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Reaction mechanism of deoxyribonucleotidase: A theoretical study
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
2005 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 42, 20004-20008 p.Article in journal (Refereed) Published
Abstract [en]

The reaction mechanism of human deoxyribonucleotidase (dN) is studied using high-level quantum-chemical methods. dN catalyzes the dephosphorylation of deoxyribonucleoside monophosphates (dNMPs) to their nucleoside form in human cells. Large quantum models are employed (99 atoms) based on a recent X-ray crystal structure [Rinaldo-Matthis et al. Nat. Struct. Biol. 2002, 9, 779]. The calculations support the proposed mechanism in which Asp41 performs a nucleophilic attack on the phosphate to form a phospho-enzyme intermediate. Asp43 acts in the first step as an acid, protonating the leaving nucleoside, and in the second step as a base, deprotonating the lytic water. No pentacoordinated intermediates could be located.

Place, publisher, year, edition, pages
2005. Vol. 109, no 42, 20004-20008 p.
Keyword [en]
density-functional thermochemistry, crystal-structure, mitochondrial deoxyribonucleotidase, angstrom resolution, molecular-energies, exchange, gradient, model, monophosphate, intermediate
Identifiers
URN: urn:nbn:se:kth:diva-15141DOI: 10.1021/jp0546150ISI: 000232857900060Scopus ID: 2-s2.0-27744514664OAI: oai:DiVA.org:kth-15141DiVA: diva2:333182
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2017-12-12Bibliographically approved

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