Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide.
Tyrosyl-DNA phosphodiesterase (Tdp1) is a member of the phospholipase D superfamily and acts as a DNA repair enzyme that removes stalled topoisomerase I- DNA complexes by hydrolyzing the bond between a tyrosine side chain and a DNA 3' phosphate. Despite the complexity of the substrate of this phosphodiesterase, vanadate succeeded in linking human Tdp1, a tyrosine-containing peptide, and a single-stranded DNA oligonucleotide into a quaternary complex that mimics the transition state for the first step of the catalytic reaction. The conformation of the bound substrate mimic gives compelling evidence that the topoisomerase I-DNA complex must undergo extensive modification prior to cleavage by Tdp1. The structure also illustrates that the use of vanadate as the central moiety in high-order complexes has the potential to be a general method for capturing protein-substrate interactions for phosphoryl transfer enzymes, even when the substrates are large, complicated, and unusual.
Davies
Douglas R
DR
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Interthal
Heidrun
H
Champoux
James J
JJ
Hol
Wim G J
WG
D003460:Crystallization; D018360:Crystallography, X-Ray; D004247:DNA / Q000378:metabolism*; D004264:DNA Topoisomerases, Type I / Q000737:chemistry*; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D018716:Molecular Mimicry; D009841:Oligonucleotides / Q000737:chemistry; D010727:Phosphoric Diester Hydrolases / Q000737:chemistry*; D011487:Protein Conformation; D014638:Vanadates / Q000737:chemistry*
D009841:Oligonucleotides; D014638:Vanadates; D004247:DNA; D010727:Phosphoric Diester Hydrolases; C498508:TDP1 protein, human; C122147:tyrosyl-DNA phosphodiesterase; D004264:DNA Topoisomerases, Type I