@article {44647, title = {Dynamics of loops at the substrate entry channel determine the specificity of iridoid synthases}, journal = {Febs Letters}, volume = {592}, year = {2018}, month = {AUG}, pages = {2624-2635}, abstract = {

Iridoid synthases belong to the family of short-chain dehydrogenase reductase involved in the biosynthesis of iridoids. Despite having high sequence and structural homology with progesterone 5 beta- reductase, these enzymes exhibit differential substrate specificities. Previously, two loops. L1 and L2 at substrate-binding pocket, were suggested to be involved in generating substrate specificity. However, the structural basis of specificity determinants was elusive. Here, combining sequence and structural analysis, site-directed mutagenesis, and molecular dynamics simulations, we have shown that iridoid synthase contains two channels for substrate entry whose geometries are altered by L1-L2 dynamics, primarily orchestrated by interactions of residues Glu161 and Gly162 of L1 and Asn358 of L2. A complex interplay of these interactions confer the substrate specificity to the enzyme.

}, keywords = {iridoid synthase, iridoids, Molecular dynamics simulations, progesterone 5 beta-reductase, Substrate specificity}, issn = {1873-3468}, doi = {10.1002/1873-3468.13174}, author = {Sandholu, Anand S. and Mohole, Madhura and Duax, William L. and Thulasiram, Hirekodathakallu V. and Sengupta, Durba and Kulkarni, Kiran} } @article {46914, title = {Structural studies on 10-hydroxygeraniol dehydrogenase: a novel linear substrate-specific dehydrogenase from Catharanthus roseus}, journal = {Proteins-Structure Function and Bioinformatics}, volume = {88}, year = {2020}, month = {SEP}, pages = {1197-1206}, type = {Article}, abstract = {

Conversion of 10-hydroxygeraniol to 10-oxogeranial is a crucial step in iridoid biosynthesis. This reaction is catalyzed by a zinc-dependent alcohol dehydrogenase, 10-hydroxygeraniol dehydrogenase, belonging to the family of medium-chain dehydrogenase/reductase (MDR). Here, we report the crystal structures of a novel 10-hydroxygeraniol dehydrogenase from Catharanthus roseus in its apo and nicotinamide adenine dinucleotide phosphate (NADP(+)) bound forms. Structural analysis and docking studies reveal how subtle conformational differences of loops L1, L2, L3, and helix alpha 9{\textquoteright} at the orifice of the catalytic site confer differential activity of the enzyme toward various substrates, by modulating the binding pocket shape and volume. The present study, first of its kind, provides insights into the structural basis of substrate specificity of MDRs specific to linear substrates. Furthermore, comparison of apo and NADP(+) bound structures suggests that the enzyme adopts open and closed states to facilitate cofactor binding.

}, keywords = {10-hydroxygeraniol dehydrogenase, iridoid biosynthesis, medium-chain dehydrogenase, monoterpene indole alkaloids, reductase, X-ray crystallography}, issn = {0887-3585}, doi = {10.1002/prot.25891, Early Access Date = MAR 2020}, author = {Sandholu, Anand S. and Mujawar, Sharmila P. and Ramakrishnan, Krithika and Thulasiram, Hirekodathakallu V. and Kulkarni, Kiran} } @article {48673, title = {Wavelet coherence phase analysis decodes the universal switching mechanism of Ras GTPase superfamily}, journal = {iScience}, volume = {26}, year = {2023}, month = {JUL}, pages = {107031}, type = {Article}, abstract = {

The Ras superfamily of GTPases regulate critical cellular processes by shuttling between GTP-bound ON and GDP-bound OFF states. This switching mechanism is attributed to the conformational changes in two loops, SWI and SWII, upon GTP binding and hydrolysis. Since these conformational changes vary across the Ras superfamily, there is no generic parameter to define their functional states. A unique wavelet coherence (WC) analysis-based approach developed here shows that the structural changes in switch regions could be mapped onto the wavelet coherence phase couplings (WPCs). Thus, WPCs could serve as unique parameters to define their functional states. Disentanglement of WPCs in oncogenic GTPases shows how breakdown of structural allostery leads to their aberrant function. These observations stand out even for simulated ensemble of switch region conformers. Overall, for the first time, we show that WPCs could unravel the latent structural deviations in Ras proteins to decode their universal switching mechanism.

}, doi = {10.1016/j.isci.2023.107031}, author = {Motiwala, Zenia and Sandholu, Anand S. and Sengupta, Durba and Kulkarni, Kiran} }