Structure of Chlorella virus DNA ligase-adenylate bound to a 5' phosphorylated nick

File:2q2t.gif


PDB ID 2q2t

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, resolution 2.300Å
Ligands: , , , , ,
Gene: A544R (Paramecium bursaria Chlorella virus 1)
Related: 1FVI, 2Q2U


Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



OverviewOverview

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.

About this StructureAbout this Structure

2Q2T is a Single protein structure of sequence from Paramecium bursaria chlorella virus 1. Full crystallographic information is available from OCA.

ReferenceReference

Structural basis for nick recognition by a minimal pluripotent DNA ligase., Nair PA, Nandakumar J, Smith P, Odell M, Lima CD, Shuman S, Nat Struct Mol Biol. 2007 Aug;14(8):770-8. Epub 2007 Jul 8. PMID:17618295

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