1MU9

Crystal Structure of a Human Tyrosyl-DNA Phosphodiesterase (Tdp1)-Vanadate Complex

Summary for 1MU9

• Entry DOI: 10.2210/pdb1mu9/pdb
• Related: 1jy1 1mu7
• Descriptor: Tyrosyl-DNA Phosphodiesterase, VANADATE ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: pld superfamily, protein-vanadate complex, hydrolase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 109876.46

Authors

Davies, D.R.,Interthal, H.,Champoux, J.J.,Hol, W.G.J. (deposition date: 2002-09-23, release date: 2003-01-07, Last modification date: 2024-02-14)

Primary citation

Davies, D.R.,Interthal, H.,Champoux, J.J.,Hol, W.G.J.
Insights Into Substrate Binding and Catalytic Mechanism of Human Tyrosyl-DNA Phosphodiesterase (Tdp1) from Vanadate- and Tungstate-Inhibited Structures
J.Mol.Biol., 324:917-932, 2002

PubMed Abstract: Tyrosyl-DNA phosphodiesterase (Tdp1) is a DNA repair enzyme that catalyzes the hydrolysis of a phosphodiester bond between a tyrosine residue and a DNA 3'-phosphate. The only known example of such a linkage in eukaryotic cells occurs normally as a transient link between a type IB topoisomerase and DNA. Thus human Tdp1 is thought to be responsible for repairing lesions that occur when topoisomerase I becomes stalled on the DNA in the cell. Tdp1 has also been shown to remove glycolate from single-stranded DNA containing a 3'-phosphoglycolate, suggesting a role for Tdp1 in repair of free-radical mediated DNA double-strand breaks. We report the three-dimensional structures of human Tdp1 bound to the phosphate transition state analogs vanadate and tungstate. Each structure shows the inhibitor covalently bound to His263, confirming that this residue is the nucleophile in the first step of the catalytic reaction. Vanadate in the Tdp1-vanadate structure has a trigonal bipyramidal geometry that mimics the transition state for hydrolysis of a phosphodiester bond, while Tdp1-tungstate displays unusual octahedral coordination. The presence of low-occupancy tungstate molecules along the narrow groove of the substrate binding cleft is suggestive evidence that this groove binds ssDNA. In both cases, glycerol from the cryoprotectant solution became liganded to the vanadate or tungstate inhibitor molecules in a bidentate 1,2-diol fashion. These structural models allow predictions to be made regarding the specific binding mode of the substrate and the mechanism of catalysis.

PubMed: 12470949
DOI: 10.1016/S0022-2836(02)01154-3

Experimental method

X-RAY DIFFRACTION (2.05 Å)