent cation triggered nick sealing in crystallo, establishing that the nick complex is a bona fide intermediate in the DNA repair pathway.</p>