Structural basis for nick recognition by a minimal pluripotent DNA ligase.
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.
Nair
Pravin A
PA
Molecular Biology and Structural Biology Programs, Sloan-Kettering Institute, New York, New York 10021, USA.
Nandakumar
Jayakrishnan
J
Smith
Paul
P
Odell
Mark
M
Lima
Christopher D
CD
Shuman
Stewart
S
D001665:Binding Sites; D018360:Crystallography, X-Ray; D053904:DNA Breaks, Single-Stranded; D011088:DNA Ligases / Q000737:chemistry* / Q000502:physiology; D008958:Models, Molecular; D009711:Nucleotides / Q000737:chemistry / Q000378:metabolism; D017434:Protein Structure, Tertiary; D013329:Structure-Activity Relationship; D014764:Viral Proteins / Q000737:chemistry* / Q000502:physiology
D009711:Nucleotides; D014764:Viral Proteins; C110456:Chlorella virus DNA ligase; D011088:DNA Ligases