2fcc

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spinqualitylabelsall models 2fcc, resolution 2.30Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with a DNA Substrate Containing Abasic Site

Overview

The base excision repair (BER) pathway for ultraviolet light (UV)-induced, cyclobutane pyrimidine dimers is initiated by DNA glycosylases that also, possess abasic (AP) site lyase activity. The prototypical enzyme known to, catalyze these reactions is the T4 pyrimidine dimer glycosylase (T4-Pdg)., The fundamental chemical reactions and the critical amino acids that lead, to both glycosyl and phosphodiester bond scission are known. Catalysis, proceeds via a protonated imine covalent intermediate between the, alpha-amino group of the N-terminal threonine residue and the C1' of the, deoxyribose sugar of the 5' pyrimidine at the dimer site. This covalent, complex can be trapped as an irreversible, reduced cross-linked, DNA-protein complex by incubation with a strong reducing agent. This, active site trapping reaction is equally efficient on DNA substrates, containing pyrimidine dimers or AP sites. Herein, we report the co-crystal, structure of T4-Pdg as a reduced covalent complex with an AP, site-containing duplex oligodeoxynucleotide. This high-resolution, structure reveals essential precatalytic and catalytic features, including, flipping of the nucleotide opposite the AP site, a sharp kink, (approximately 66 degrees ) in the DNA at the dimer site and the covalent, bond linking the enzyme to the DNA. Superposition of this structure with a, previously published co-crystal structure of a catalytically incompetent, mutant of T4-Pdg with cyclobutane dimer-containing DNA reveals new, insights into the structural requirements and the mechanisms involved in, DNA bending, nucleotide flipping and catalytic reaction.

About this Structure

2FCC is a Single protein structure of sequence from Bacteriophage t4 with SO4 and GOL as ligands. Active as Deoxyribonuclease (pyrimidine dimer), with EC number 3.1.25.1 Full crystallographic information is available from OCA.

Reference

Structure of T4 pyrimidine dimer glycosylase in a reduced imine covalent complex with abasic site-containing DNA., Golan G, Zharkov DO, Grollman AP, Dodson ML, McCullough AK, Lloyd RS, Shoham G, J Mol Biol. 2006 Sep 15;362(2):241-58. Epub 2006 Jul 7. PMID:16916523

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