SNAP output for PDB entry 3spd [SNAP web server]

PDB-id

3spd; SNAP-derived features in text and JSON formats; DNAproDB

Class

hydrolase-DNA

Method

X-ray (1.912 Å)

Summary

Crystal structure of aprataxin ortholog hnt3 in complex with DNA

Reference

Gong Y, Zhu D, Ding J, Dou C, Ren X, Gu L, Jiang T, Wang D (2011): "Crystal structures of aprataxin ortholog Hnt3 reveal the mechanism for reversal of 5'-adenylated DNA." Nat.Struct.Mol.Biol., 18, 1297-1299. doi: 10.1038/nsmb.2145.

Abstract

Aprataxin is a DNA deadenylase that resolves DNA 5'-AMP termini and reverses abortive DNA ligation. The crystal structures of Schizosaccharomyces pombe aprataxin Hnt3 in its apo form and in complex to dsDNA and dsDNA-AMP reveal how Hnt3 recognizes and processes 5'-adenylated DNA in a structure-specific manner. The bound DNA adopts a 5'-flap conformation that facilitates 5'-AMP access to the active site, where AMP cleavage occurs by a canonical catalytic mechanism.