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1. Catalytic and post-translational maturation roles of a conserved active site serine residue in nitrile hydratases

   https://doi.org/10.1016/j.jinorgbio.2024.112763  

   Miller, Callie; Knutson, Kylie; Liu, Dali; Bennett, Brian; Holz, Richard C (January 2025, Journal of Inorganic Biochemistry)

   NA (Ed.)

   A highly conserved second-sphere active site αSer residue in nitrile hydratase (NHase), that forms a hydrogen bond with the axial metal-bound water molecule, was mutated to Ala, Asp, and Thr, in the Co-type NHase from Pseudonocardia thermophila JCM 3095 (PtNHase) and to Ala and Thr in the Fe-type NHase from Rhodococcus equi TG328–2 (ReNHase). All five mutants were successfully purified; metal analysis via ICP-AES indicated that all three Co-type PtNHase mutants were in their apo-form while the Fe-type αSer117Ala and αSer117Thr mutants contained 85 and 50 % of their active site Fe(III) ions, respectively. The kcat values obtained for the PtNHase mutant enzymes were between 0.03 ± 0.01 and 0.2 ± 0.02 s− 1 amounting to <0.8 % of the kcat value observed for WT PtNHase. The Fe-type ReNHase mutants retained some detectable activity with kcat values of 93 ± 3 and 40 ± 2 s− 1 for the αSer117Ala and αSer117Thr mutants, respectively, which is ~5 % of WT ReNHase activity towards acrylonitrile. UV–Vis spectra coupled with EPR data obtained on the ReNHase mutant enzymes showed subtle changes in the electronic environment around the active site Fe(III) ions, consistent with altering the hydrogen bonding interaction with the axial water ligand. X-ray crystal structures of the three PtNHase mutant enzymes confirmed the mutation and the lack of active site metal, while also providing insight into the active site hydrogen bonding network. Taken together, these data confirm that the conserved active site αSer residue plays an important catalytic role but is not essential for catalysis. They also confirm the necessity of the conserved second-sphere αSer residue for the metalation process and subsequent post-translational modification of the α-subunit in Co-type NHases but not Fe-type NHases, suggesting different mechanisms for the two types of NHases. 

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2. Examination of the Catalytic Role of the Axial Cystine Ligand in the Co-Type Nitrile Hydratase from Pseudonocardia thermophila JCM 3095

   https://doi.org/10.3390/catal11111381  

   Ogutu, Irene R.; St. Maurice, Martin; Bennett, Brian; Holz, Richard C. (November 2021, Catalysts)

   The strictly conserved αSer162 residue in the Co-type nitrile hydratase from Pseudonocardia thermophila JCM 3095 (PtNHase), which forms a hydrogen bond to the axial αCys108-S atom, was mutated into an Ala residue. The αSer162Ala yielded two different protein species: one was the apoform (αSerA) that exhibited no observable activity, and the second (αSerB) contained its full complement of cobalt ions and was active with a kcat value of 63 ± 3 s−1 towards acrylonitrile at pH 7.5. The X-ray crystal structure of αSerA was determined at 1.85 Å resolution and contained no detectable cobalt per α2β2 heterotetramer. The axial αCys108 ligand itself was also mutated into Ser, Met, and His ligands. All three of these αCys108 mutant enzymes contained only half of the cobalt complement of wild-type PtNHase, but were able to hydrate acrylonitrile with kcat values of 120 ± 6, 29 ± 3, and 14 ± 1 s−1 for the αCys108His, Ser, and Met mutant enzymes, respectively. As all three of these mutant enzymes are catalytically competent, these data provide the first experimental evidence that transient disulfide bond formation is not catalytically essential for NHases. 

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3. Adrenodoxin alters human cytochrome P450 27A1 structure and reaction efficiency beyond supplying electrons

   https://doi.org/10.1016/j.abb.2025.110700  

   Vu, Quoc T; May, Katherine C; Collins, Leonard B; Xi, Ying; Davis, Zachary B; Bartholomew-Schoch, Jackson L; Vaughn, Lindsay R; Provost, Katherine R; Arnold, Noah L; Harris, Ethan F; et al (February 2026, Archives of Biochemistry and Biophysics)

   Human cytochrome P450 (P450) 27A1 catalyzes the hydroxylation of cholesterol and vitamin D derivatives. P450 27A1 is localized in the mitochondria and is reduced by its redox partner protein adrenodoxin twice for each catalytic cycle. The reliance on adrenodoxin is conserved across all human mitochondrial P450 enzymes. This study examines the adrenodoxin interaction with P450 27A1 and draws comparisons with studies of other P450 enzymes to determine if differences exist. The P450-adrenodoxin complex structure was examined by chemical crosslinking and analyzed by mass spectrometry. The effect of adrenodoxin concentration on P450 27A1 function was assessed by studying effects on steady state enzyme kinetics parameters and equilibrium substrate binding. The results suggest that adrenodoxin binds to P450 27A1 at a proximal site like other P450 enzymes but differs in the specific residues involved. Furthermore, the presence of adrenodoxin and/or substrate decreases the number of interprotein and intraprotein crosslinks observed, indicating that these components change the conformation of the P450 enzyme. Increased adrenodoxin concentration causes the P450 and vitamin D3 kcat value to increase, the kcat/Km value to decrease, and the substrate Kd to remain constant. These results suggest adrenodoxin alters enzyme efficiency beyond electron transfer without affecting substrate loading. The adrenodoxin effects on P450 27A1 kinetics and equilibrium constants differ from those of other human mitochondrial P450 enzymes. In total, these structural and functional studies suggest that while the general adrenodoxin binding site and function is conserved across P450 enzymes, the details and additional effects of this interaction vary. 

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4. Gcn5-Related N-Acetyltransferases (GNATs) With a Catalytic Serine Residue Can Play Ping-Pong Too

   https://doi.org/10.3389/fmolb.2021.646046  

   Baumgartner, Jackson T.; Habeeb Mohammad, Thahani S.; Czub, Mateusz P.; Majorek, Karolina A.; Arolli, Xhulio; Variot, Cillian; Anonick, Madison; Minor, Wladek; Ballicora, Miguel A.; Becker, Daniel P.; et al (April 2021, Frontiers in Molecular Biosciences)

   Enzymes in the Gcn5-related N- acetyltransferase (GNAT) superfamily are widespread and critically involved in multiple cellular processes ranging from antibiotic resistance to histone modification. While acetyl transfer is the most widely catalyzed reaction, recent studies have revealed that these enzymes are also capable of performing succinylation, condensation, decarboxylation, and methylcarbamoylation reactions. The canonical chemical mechanism attributed to GNATs is a general acid/base mechanism; however, mounting evidence has cast doubt on the applicability of this mechanism to all GNATs. This study shows that the Pseudomonas aeruginosa PA3944 enzyme uses a nucleophilic serine residue and a hybrid ping-pong mechanism for catalysis instead of a general acid/base mechanism. To simplify this enzyme’s kinetic characterization, we synthesized a polymyxin B substrate analog and performed molecular docking experiments. We performed site-directed mutagenesis of key active site residues (S148 and E102) and determined the structure of the E102A mutant. We found that the serine residue is essential for catalysis toward the synthetic substrate analog and polymyxin B, but the glutamate residue is more likely important for substrate recognition or stabilization. Our results challenge the current paradigm of GNAT mechanisms and show that this common enzyme scaffold utilizes different active site residues to accomplish a diversity of catalytic reactions. 

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5. The number of catalytic cycles in an enzyme’s lifetime and why it matters to metabolic engineering

   https://doi.org/10.1073/pnas.2023348118  

   Hanson, Andrew D.; McCarty, Donald R.; Henry, Christopher S.; Xian, Xiaochen; Joshi, Jaya; Patterson, Jenelle A.; García-García, Jorge D.; Fleischmann, Scott D.; Tivendale, Nathan D.; Millar, A. Harvey (March 2021, Proceedings of the National Academy of Sciences)

   Metabolic engineering uses enzymes as parts to build biosystems for specified tasks. Although a part’s working life and failure modes are key engineering performance indicators, this is not yet so in metabolic engineering because it is not known how long enzymes remain functional in vivo or whether cumulative deterioration (wear-out), sudden random failure, or other causes drive replacement. Consequently, enzymes cannot be engineered to extend life and cut the high energy costs of replacement. Guided by catalyst engineering, we adopted catalytic cycles until replacement (CCR) as a metric for enzyme functional life span in vivo. CCR is the number of catalytic cycles that an enzyme mediates in vivo before failure or replacement, i.e., metabolic flux rate/protein turnover rate. We used estimated fluxes and measured protein turnover rates to calculate CCRs for ∼100–200 enzymes each from Lactococcus lactis , yeast, and Arabidopsis . CCRs in these organisms had similar ranges (<10 3 to >10 7 ) but different median values (3–4 × 10 4 in L. lactis and yeast versus 4 × 10 5 in Arabidopsis ). In all organisms, enzymes whose substrates, products, or mechanisms can attack reactive amino acid residues had significantly lower median CCR values than other enzymes. Taken with literature on mechanism-based inactivation, the latter finding supports the proposal that 1) random active-site damage by reaction chemistry is an important cause of enzyme failure, and 2) reactive noncatalytic residues in the active-site region are likely contributors to damage susceptibility. Enzyme engineering to raise CCRs and lower replacement costs may thus be both beneficial and feasible. 

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