DNA Polymerases: An Insight into Their Active Sites and Catalytic Mechanism.
Loading...
Date
2013-07
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
Abstract
To analyze the active sites of various prokaryotic and eukaryotic DNA polymerases and
propose a plausible mechanism of action for the polymerases with the Escherichia coli DNA
polymerase I as a model system.
Study Design: Bioinformatics, Biochemical and X-ray crystallographic data were analyzed.
Place and Duration of Study: Department of Molecular Microbiology, School of
Biotechnology, Madurai Kamaraj University, Madurai – 625 021, India. From 2007 to 2012.
Methodology: The advanced version of T-COFFEE was used to analyze both prokaryotic
and eukaryotic DNA polymerase sequences. Along with this bioinformatics data, X-ray
crystallographic and biochemical data were used to confirm the possible amino acids in the
active sites of different types of polymerases from various sources.
Results: Multiple sequence analyses of various polymerases from different sources show
only a few highly conserved motifs among these enzymes except eukaryotic epsilon
polymerases where a large number of highly conserved sequences are found. Possible
catalytic/active site regions in all these polymerases show a highly conserved catalytic amino
acid K/R and the YG/A pair. A distance conservation is also observed between the active
sites. Furthermore, two highly conserved Ds and DXD motifs are also observed.
Conclusion: The highly conserved amino acid K/R acts as the proton abstractor in catalysis
and the YG/A pair acts as a “steric gate” in selection of only dNTPS for polymerization
reactions. The two highly conserved Ds act as the “charge shielder” of dNTPs and orient the alpha phosphate of incoming dNTPs to the 3’-OH end of the growing primer.
Description
Keywords
DNA polymerases, T-COFFEE, conserved motifs, active sites, E. coli DNA polymerase I, polymerase active site, polymerization mechanism, exonuclease active site, proof-reading mechanism
Citation
Palanivelu P. DNA Polymerases: An Insight into Their Active Sites and Catalytic Mechanism. International Journal of Biochemistry Research & Review 2013 Jul-Sept ; 3 (3) : 206-247.