title: Evidence of the crucial role of the linker domain on the catalytic activity of human topoisomerase I by experimental and simulative characterization of the Lys681Ala mutant.
abstract: The functional and structural-dynamical properties of the Lys681Ala mutation in the human topoisomerase IB linker domain have been investigated by catalytic assays and molecular dynamics simulation. The mutant is characterized by a comparable cleavage and a strongly reduced religation rate when compared to the wild type protein. The mutant also displays perturbed linker dynamics, as shown by analysis of the principal components of the motion, and a reduced electrostatic interaction with DNA. Inspection of the inter atomic distances in proximity of the active site shows that in the mutant the distance between the amino group of Lys532 side chain and the 5' OH of the scissile phosphate is longer than the wild type enzyme, providing an atomic explanation for the reduced religation rate of the mutant. Taken together these results indicate the existence of a long range communication between the linker domain and the active site region and points out the crucial role of the linker in the modulation of the catalytic activity.
authors.affiliation: Department of Biology, University of Rome Tor Vergata, CNR National Research Council, INFM National Institute for the Physics of Matter, Rome 00133, Italy.
authors.forename: Paola
authors.initials: P
authors.lastname: Fiorani
authors.forename: Cinzia
authors.initials: C
authors.lastname: Tesauro
authors.forename: Giordano
authors.initials: G
authors.lastname: Mancini
authors.forename: Giovanni
authors.initials: G
authors.lastname: Chillemi
authors.forename: Ilda
authors.initials: I
authors.lastname: D'Annessa
authors.forename: Grazia
authors.initials: G
authors.lastname: Graziani
authors.forename: Lucio
authors.initials: L
authors.lastname: Tentori
authors.forename: Alessia
authors.initials: A
authors.lastname: Muzi
authors.forename: Alessandro
authors.initials: A
authors.lastname: Desideri
mesh_terms: D000409:Alanine / Q000235:genetics; D001483:Base Sequence; D002384:Catalysis; D020134:Catalytic Domain; D004264:DNA Topoisomerases, Type I / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D008239:Lysine / Q000235:genetics; D008969:Molecular Sequence Data; D009154:Mutation; D017354:Point Mutation; D017434:Protein Structure, Tertiary; D055672:Static Electricity
chemical_list: D004264:DNA Topoisomerases, Type I; D008239:Lysine; D000409:Alanine