Skip to main content

DNA Polymerases: An Insight into Their Active Sites and Catalytic Mechanism | Chapter 02 | Recent Advances in Biological Research Vol. 1

Introduction: DNA polymerases are cardinal enzymes, which play a vital role in preserving as well as maintaining the blueprint of life in all living cells. Furthermore, in-depth analyses of DNA and RNA polymerases, which are the crucial catalysts of life, not only reveal fundamental information about their emergence but also on the evolution of life on the planet earth.

Aim: 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, Genetic, Site-Directed Mutagenesis (SDM) analyses 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, SDM analysis data were also 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 showed only a few highly conserved motifs among these enzymes except eukaryotic epsilon polymerases where a large number of highly conserved sequences were found. Possible catalytic/active site regions in all these polymerases showed 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 and implicated in catalysis.

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” and along with a completely conserved R, select 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. Multiple sequence analyses have shown that a basic amino acid K/R and an YG pair are highly conserved in almost all DNA polymerases except in error-prone polymerases where the YG pair is not found at the expected distance from the catalytic K/R. SDM, biochemical and X-ray crystallographic analyses of DNA polymerase I from E. coli have also suggested their involvement in substrate binding and catalysis. Large numbers of highly/completely conserved monos, diads, triads are also found among different groups of DNA polymerases and they may play an important role in folding the proteins to the correct 3D structure. Based on these results, a mechanism of action is proposed for the polymerization reactions as well as for the proof-reading function of DNA polymerase I from E. coli as a model enzyme. A similar mechanism may be followed by other polymerases as the almost completely conserved K/R and YG pair are present in all of them.

Biography of author(s)

Dr. Peramachi Palanivelu
Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai – 625 021, India.



Comments

Popular posts from this blog

Greening Regional Airports: A Vision for Carbon Neutral Infrastructure | Chapter 12 | Contemporary Perspective on Science, Technology and Research Vol. 3

 This study provides an overview of the energy demand of a regional airport, divided into individual time horizons. The electrification of aircraft systems raises the question of whether airports will be among the largest electricity consumers in our infrastructure in the future. Sustainability and especially emission reductions are significant challenges for airports that are currently being addressed. The Clean Sky 2 project GENESIS addresses the environmental sustainability of hybrid-electric 50-passenger aircraft systems in a life cycle perspective to support the development of a technology roadmap for the transition to sustainable and competitive electric aircraft systems. This article originates from the GENESIS research and describes various options for ground power supply at a regional airport. Potential solutions for airport infrastructure with a short (2030), medium (2040), and long (2050) time horizon are proposed. In addition to the environmental and conservation benefi...

Occipital Dermal Sinus Tract Causing Craniospinal Infection: A Review | Chapter 13 | New Visions in Medicine and Medical Science Vol. 4

  Dermal sinus is a rare congenital condition characterized by a pathological tract connecting the skin to deeper tissues of the central nervous system, potentially leading to severe infectious complications. It arises from a failure in the separation of ectodermal layers during early gestation. Diagnosing dermal sinus tract in newborns requires a careful physical examination, focusing on midline dimples in the occipital region associated with cutaneous abnormalities like hairy nevus or hyperpigmentation. The presence of drainage, abnormal hair distribution, or localized swelling may indicate a sinus tract. Regular examination for dimples or sinuses is recommended for infants and children with recurrent meningitis or infections. Early detection is crucial to prevent severe complications like meningitis, with Staphylococcus aureus being a common causative organism. Neuroradiological studies, including computed tomography (CT) scan and magnetic resonance imaging (MRI), with histopath...

Alkali Element Modification of Glucose Molecules as a Method to Dissolve Cancer Cells | Chapter 12 | New Visions in Medicine and Medical Science Vol. 4

  The present study highlights about alkali element modification of glucose molecules as a method to dissolve cancer cells. The central regulation of the mechanisms governing cell proliferation has little effect on cancer cells. Cancer cells are entirely independent of the central command and divide and proliferate on their own, making it challenging to activate their response mechanism. Precisely, this is the reason why they are at risk to the health of humans and/or any biological entities. Instead of trying to reconnect the central command of the growth control mechanism to cancer cells that are already out of the range, we present a method of using the cancer cell’s own irresponsive and uncontrolled growth mechanism to their disadvantage and destroy the cancer cells. We found that this is achievable in an atomic/molecular level study of the glucose molecule, which is the primary food source used for growth and energy generation by all cells in the body, including the cancer cel...