Active Site Motif Research Articles

Identification and functional analysis of lysophosphatidic acid phosphatase type 6 (ACP6) gene in golden pompano (Trachinotusovatus)

Golden pompano (Trachinotus ovatus), a marine farmed fish, is economically valuable in China. Lysophosphatidic acid phosphatase type 6 (ACP6) is a type of histidine acid phosphatase and plays an important role in regulating host inflammatory responses and anti-cancer effects in mammals. However, its function in teleost remains unknown. The present study aimed to investigate ACP6 function in golden pompano. ACP6 from golden pompano was identified, cloned, and named TroACP6. The open reading frame of TroACP6 was 1275 bp in length, encoding 424 amino acids. The TroACP6 protein shared high sequence identity (43.32%–90.57 %) with the ACP6 of other species. It contained a histidine phosphatase domain with the active site motif “RHGART” and the catalytic dipeptide HD (histidine and aspartate). Meanwhile, TroACP6 mRNA was widely distributed in the various tissues of healthy golden pompano, with the maximum expression in the head kidney. The function of TroACP6 was analyzed both in vitro and in vivo, and the results revealed that the purified recombinant TroACP6 protein exhibited optimum phosphatase activity at pH 6.0 and 50 °C in vitro. Meanwhile, upon Edwardsiella tarda challenge, TroACP6 expression in tissues increased significantly in vivo. In addition, TroACP6 overexpression enhanced the respiratory burst activity and superoxide dismutase activity of head kidney macrophages in vivo. Furthermore, the overexpression and knockdown of TroACP6 in vivo had a significant effect on bacterial infection. In summary, the study findings indicate that TroACP6 in golden pompano is involved in host defense against bacterial infection.

Structure-aided function assignment to the transcriptomic conopeptide Am931

Implementation of the next-generation technologies for gene sequencing of venom duct transcriptome has provided a large number of peptide sequences of marine cone snails. Emerging technologies on computational platforms are now rapidly evolving for the accurate predictions of the 3D structure of the polypeptide using the primary sequence. The current report aims to integrate the information derived from these two technologies to develop the concept of structure-aided function assignment of Conus peptides. The proof of the concept was demonstrated using the transcriptomic peptide Am931 of C. amadis. The 3D structure of Am931 was computed using Density Functional Theory (DFT) and the quality of the predicted structure was confirmed using 2D NMR spectroscopy of the corresponding synthetic peptide. The computed structure of Am931 aligns with the active site motif of thioredoxins, possess catalytic disulfide conformation of (+, −)AntiRHHook and selectively modulate the N-terminal Cys3 thiol. These structural features indicate that Am931 may act as a disulfide isomerase and modulate the oxidative folding of conotoxins. Synthetic peptide Am931 provides proof-of-function by exhibiting catalytic activity on the oxidative folding of α-conotoxin ImI and improving the yield of native globular fold. The approach of integration of new technologies in the Conus peptide research may help to accelerate the discovery pipeline of new/improved conotoxin functional.

Redox-Active Conopeptide Li520 Has Evolved to Catalyze Oxidative Folding of Conotoxins.

The evolution of miniature conopeptide Li520 (COWC*, *: C-terminal amidation) to exhibit the disulfide isomerase activity was probed using structure, function, disulfide conformation, and the precursor gene sequence. The peptides Li520, Li504, [O2A]Li520, [W3A]Li520, and Grx506, homologues active-site motif of glutaredoxin, were chemically synthesized and assessed for their disulfide reduction potential, intrinsic folding of disulfides, and disulfide isomerization activity on α-conotoxin ImI. The reduction potential of the disulfide of peptides varies from -189 to -344 mV, which is within the range observed for the redox family of proteins that modulates the folding of protein disulfides. The oxidative folding studies confirm the significance of the tryptophan residue in engaging Li520 in disulfide-exchange reactions and the role of proline hydroxylation in extending the lifetime of Li520 in a reduced free thiol state. Studies of quenching of tryptophan fluorescence by the disulfide in situ folding reaction in conjunction with the optimized structures by density functional theory (DFT) confirm the difference in conformation of disulfides between the native and mutant peptides. Interestingly, the native peptide Li520/Li504 shares a similar disulfide conformation of (-,-)AntiRHHook with the redox family of proteins known to modulate disulfides, particularly in lieu of the tetrapeptide of glutaredoxin, deviating from its disulfide conformation compared to its naive protein. Analysis of the precursor gene sequences of M-superfamily conotoxins revealed the presence of Li520 in different cone snail species with distinct food habits and possible modes of evolution through the diversification of cysteine motifs. The results of the report suggest that the short redox conopeptide Li520 has evolved to facilitate the oxidative folding of conotoxins and may be useful to develop as reagents for the synthesis of therapeutically important cysteine-rich peptides.

Discovery of the selenium-containing antioxidant ovoselenol derived from convergent evolution.

Selenium is an essential micronutrient, but its presence in biology has been limited to protein and nucleic acid biopolymers. The recent identification of a biosynthetic pathway for selenium-containing small molecules suggests that there is a larger family of selenometabolites that remains to be discovered. Here we identify a recently evolved branch of abundant and uncharacterized metalloenzymes that we predict are involved in selenometabolite biosynthesis using a bioinformatic search strategy that relies on the mapping of composite active site motifs. Biochemical studies confirm this prediction and show that these enzymes form an unusual C-Se bond onto histidine, thus giving rise to a distinct selenometabolite and potent antioxidant that we have termed ovoselenol. Aside from providing insights into the evolution of this enzyme class and the structural basis of C-Se bond formation, our work offers a blueprint for charting the microbial selenometabolome in the future.

Amorphous molybdenum sulfide nanosheets composed of [Mo3S13]2- active-site motifs for enhancing conversion of Fe3+/Fe2+ in Fenton reaction under neutral condition

Molybdenum disulfide (MoS2) edges have been considered as effective active sites to promote Fenton reaction, whereas the basal plane is inert. It is dauntingly challenging to maximally exposure edge active sites and active the basal plane. Inspired that [Mo3S13]2- clusters is basic structural unit of MoS2 edge, amorphous molybdenum sulfide (a-MoSx) nanosheets composed of [Mo3S13]2- active-site motifs may be an ideal co-catalyst for Fenton reaction. Herein, accordion-like a-MoSx nanosheets were successfully designed and prepared by one step oil-heating method. The as-synthesized a-MoSx exhibited superior activity in co-catalytic Fenton degradation of tetracycline (TC, 10 mg/L) than that of MoS2, which could reach 94.73 % within 5 min under neutral condition. This is attributed to the better Mo-S coordination mode or surrounding environment to accelerate the rate-limiting step of Fe3+/Fe2+ conversion, with DFT calculations indicating for Fe3+ on Mo4+ or S2-/S22- sites in a-MoSx a higher electron aggregation density and lower adsorption energy. Impressively, all the S atoms in a-MoSx have low adsorption energy with H atom, making that the co-catalytic Fenton reaction can be performed under neutral conditions. For a scale-up experiment, 5 L of TC wastewater (50 mg/L) was almost completely degraded after 120 min in the nickel foam/a-MoSx + H2O2 + Fe2+ system.

Distinct Site Motifs Activate O2 and H2 on Supported Au Nanoparticles in Liquid Water.

Au nanoparticles catalyze the activation and conversion of small molecules with rates and kinetic barriers that depend on the dimensions of the nanoparticle, composition of the support, and presence of catalytically culpable water molecules that solvate these interfaces. Here, molecular interpretations of steady-state rate measurements, kinetic isotope effects, and structural characterizations reveal how the interface of Au nanoparticles, liquid water, and metal oxide supports mediate the kinetically relevant activation of H2 and sequential reduction of O2-derived intermediates during the formation of H2O2 and H2O. Rates of H2 consumption are 10-100 fold greater on Au nanoparticles supported on metal oxides (e.g., titania) compared to more inert and hydrophobic materials (carbon, boron nitride). Similarly, Au nanoparticles on reducible and Lewis acidic supports (e.g., lanthana) bind dioxygen intermediates more strongly and present lower barriers (<22 kJ mol-1) for O-O bond dissociation than inert interfaces formed with silica (>70 kJ mol-1). Selectivities for H2O2 formation increase significantly as the diameters of the Au nanoparticles increase because differences in nanoparticle size change the relative fractions of exposed sites that exist at Au-support interfaces. In contrast, site-normalized rates and barriers for H2 activation depend weakly on the size of Au nanoparticles and the associated differences in active site motifs. These findings suggest that H2O aids the activation of H2 at sites present across all surface Au atoms when nanoparticles are solvated by water. However, molecular O2 preferentially binds and dissociates at Au-support interfaces, leading to greater structure sensitivity for barriers of O-O dissociation across different support identities and sizes of Au nanoparticles. These insights differ from prior knowledge from studies of gas-phase reactions of H2 and O2 upon Au nanoparticle catalysts within dilute vapor pressures of water (10-4 to 0.1 kPa H2O), in which catalysis occurs at the perimeter of the Au-support interface. In contrast, contacting Au catalysts with liquid water (55.5 M H2O) expands catalysis to all surface Au atoms and enables appreciable H2O2 formation.

Enzymatic characterization of five thioredoxins and a thioredoxin reductase from Myxococcus xanthus.

Thioredoxin (Trx) is a disulfide-containing redox protein that functions as a disulfide oxidoreductase. Myxococcus xanthus contains five Trxs (Trx1-Trx5) and one Trx reductase (TrxR). Trxs typically have a CGPC active-site motif; however, M. xanthus Trxs have slightly different active-site sequences, with the exception of Trx4. The five Trxs of M. xanthus exhibited reduced activities against insulin, 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB), cystine, glutathione disulfide (GSSG), S-nitrosoglutathione (GSNO), and H2O2 in the presence of TrxR. Myxococcus xanthus adenylate kinase and serine/threonine phosphatase activities, which were increased by the addition of dithiothreitol, were activated by the addition of Trxs and TrxR. Among these, Trx1, which has a CAPC sequence in its active site, exhibited the highest reducing activity with the exception of GSNO. Myxococcus xanthus TrxR showed weak reducing activity towards DTNB, GSSG, GSNO, and H2O2, suggesting that it has broad substrate specificity, unlike previously reported low-molecular-weight TrxRs. TrxR reduced oxidized Trx1 as the best substrate, with a kcat/Km value of 0.253 min-1 µM-1, which was 10-28-fold higher than that of the other Trxs. These results suggest that all Trxs possess reducing activity and that Trx1 may be the most functional in M. xanthus because TrxR most efficiently reduces oxidized Trx1.

Theoretical insights into layered IrO2 for the oxygen evolution reaction.

Here we present the density functional theory-based exploration of layered IrO2 polymorphs for the oxygen evolution reaction, as well as a data-driven geometric descriptor for catalytic activity. The layer edges are identified as promising active site motifs with not only low theoretical overpotential but also intriguing structural flexibility and to break the universal energetic scaling through torsional distortion.

Utilizing the Complexity of Transition Metal Phosphide Surfaces to Tune Nitrate Reduction Selectivity

Electrocatalytic nitrate reduction (NO3RR) is one exciting method of upcycling nitrate in wastewater by conversion to ammonia, an essential component in fertilizers and a potential liquid fuel. Nitrate reduction to NH3 is impeded by the formation of other products such as NO2 - or H2 via the hydrogen evolution reaction (HER). Transition metal phosphide (TMP) nanocrystals have a non-uniform surface charge distribution due to their binary compositions, which leads to a variety of active sites with different binding affinities. We hypothesize that the diversity of active sites on Ni2P can be leveraged to perform complex electrocatalytic reactions such as the NO3RR. Specifically, a diversity of surface sites can create local active site motifs that promote the adsorption of different intermediates, e.g., *NO3 - and *H, that can readily react for the NO3RR. We prepare 5 nm Ni2P and Ni nanocrystals using colloidal syntheses and deposit them onto a carbon support to compare the simpler catalytic surface of Ni with the more complex Ni2P surface. We compare their NO3RR activities with cyclic voltammetry in neutral, buffered aqueous conditions. We also investigate the selectivity between the NO3RR and HER with bulk electrolysis coupled with a colorimetric assay, where Ni2P on carbon shows higher selectivity toward NH3 over NO2 - and H2. With these experiments, we evaluate our hypothesis that the surface complexity of Ni2P will lead to enhanced NO3RR selectivity relative to Ni. This work sets the stage for developing selective electrocatalysts by utilizing ensembles of active sites to drive electrocatalytic selectivity.

Substrate selectivity and catalytic activation of the type III CRISPR ancillary nuclease Can2.

Type III CRISPR-Cas systems provide adaptive immunity against foreign mobile genetic elements through RNA-guided interference. Sequence-specific recognition of RNA targets by the type III effector complex triggers the generation of cyclic oligoadenylate (cOA) second messengers that activate ancillary effector proteins, thus reinforcing the host immune response. The ancillary nuclease Can2 is activated by cyclic tetra-AMP (cA4); however, the mechanisms underlying cA4-mediated activation and substrate selectivity remain elusive. Here we report crystal structures of Thermoanaerobacter brockii Can2 (TbrCan2) in substrate- and product-bound complexes. We show that TbrCan2 is a single strand-selective DNase and RNase that binds substrates via a conserved SxTTS active site motif, and reveal molecular interactions underpinning its sequence preference for CA dinucleotides. Furthermore, we identify a molecular interaction relay linking the cA4 binding site and the nuclease catalytic site to enable divalent metal cation coordination and catalytic activation. These findings provide key insights into the molecular mechanisms of Can2 nucleases in type III CRISPR-Cas immunity and may guide their technological development for nucleic acid detection applications.

RIBOSOME-INACTIVATED PROTEINS (RIPS) OF THE BLACK ELDER SAMBUCUS NIGRA

The aim of this work is to study the composition of ribosome-inactivating proteins from the bark and berries of the black elderberry Sambucus nigra L., growing on the territory of the Republic of Uzbekistan.&#x0D; The composition of ribosome-inactivating proteins in the bark and berries of black elder Sambucus nigra L., collected in the Botanical Garden of the Republic of Uzbekistan, was studied. According to HPLC-MS/MS sequencing, the bark sample revealed the presence of 9 RIP-2. Based on the obtained amino acid sequences using the CLUSTAL O (1.2.4) program, the amino acid sequence of the identified type 2 RIPs was compared and similar and conserved residues were identified, which will further help identify new RIPs. In the course of the studies, the tryptic peptide LSLVVLQMVSEAAR containing the RIP active site motif (EAAR) was identified with a high degree of probability. Mass spectral data on this fragment will allow further identification of other RIP-1/2 from other samples of natural origin.&#x0D; 2 RIPs were isolated from berries, one of which is in a reduced form containing one chain. Establishing the amino acid sequence in the isolated RIP from black elderberries with a molecular mass of 62337 Da confirmed our hypothesis of identification by the tryptic peptide containing the RIP active center (EAAR).

A Malassezia pseudoprotease dominates the secreted hydrolase landscape and is a potential allergen on skin

Malassezia globosa is abundant and prevalent on sebaceous areas of the human skin. Genome annotation reveals that M. globosa possesses a repertoire of secreted hydrolytic enzymes relevant for lipid and protein metabolism. However, the functional significance of these enzymes is uncertain and presence of these genes in the genome does not always translate to expression at the cutaneous surface. In this study we utilized targeted RNA sequencing from samples isolated directly from the skin to quantify gene expression of M. globosa secreted proteases, lipases, phospholipases and sphingomyelinases. Our findings indicate that the expression of these enzymes is dynamically regulated by the environment in which the fungus resides, as different growth phases of the planktonic culture of M. globosa show distinct expression levels. Furthermore, we observed significant differences in the expression of these enzymes in culture compared to healthy sebaceous skin sites. By examining the in situ gene expression of M. globosa's secreted hydrolases, we identified a predicted aspartyl protease, MGL_3331, which is highly expressed on both healthy and disease-affected dermatological sites. However, molecular modeling and biochemical studies revealed that this protein has a non-canonical active site motif and lacks measurable proteolytic activity. This pseudoprotease MGL_3331 elicits a heightened IgE-reactivity in blood plasma isolated from patients with atopic dermatitis compared to healthy individuals and invokes a pro-inflammatory response in peripheral blood mononuclear cells. Overall, our study highlights the importance of studying fungal proteins expressed in physiologically relevant environments and underscores the notion that secreted inactive enzymes may have important functions in influencing host immunity.

Antiviral mechanisms of sorafenib against foot-and-mouth disease virus via c-RAF and AKT/PI3K pathways.

Foot-and-mouth disease virus (FMDV) is a highly contagious pathogen that poses a significant threat to the global livestock industry. However, specific antiviral treatments against FMDV are currently unavailable. This study aimed to evaluate the antiviral activity of anticancer drugs, including kinase and non-kinase inhibitors against FMDV replication in BHK-21 cells. Sorafenib, a multi-kinase inhibitor, demonstrated a significant dose-dependent reduction in FMDV replication. It exhibited a half maximal effective concentration (EC50) value of 2.46µM at the pre-viral entry stage and 2.03µM at the post-viral entry stage. Further intracellular assays revealed that sorafenib effectively decreased 3Dpol activity with a half maximal inhibitory concentration (IC50) of 155nM, while not affecting 3Cpro function. The study indicates that sorafenib influences host protein pathways during FMDV infection, primarily by potentiating the c-RAF canonical pathway and AKT/PI3K pathway. Molecular docking analysis demonstrated specific binding of sorafenib to the active site of FMDV 3Dpol, interacting with crucial catalytic residues, including D245, D338, S298, and N307. Additionally, sorafenib exhibited significant binding affinity to the active site motifs of cellular kinases, namely c-RAF, AKT, and PI3K, which play critical roles in the viral life cycle. The findings suggest that sorafenib holds promise as a therapeutic agent against FMDV infection. Its mechanism of action may involve inhibiting FMDV replication by reducing 3Dpol activity and regulating cellular kinases. This study provides insights for the development of novel therapeutic strategies to combat FMDV infections.

Topology and Function of the S. cerevisiae Autophagy Protein Atg15.

The putative phospholipase Atg15 is required for the intravacuolar lysis of autophagic bodies and MVB vesicles. Intracellular membrane lysis is a highly sophisticated mechanism that is not fully understood. The amino-terminal transmembrane domain of Atg15 contains the sorting signal for entry into the MVB pathway. By replacing this domain, we generated chimeras located in the cytosol, the vacuole membrane, and the lumen. The variants at the vacuole membrane and in the lumen were highly active. Together with the absence of Atg15 from the phagophore and autophagic bodies, this suggests that, within the vacuole, Atg15 can lyse vesicles where it is not embedded. In-depth topological analyses showed that Atg15 is a single membrane-spanning protein with the amino-terminus in the cytosol and the rest, including the active site motif, in the ER lumen. Remarkably, only membrane-embedded Atg15 variants affected growth when overexpressed. The growth defects depended on its active site serine 332, showing that it was linked to the enzymatic activity of Atg15. Interestingly, the growth defects were independent of vacuolar proteinase A and vacuolar acidification.

Theoretical study of the mechanism of the hydrogen evolution reaction on the V2C MXene: Thermodynamic and kinetic aspects

Both experimentally and theoretically, the MXene family has shown promising hydrogen evolution reaction (HER) capabilities. However, so far, the theoretical approach has been relying on the well-known thermodynamic descriptor, ΔGH, whereas experimental studies report Tafel plots, containing kinetic rather than thermodynamic information. Aiming to link theory to experiments, the present study explores five different HER pathways over the exemplary V2C (0001) MXene by density functional theory calculations. While the surface coverage under HER conditions (with either H* or OH* adsorbates) is extracted from a Pourbaix diagram, we determine the energetics of the reaction intermediates and transition states for both surface species as active sites. This enables the construction of free-energy diagrams for the Volmer-Heyrovsky and Volmer-Tafel mechanisms and allows for the simulation of Tafel plots by a rigorous microkinetic framework. While the active-site motif V2C-OH seems to be less relevant for the HER under typical reaction conditions, we demonstrate that the HER is kinetically facile on the V2C-H surface. For this surface termination, we report a potential-depending switching of the preferred mechanism from the Volmer-Heyrovsky to the Volmer-Tafel description with increasing overpotential while encountering similarities to the HER over Pt.

Functional and Phylogenetic Diversity of Cas10 Proteins.

Cas10 proteins are large subunits of type III CRISPR RNA (crRNA)-guided surveillance complexes, many of which have nuclease and cyclase activities. Here, we use computational and phylogenetic methods to identify and analyze 2014 Cas10 sequences from genomic and metagenomic databases. Cas10 proteins cluster into five distinct clades that mirror previously established CRISPR-Cas subtypes. Most Cas10 proteins (85.0%) have conserved polymerase active-site motifs, while HD-nuclease domains are less well conserved (36.0%). We identify Cas10 variants that are split over multiple genes or genetically fused to nucleases activated by cyclic nucleotides (i.e., NucC) or components of toxin-antitoxin systems (i.e., AbiEii). To clarify the functional diversification of Cas10 proteins, we cloned, expressed, and purified five representatives from three phylogenetically distinct clades. None of the Cas10s are functional cyclases in isolation, and activity assays performed with polymerase domain active site mutants indicate that previously reported Cas10 DNA-polymerase activity may be a result of contamination. Collectively, this work helps clarify the phylogenetic and functional diversity of Cas10 proteins in type III CRISPR systems.

Human and bacterial TatD enzymes exhibit apurinic/apyrimidinic (AP) endonuclease activity.

TatD enzymes are evolutionarily conserved deoxyribonucleases associated with DNA repair, apoptosis, development, and parasite virulence. Three TatD paralogs exist in humans, but their nuclease functions are unknown. Here, we describe the nuclease activities of two of the three human TatD paralogs, TATDN1 and TATDN3, which represent two phylogenetically distinct clades based on unique active site motifs. We found that in addition to 3'-5' exonuclease activity associated with other TatD proteins, both TATDN1 and TATDN3 exhibited apurinic/apyrimidinic (AP) endonuclease activity. The AP endonuclease activity was observed only in double-stranded DNA, whereas exonuclease activity was operative primarily in single-stranded DNA. Both nuclease activities were observed in the presence of Mg2+ or Mn2+, and we identified several divalent metal cofactors that inhibited exonuclease and supported AP endonuclease activity. Biochemical analysis and a crystal structure of TATDN1 bound to 2'-deoxyadenosine 5'-monophosphate in the active site are consistent with two-metal ion catalysis, and we identify several residues that differentiate nuclease activities in the two proteins. In addition, we show that the three Escherichia coli TatD paralogs are also AP endonucleases, indicating that this activity is conserved across evolution. Together, these results indicate that TatD enzymes constitute a family of ancient AP endonucleases.

Activation loop phosphorylation tunes conformational dynamics underlying Pyk2 tyrosine kinase activation

Pyk2 is a multidomain non-receptor tyrosine kinase that undergoes a multistage activation mechanism. Activation is instigated by conformational rearrangements relieving autoinhibitory FERM domain interactions. The kinase autophosphorylates a central linker residue to recruit Src kinase. Pyk2 and Src mutually phosphorylate activation loops to confer full activation. While the mechanisms of autoinhibition are established, the conformational dynamics associated with autophosphorylation and Src recruitment remain unclear. We employ hydrogen/deuterium exchange mass spectrometry and kinase activity profiling to map the conformational dynamics associated with substrate binding and Src-mediated activation loop phosphorylation. Nucleotide engagement stabilizes the autoinhibitory interface, while phosphorylation deprotects both FERM and kinase regulatory surfaces. Phosphorylation organizes active site motifs linking catalytic loop with activation segment. Dynamics of the activation segment anchor propagate to EF/G helices to prevent reversion of the autoinhibitory FERM interaction. We employ targeted mutagenesis to dissect how phosphorylation-induced conformational rearrangements elevate kinase activity above the basal autophosphorylation rate.

Roles of conserved active site residues in the IscS cysteine desulfurase reaction.

Escherichia coli cysteine desulfurase (CD), IscS, modifies basal metabolism by transferring sulphur (S) from L-cysteine to numerous cellular pathways, whereas NFS1, a human CD, is active only in the formation of the [Acp]2:[ISD11]2:[NFS1]2 complex. Despite the accumulation of red-coloured IscS in E. coli cells as a result of the deficiency of accessible iron, as revealed in our previous studies, the mechanism of the potential enzymatic reaction remains unclear. In this study, the N-terminus of IscS was fused with the C-terminus of NFS1, which was reported to be almost fully active as IscS and exhibits a pyridoxal 5'-phosphate (PLP) absorption peak at 395 nm. Moreover, SUMO-EH-IscS exhibited significant growth recovery and NADH-dehydrogenase I activity in the iscS mutant cells. Furthermore, through in vitro and in vivo experiments combined with high-performance liquid chromatography and ultra-performance liquid chromatography-tandem mass spectrometry, it was shown that the new absorption peaks of the IscS H104Q, IscS Q183E, IscS K206A, and IscS K206A&C328S variants at 340 and 350 nm may correspond to the enzyme reaction intermediates, Cys-ketimine and Cys-aldimine, respectively. However, after mutation of the conserved active-site residues, additional absorption peaks at 420 and 430 nm were associated with PLP migration in the active-site pocket. Additionally, the corresponding absorption peaks of Cys-quinonoid, Ala-ketimine, and Ala-aldimine intermediates in IscS were 510, 325, and 345 nm, respectively, as determined by site-directed mutagenesis and substrate/product-binding analyses during the CD reaction process. Notably, red IscS formed in vitro by incubating IscS variants (Q183E and K206A) with excess L-alanine and sulphide under aerobic conditions produced an absorption peak similar to the wild-type IscS, at 510 nm. Interestingly, site-directed mutation of IscS with hydrogen bonds to PLP at Asp180 and Gln183 resulted in a loss of enzymatic activity followed by an absorption peak consistent with NFS1 (420 nm). Furthermore, mutations at Asp180 or Lys206 inhibited the reaction of IscS in vitro with L-cysteine (substrate) and L-alanine (product). These results suggest that the conserved active site residues (His104, Asp180, and Gln183) and their hydrogen bond with PLP in the N-terminus of IscS play a key role in determining whether the L-cysteine substrate can enter the active-site pocket and regulate the enzymatic reaction process. Therefore, our findings provide a framework for evaluating the roles of conserved active-site residues, motifs, and domains in CDs.

Identifying esterase and lipase activity in proteins of unknown function.

Over 3800 structures in the Protein Data Bank (PDB) have unknown function. The Biochemistry Authentic Scientific Inquiry Lab (BASIL) curriculum uses authentic inquiry to teach students to use structural bioinformatics tools to compare these structures to known enzymes and predict a function. We have predicted esterase or lipase function for several structures after performing both global and local structure alignments to identify similar structures in the PDB as well as specific amino acids that may be active site motifs. This function was supported by sequence alignment data from BLAST and PFam. SwissDock was then used for ligand docking to determine ester and lipid substrates to use for testing activity. Students in the biochemistry lab next used standard wet-lab biochemistry techniques to express and purify the target enzymes and performed kinetic assays using p-nitrophenyl acetate to test for esterase activity. After completing the BASIL curriculum, students continued with independent research projects to develop assays to test for lipase function. We have focused our efforts on the protein structures with PDB IDs 2O14 and 4Q7Q, as they showed the most promise through initial enzymatic testing. Both proteins show significant esterase activity in hydrolyzing both p-nitrophenyl acetate and p-nitrophenyl butyrate. Additionally, both proteins are able to hydrolyze p-nitrophenyl dodecanoate when sodium deoxycholate is present in the buffer solution for solubility of the substrate. We have also incorporated the p-nitrophenyl dodecanoate in DMPC vesicles, and testing of substrate hydrolysis with these vesicles is underway. We have also tested pancreatic lipase under all these conditions as a positive control for the experiments. Students will be creating a Proteopedia page for each protein. This project has been supported in part by NSF IUSE 1709355 and 2141908.