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1. Kinetic characterization of methylthio-d-ribose-1-phosphate isomerase

   https://doi.org/10.1016/bs.mie.2023.03.015  

   Veeramachineni, Vamsee M; Ubayawardhana, Subashi T; Murkin, Andrew S (January 2023, Methods in enzymology)

   Methylthio-D-ribose-1-phosphate (MTR1P) isomerase (MtnA) catalyzes the reversible isomerization of the aldose MTR1P into the ketose methylthio-D-ribulose 1-phosphate. It serves as a member of the methionine salvage pathway that many organisms require for recycling methylthio-D-adenosine, a byproduct of S-adenosylmethionine metabolism, back to methionine. MtnA is of mechanistic interest because unlike most other aldose–ketose isomerases, its substrate exists as an anomeric phosphate ester and therefore cannot equilibrate with a ring-opened aldehyde that is otherwise required to promote isomerization. To investigate the mechanism of MtnA, it is necessary to establish reliable methods for determining the concentration of MTR1P and to measure enzyme activity in a continuous assay. This chapter describes several such protocols needed to perform steady-state kinetics measurements. It additionally outlines the preparation of [32P]MTR1P, its use in radioactively labeling the enzyme, and the characterization of the resulting phosphoryl adduct. 

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2. Evidence for the chemical mechanism of RibB (3,4-dihydroxy-2-butanone 4-phosphate synthase) of riboflavin biosynthesis.

   Nikola Kenjić, Kathleen M. (July 2022, Journal of the American Chemical Society)

   RibB (3,4-dihydroxy-2-butanone 4-phosphate synthase) is a magnesium-dependent enzyme that excis-es the C4 of D-ribulose-5-phosphate (D-Ru5P) as formate. This chemistry forms the four-carbon sub-strate for RibE (lumazine synthase) that is incorporated into the xylene moiety of lumazine and ulti-mately the riboflavin isoalloxazine. The reaction was first identified in studies by Bacher and cowork-ers in the early 1990s and a chemical mechanism hypothesis offered by these researchers has become the consensus mechanism despite minimal direct evidence. In addition, X-ray crystal structures of RibB typically show two metal ions when solved in the presence of non-native metals and/or liganding non-substrate analogues and the concensus hypothetical mechanism has incorporated this cofactor set. We have used a variety of biochemical approaches to further characterize the chemistry catalyzed by RibB from Vibrio cholera (VcRibB). We show that full activity is achieved at metal ion concentra-tions equal to the enzyme concentration indicating that only one metal ion is required for catalysis. This was confirmed from EPR of the enzyme reconstituted with manganese and crystal structures ob-tained from soaking with the native substrate, D-Ru5P. These data definitively show the involvement of a single active site metal ion. The slow rate of turnover of VcRibB was used to identify two transient species prior to the formation of products using acid quench of single turnover reactions in combina-tion with NMR for singly and fully 13C-labelled D-Ru5P. The data indicate that dehydration of C1 forms the first transient species that then undergoes rearrangement by a 1,2 migration that fuses C5 to C3 and renders C4 hydrated as a gem diol that is poised for elimination as formate. Time-dependent Mn2+ soaks of VcRibB-D-Ru5P co-crystals provided structures that show accumulation in crystallo of the same intermediate states as observed with acid-quench and NMR. Collectively these data reveal for the first time crucial transient chemical states in the mechanism of RibB. 

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3. F1FO ATP synthase molecular motor mechanisms

   https://doi.org/10.3389/fmicb.2022.965620  

   Frasch, Wayne D.; Bukhari, Zain A.; Yanagisawa, Seiga (August 2022, Frontiers in Microbiology)

   The F-ATP synthase, consisting of F 1 and F O motors connected by a central rotor and the stators, is the enzyme responsible for synthesizing the majority of ATP in all organisms. The F 1 (αβ) 3 ring stator contains three catalytic sites. Single-molecule F 1 rotation studies revealed that ATP hydrolysis at each catalytic site (0°) precedes a power-stroke that rotates subunit-γ 120° with angular velocities that vary with rotational position. Catalytic site conformations vary relative to subunit-γ position (β E , empty; β D , ADP bound; β T , ATP-bound). During a power stroke, β E binds ATP (0°–60°) and β D releases ADP (60°–120°). Årrhenius analysis of the power stroke revealed that elastic energy powers rotation via unwinding the γ-subunit coiled-coil. Energy from ATP binding at 34° closes β E upon subunit-γ to drive rotation to 120° and forcing the subunit-γ to exchange its tether from β E to β D , which changes catalytic site conformations. In F 1 F O , the membrane-bound F O complex contains a ring of c-subunits that is attached to subunit-γ. This c-ring rotates relative to the subunit-a stator in response to transmembrane proton flow driven by a pH gradient, which drives subunit-γ rotation in the opposite direction to force ATP synthesis in F 1 . Single-molecule studies of F 1 F O embedded in lipid bilayer nanodisks showed that the c-ring transiently stopped F 1 -ATPase-driven rotation every 36° (at each c-subunit in the c 10 -ring of E. coli F 1 F O ) and was able to rotate 11° in the direction of ATP synthesis. Protonation and deprotonation of the conserved carboxyl group on each c-subunit is facilitated by separate groups of subunit-a residues, which were determined to have different pKa’s. Mutations of any of any residue from either group changed both pKa values, which changed the occurrence of the 11° rotation proportionately. This supports a Grotthuss mechanism for proton translocation and indicates that proton translocation occurs during the 11° steps. This is consistent with a mechanism in which each 36° of rotation the c-ring during ATP synthesis involves a proton translocation-dependent 11° rotation of the c-ring, followed by a 25° rotation driven by electrostatic interaction of the negatively charged unprotonated carboxyl group to the positively charged essential arginine in subunit-a. 

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4. Design, Synthesis, and Mechanistic Studies of ( R )-3-Amino-5,5-difluorocyclohex-1-ene-1-carboxylic Acid as an Inactivator of Human Ornithine Aminotransferase

   https://doi.org/10.1021/acschembio.4c00022  

   Devitt, Allison N; Vargas, Abigail L; Zhu, Wei; Des_Soye, Benjamin James; Butun, Fatma Ayaloglu; Alt, Tyler; Kaley, Nicholas; Ferreira, Glaucio M; Moran, Graham R; Kelleher, Neil L; et al (May 2024, ACS Chemical Biology)

   He, Chuan (Ed.)

   Human ornithine aminotransferase (hOAT), a pyridoxal 5'-phosphate (PLP)-dependent enzyme, has been shown to play an essential role in the metabolic reprogramming and progression of hepatocellular carcinoma (HCC). HCC accounts for approximately 75% of primary liver cancers and is within the top three causes of cancer death worldwide. As a result of treatment limitations, the overall 5-year survival rate for all patients with HCC is under 20%. The prevalence of HCC necessitates continued development of novel and effective treatment methods. In recent years, the therapeutic potential of selective inactivation of hOAT has been demonstrated for the treatment of HCC. Inspired by previous increased selectivity for hOAT by the expansion of the cyclopentene ring scaffold to a cyclohexene, we designed, synthesized, and evaluated a series of novel fluorinated cyclohexene analogues and identified (R)-3-amino-5,5-difluorocyclohex-1-ene-1-carboxylic acid as a time-dependent inhibitor of hOAT. Structural and mechanistic studies have elucidated the mechanism of inactivation of hOAT by 5, resulting in a PLP-inactivator adduct tightly bound to the active site of the enzyme. Intact protein mass spectrometry, 19F NMR spectroscopy, transient state kinetic studies, and X-ray crystallography were used to determine the structure of the final adduct and elucidate the mechanisms of inactivation. Interestingly, despite the highly electrophilic intermediate species conferred by fluorine and structural evidence of solvent accessibility in the hOAT active site, Lys292 and water did not participate in nucleophilic addition during the inactivation mechanism of hOAT by 5. Instead, rapid aromatization to yield the final adduct was favored. 

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5. Nitrene transfer from a sterically confined copper nitrenoid dipyrrin complex

   Carsch, Kurtis M.; North, Sasha C.; DiMucci, Ida M.; Iliescu, Andrei; Vojackova, Petra; Khazanov, Thomas; Zheng, Shao-Liang; Cundari, Thomas R.; Lancaster, Kyle M.; Betley, Theodore A. (September 2023, Chemical Science)

   Despite the myriad Cu-catalyzed nitrene transfer methodologies to form new C–N bonds (e.g.,amination, aziridination), the critical reaction intermediates have largely eluded direct characterization due to their inherent reactivity. Herein, we report the synthesis of dipyrrin-supported Cu nitrenoid adducts, investigate their spectroscopic features, and probe their nitrene transfer chemistry through detailed mechanistic analyses. Treatment of the dipyrrin CuI complexes with substituted organoazides affords terminally ligated organoazide adducts with minimal activation of the azide unit as evidenced by vibrational spectroscopy and single crystal X-ray diffraction. The Cu nitrenoid, with an electronic structure most consistent with a triplet nitrene adduct of CuI, is accessed following geometric rearrangement of the azide adduct from k1-N terminal ligation to k1-N internal ligation with subsequent expulsion of N2. For perfluorinated arylazides, stoichiometric and catalytic C–H amination and aziridination was observed. Mechanistic analysis employing substrate competition reveals an enthalpically-controlled, electrophilic nitrene transfer for primary and secondary C–H bonds. Kinetic analyses for catalytic amination using tetrahydrofuran as a model substrate reveal pseudo-first order kineticsunderrelevantaminationconditionswithafirst-orderdependenceonbothCuandorganoazide. Activation parameters determined from Eyring analysis(DH‡=9.2(2)kcalmol−1,DS‡=−42(2)calmol−1 K−1, DG‡ 298K =21.7(2) kcal mol−1) and parallel kinetic isotope effect measurements (1.10(2)) are consistent with rate-limiting Cu nitrenoid formation, followed by a proposed stepwise hydrogen-atom abstraction and rapid radical recombination to furnish the resulting C–N bond. The proposed mechanism and experimental analysis are further corroborated by density functional theory calculations. Multiconfigurational calculations provide insight into the electronic structure of the catalytically relevant Cu nitrene intermediates. The findings presented herein will assist in the development of future methodology for Cu-mediated C–N bond forming catalysis. 

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