@article {30082, title = {Structural basis for substrate discrimination by E. coli repair enzyme, AlkB}, journal = {RSC ADVANCES}, volume = {8}, year = {2018}, month = {2018}, pages = {1281-1291}, abstract = {

E. coli AlkB, a repair enzyme of the dioxygenase family, catalyses the removal of mutagenic methylated nucleotides from the genome. Known for substrate promiscuity, AlkB{\textquoteright}s catalytic mechanism and conformational changes accompanying substrate binding have been extensively dissected. However, the structural parameters of various substrates governing their recognition by AlkB still remain elusive. In this work, through solution-state vibrational spectra of methylated substrates bound to AlkB in combination with computational analysis, we show that the recognition specificity is dictated by the protonation states of the substrates. Specificity is conferred predominantly through hydrogen bonding and cation{\textendash}π interactions. Furthermore, we report on the interaction of AlkB with normal, unmodified nucleotides, wherein the presence of an exocyclic amino group serves as an essential criterion for the initial process of substrate recognition. Taken together, these results provide a rationale for structural determinants of substrate specificity as well as mode of lesion discrimination employed by AlkB.

}, doi = {10.1039/c7ra11333a}, author = {Jayanth, Namrata and Ogirala, Nirmala and Yadav, Anil and Puranik, Mrinalini} } @article {18680, title = {Mechanism of Discrimination of 8-Oxoguanosine versus Guanosine by Escherichia coli Fpg.}, journal = {J Phys Chem B}, year = {2017}, month = {2017 Jun 07}, abstract = {

The mutagenic 8-oxoguanosine monophosphate, the predominant product of DNA oxidation, is excised by formamidopyrimidine glycosylase (Fpg) in bacteria. The mechanism of recognition of 8-oxodG, which differs subtly from its normal counterpart, guanosine monophosphate (dG), by Escherichia coli Fpg remains elusive due to the lack of structural data of E. coli Fpg bound to 8-oxodG. Here, we present solution-state structure of 8-oxodG oligomer bound to E. coli E3Q Fpg using UV resonance Raman (UVRR) spectroscopy. The vibrational spectra report on the π-stacking and hydrogen bonding interactions established by 8-oxodG with E. coli E3Q Fpg. Furthermore, we report on the interactions of E. coli E3Q Fpg with the normal, undamaged nucleotide, dG. We show that E. coli Fpg recognizes 8-oxodG and dG through their C2-amino group but only 8-oxodG forms extensive contacts with E. coli Fpg. Our findings provide a basis for mechanism of lesion recognition by E. coli Fpg.

}, issn = {1520-5207}, doi = {10.1021/acs.jpcb.7b00205}, author = {Jayanth, Namrata and Puranik, Mrinalini} }