2q2t
Structure of Chlorella virus DNA ligase-adenylate bound to a 5' phosphorylated nick
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| , resolution 2.300Å | |||||||
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| Ligands: | |||||||
| Gene: | A544R (Paramecium bursaria Chlorella virus 1) | ||||||
| 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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