Nucleic Acids Research Advance Access originally published online on September 18, 2009
Nucleic Acids Research 2009 37(20):6849-6858; doi:10.1093/nar/gkp669
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Nucleic Acids Research, 2009, Vol. 37, No. 20 6849-6858
© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Nucleic Acid Enzymes |
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
1CNR National Research Council, INFM National Institute for the Physics of Matter and Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, 2CASPUR Interuniversities Consortium for Supercomputing Applications, Via dei Tizii 6b, Rome 00185 and 3Department of Neuroscience, University of Rome ‘Tor Vergata’ Via Montpellier 1, 00133 Rome, Italy
*To whom correspondence should be addressed. Tel: +39 0672594376; Fax: +39 0672594326; Email: desideri{at}uniroma2.it
Received May 14, 2009. Accepted August 29, 2009.
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.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.