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

PDB-id

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

Class

transferase-DNA

Method

X-ray (3.1 Å)

Summary

Polymerase domain from mycobacterium tuberculosis ligase d in complex with DNA, utp and manganese.

Reference

Brissett NC, Martin MJ, Pitcher RS, Bianchi J, Juarez R, Green AJ, Fox GC, Blanco L, Doherty AJ (2011): "Structure of a Preternary Complex Involving a Prokaryotic NHEJ DNA Polymerase." Mol.Cell, 41, 221-231. doi: 10.1016/j.molcel.2010.12.026.

Abstract

In many prokaryotes, a specific DNA primase/polymerase (PolDom) is required for nonhomologous end joining (NHEJ) repair of DNA double-strand breaks (DSBs). Here, we report the crystal structure of a catalytically active conformation of Mycobacterium tuberculosis PolDom, consisting of a polymerase bound to a DNA end with a 3' overhang, two metal ions, and an incoming nucleotide but, significantly, lacking a primer strand. This structure represents a polymerase:DNA complex in a preternary intermediate state. This polymerase complex occurs in solution, stabilizing the enzyme on DNA ends and promoting nucleotide extension of short incoming termini. We also demonstrate that the invariant Arg(220), contained in a conserved loop (loop 2), plays an essential role in catalysis by regulating binding of a second metal ion in the active site. We propose that this NHEJ intermediate facilitates extension reactions involving critically short or noncomplementary DNA ends, thus promoting break repair and minimizing sequence loss during DSB repair.