Conformational Dynamics, Ligand Binding and Effects of Mutations in NirE an S-Adenosyl-L-Methionine Dependent Methyltransferase

Abstract

Heme d1, a vital tetrapyrrol involved in the denitrification processes is synthesized from its precursor molecule precorrin-2 in a chemical reaction catalysed by an S-adenosyl-L-methionine (SAM) dependent Methyltransferase (NirE). The NirE enzyme catalyses the transfer of a methyl group from the SAM to uroporphyrinogen III and serves as a novel potential drug target for the pharmaceutical industry. An important insight into the structure-activity relationships of NirE has been revealed by elucidating its crystal structure, but there is still no understanding about how conformational flexibility influences structure, cofactor and substrate binding by the enzyme as well as the structural effects of mutations of residues involved in binding and catalysis. In order to provide this missing but very important information we performed a comprehensive atomistic molecular dynamics study which revealed that i) the binding of the substrate contributes to the stabilization of the structure of the full complex; ii) conformational changes influence the orientation of the pyrrole rings in the substrate, iii) more open conformation of enzyme active site to accommodate the substrate as an outcome of conformational motions; and iv) the mutations of binding and active site residues lead to sensitive structural changes which influence binding and catalysis.

Effects of Mutations on Structure–Function Relationships of Matrix Metalloproteinase-1

“…With the exception of the E200A mutant, there are no X-ray crystallographic structures of MMP-1•THP with mutated residues, and the present study provides this missing structural information and asserts that the mutations have delicate, distinct, and specific effects on the structure, interactions, and dynamics in MMP-1•THP. The magnitude of the changes in the local interactions and dynamics are in agreement with the effects of mutations in other proteins [13,14,15,16]. …”

“…MD simulations are applied herein to understand how MMP-1 mutations perturbed the local structure and also to investigate the long-range effects on MMP-1 structure, dynamics, and interactions with a THP. MD simulations have been successfully applied previously to study the effect of mutations on key structural determinants in different enzymes [13,14,15,16]. In order to understand their influence on MMP-1 structure–function relationships, MD simulations were performed on the seven previously described mutants [5,6,7]: E200A, F301Y, F289A/Y290A/P291A, I271A/R272A, L338A/H339A, R272A, and L295S.…”

Carbon isotopic heterogeneity of coenzyme F430 and membrane lipids in methane‐oxidizing archaea

“…Regardless of how glutamate is formed, tetrapyrrole biosynthesis proceeds by combining eight glutamate molecules into the 40‐carbon uroporphyrinogen III. Two additional methyl carbons are added to uroporphyrinogen III from methionine, via a S ‐adenosyl methionine (SAM) reaction to form precorrin‐2 (Boss, Oehme, Billig, Birkemeyer, & Layer, ; Singh et al, ; Storbeck et al, , ; Zajicek et al, ). These methyl groups likely come from methyl‐H 4 MPT which delivers the methyl group to homocysteine to form methionine.…”

“…The oxidative pathway in class II methanogens produces 2-oxoglutarate with this ratio at 2:3. Birkemeyer, & Layer, 2017;Singh et al, 2016;Storbeck et al, 2011Storbeck et al, , 2009Zajicek et al, 2009). These methyl groups likely come from methyl-H 4 MPT which delivers the methyl group to homocysteine to form methionine.…”

Protein-protein Interactions of Bacterial Topoisomerase I

“…The conformational dynamics of proteins as flexible macromolecules can be related to its function (Karplus et al, 2002). In silico studies can provide insights into the influence of a protein conformation on its binding partner and the strength of binding (Singh et al, 2016). The structural features of RNAP-EcTopoI complex were modelled by all-atom molecular dynamic simulations of the complex predicted by molecular docking.…”