There is considerable interest in how "second-shell" interactions between protein side chains and metal ligands might modulate Mn(II) ion redox properties and reactivity in metalloenzymes. One such Mn-dependent enzyme is oxalate decarboxylase (OxDC), which catalyzes the disproportionation of oxalate monoanion into formate and CO. Electron paramagnetic resonance (EPR) studies have shown that a mononuclear Mn(III) ion is formed in OxDC during catalytic turnover and that the removal of a hydrogen bond between one of the metal ligands (Glu101) and a conserved, second-shell tryptophan residue (Trp132) gives rise to altered zero-field splitting parameters for the catalytically important Mn(II) ion. We now report heavy-atom kinetic isotope effect measurements on the W132F OxDC variant, which test the hypothesis that the Glu101/Trp132 hydrogen bond modulates the stability of the Mn(III) ion during catalytic turnover. Our results suggest that removing the Glu101/Trp132 hydrogen bond increases the energy of the oxalate radical intermediate from which decarboxylation takes place. This finding is consistent with a model in which the Glu101/Trp132 hydrogen bond in WT OxDC modulates the redox properties of the Mn(II) ion.
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http://dx.doi.org/10.1021/acs.biochem.8b00214 | DOI Listing |
Int J Biol Macromol
January 2025
Department of Life Sciences and Systems Biology, University of Torino, Italy.
A new gene coding for an iron-containing enzyme was identified in the genome of Acinetobacter radioresistens. Bioinformatics analysis allowed the assignment of the protein to DyP peroxidases, due to the presence of conserved residues involved in heme binding and catalysis. Moreover, Ar-DyP is located in an operon coding also for other enzymes involved in iron uptake and regulation.
View Article and Find Full Text PDFChemosphere
January 2025
Environment Research Institute, Shandong University, Qingdao, 266237, PR China.
Polyethylene terephthalate (PET) waste significantly contributes to the global plastic crisis, but enzymatic conversion has become an efficient and environmentally friendly strategy to combat it. Therefore, this study explored the Re-face selective depolymerization mechanisms of a novel PET-degradation peptidase, hydrolase 202. Theoretical calculations revealed that the first step, a catalytic triad-assisted nucleophilic attack, is the rate-determining step.
View Article and Find Full Text PDFJ Med Chem
January 2025
Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig 38124, Germany.
The main protease M is a clinically validated target to treat infections by the coronavirus SARS-CoV-2. Among the first reported M inhibitors was the peptidomimetic α-ketoamide , whose cocrystal structure with M paved the way for multiple lead-finding studies. We established structure-activity relationships for the series by modifying residues at the P1', P3, and P4 sites.
View Article and Find Full Text PDFJ Am Chem Soc
January 2025
Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
The local electric field (LEF) plays an important role in the catalytic process; however, the precise construction and manipulation of the electric field microenvironment around the active site remains a significant challenge. Here, we have developed a supramolecular strategy for the implementation of a LEF by introducing the host macrocycle 18-crown-6 (18C6) into a cobalt phthalocyanine (CoPc)-containing covalent organic framework (COF). Utilizing the supramolecular interaction between 18C6 and potassium ion (K), a locally enhanced K concentration around CoPc can be built to generate a LEF microenvironment around the catalytically active Co site.
View Article and Find Full Text PDFChemistry
January 2025
Brandeis University, Chemistry, 415 South Street,, Waltham, 02453, UNITED STATES OF AMERICA.
We designed and synthesized three diacetylene monomers M1-M3 having two NH2 groups. As anticipated, the NH2 groups aided the preorganization of these monomers by N-H…N hydrogen bonding. In the crystals of monomer M1 and M2, the intermolecular N-H…N hydrogen bonding preorganized the diyne units in an orientation suitable for their topochemical polymerization, but in the case of monomer M3, the distance was slightly larger than that recommended for the topochemical reaction.
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