Structural plasticity inMycobacterium tuberculosisuracil-DNA glycosylase (MtUng) and its functional implications

Abstract

17 independent crystal structures of family I uracil-DNA glycosylase from Mycobacterium tuberculosis (MtUng) and its complexes with uracil and its derivatives, distributed among five distinct crystal forms, have been determined. Thermodynamic parameters of binding in the complexes have been measured using isothermal titration calorimetry. The two-domain protein exhibits open and closed conformations, suggesting that the closure of the domain on DNA binding involves conformational selection. Segmental mobility in the enzyme molecule is confined to a 32-residue stretch which plays a major role in DNA binding. Uracil and its derivatives can bind to the protein in two possible orientations. Only one of them is possible when there is a bulky substituent at the 5' position. The crystal structures of the complexes provide a reasonable rationale for the observed thermodynamic parameters. In addition to providing fresh insights into the structure, plasticity and interactions of the protein molecule, the results of the present investigation provide a platform for structure-based inhibitor design.

Targeting Uracil-DNA Glycosylases for Therapeutic Outcomes Using Insights from Virus Evolution

“…The structures of Ung catalytic domains in complex with dsDNA, demonstrate a subtle global closure of the domain upon occupation of the Ung DNA binding cleft ( Figure 3). Detailed analysis of similarities and differences in domain closure under different circumstances implicates positions of possible interest in drug development [13,36,44]. The closure due to dsDNA has also shed light upon the mode of interrogation of DNA bases by Ung [42,43].…”

“…In the case of pathogenic states of commensal bacteria, inhibition of microbial Ung could in principle be used to potentiate the action of compounds that cause lethal DNA damage in the absence of Ung. The key residue type or geometry nuances between UNG2 and those of, for example, pathogenic Mycobacteria (Figure 2, Table 1) could permit the possibility of development of selective Ung inhibitors [35,36,44]. These differences include markedly different interaction profiles for Mycobacterial Ung, versus UNG2, when either is complexed with the virus-encoded inhibitor protein, Ugi [35].…”

“…The Ung DNA binding cleft need not be fully occupied to trigger domain closure, since closed conformations of Ung have been observed under different circumstances [44]. Thus, the drug we can envisage in development could be based upon a molecule arising from a library that samples the cleft area of Ung, and for which domain closure, or just tight binding, is the readout of interest.…”

An Efficient Synthesis and In vitro Cytostatic Activity of 5-Aminosulfonyl Uracil Derivatives

“…They also represent good starting material for the synthesis of the fluorescent uracil derivatives suitable for incorporation into PNA's or nucleic acids. [24][25][26][27][28][29] Our group has a long-term experience in design, synthesis, and characterization of biologically active nucleoside derivatives. [30][31][32][33] Previously, we have synthesized N-sulfonylpyrimidine derivatives I (Figure 2) as a new type of sulfonylcycloureas.…”

Protein crystallography beamline (PX-BL21) at Indus-2 synchrotron

“…PX-BL21 is primarily aimed to cater for the needs of more than 100 independent research groups in India working in the area of structural biology. The first diffraction data on single crystals of the lysozyme protein were recorded during mid-2012 and since then the beamline has been used by several users (Goyal et al, 2014;Arif et al, 2015;Sonani et al, 2015;Agarwal et al, 2015).…”