Active Site Motif Research Articles

Response of a novel selenium-dependent glutathione peroxidase from thick shell mussel Mytilus coruscus exposed to lipopolysaccharide, copper and benzo[α]pyrene

Glutathione peroxidase (GPx) plays an important antioxidant role in cellular defense against environmental stress. In the present study, a novel selenium-dependent glutathione peroxidase termed McSeGPx firstly identified in thick shell mussel Mytilus coruscus. McSeGPx consists of 197 amino acid residues, characterized with one selenocysteine residue encoded by an opal stop codon TGA, one selenocysteine insertion sequence (SECIS) in the 3ʹ untranslated region (UTR), two active site motifs and one signature sequence motif. McSeGPx transcripts were constitutively expressed in all examined tissues, and were significantly induced in gills and digestive glands with the stimulations of lipopolysaccharide (LPS), copper (Cu) and benzo[α]pyrene (B[α]P). Additionally, rough increases in McSeGPx activity were detected in both tissues under the challenge of LPS, Cu and B[α]P. Collectively, these results suggested that McSeGPx affiliate to selenocysteine dependent GPx (SeGPx) family and might play an important role in mediating the environmental stressors and antioxidant response in M. coruscus.

Molecular characterization of caspase-8-like and its expression induced by microcystin-LR in grass carp (Ctenopharygodon idella)

Caspase-8, an initiator caspase, plays a vital role in apoptosis. In this study, caspase-8-like (named as Cicaspase-8-like), a homologue of caspase-8, was identified in grass carp (Ctenopharygodon idella). The full-length cDNA sequence of CiCaspase-8-like was 1409 bp and contained a 162 bp 5′-UTR, a 239 bp 3′-UTR and a 1008 bp coding sequence. The putative amino acids sequence was 335 residues long, including a large subunit (P20) and a small subunit (P10), but lacking conserved death effector domains. A histidine active site DHSQMDAFVCCVLSHG and a cysteine active-site motif KPKLFFIQACQG were found in P20. Phylogenetic analysis showed that Cicaspase-8-like clustered with the caspase-8 and caspase-8-like of other fish and grouped closely with Carassius auratus caspase-8-like. Quantitative real-time PCR revealed that the Cicaspase-8-like mRNA were expressed constitutively in all tested tissues from healthy grass carp, with high expression level in the blood, spleen, liver and gill, indicating its role in immune reaction. The expression of Cicaspase-8-like mRNA was decreased significantly in the liver because of the stress caused by microcystin-LR (MC-LR) (75 and 100 μg MC-LR/kg BW) at 24 h and 96 h post injection (P < 0.05), but it was increased significantly in grass carp treated with 25 μg MC-LR/kg BW at 24 h (P < 0.05) post injection. Cleaved fragments of Cicaspase-8-like were observed using western blot analysis, and the expression of Cicaspase-8-like protein was increased after MC-LR treatments. Moreover, the expression of both caspase-9 and caspase-3 mRNA increased significantly after treatment with the three doses of MC-LR. TUNEL assay results showed remarkable changes in apoptosis after the MC-LR treatment. These results suggest that Cicaspase-8-like is an important caspase and plays an essential role in MC-LR-induced apoptosis.

Predicting Adsorption Properties of Catalytic Descriptors on Bimetallic Nanoalloys with Site-Specific Precision.

Bimetallic nanoparticles present a vastly tunable structural and compositional design space rendering them promising materials for catalytic and energy applications. Yet it remains an enduring challenge to efficiently screen candidate alloys with atomic level specificity while explicitly accounting for their inherent stabilities under reaction conditions. Herein, by leveraging correlations between binding energies of metal adsorption sites and metal-adsorbate complexes, we predict adsorption energies of typical catalytic descriptors (OH*, CH3*, CH*, and CO*) on bimetallic alloys with site-specific resolution. We demonstrate that our approach predicts adsorption energies on top and bridge sites of bimetallic nanoparticles having generic morphologies and chemical environments with errors between 0.09 and 0.18 eV. By forging a link between the inherent stability of an alloy and the adsorption properties of catalytic descriptors, we can now identify active site motifs in nanoalloys that possess targeted catalytic descriptor values while being thermodynamically stable under working conditions.

MOLECULAR MODELING AND IN SILICO CHARACTERIZATION OF NITROGEN METABOLITE REPRESSOR NmrA OF OPPORTUNISTIC HUMAN PATHOGEN Aspergillus fumigatus

The most prevalent airborne human pathogenic fungus Aspergillus fumigatus is ubiquitous in soil and like other ascomycotous fungi it can utilize a variety of nitrogen sources. Nitrogen metabolite repression (NMR) may induce virulence in A. fumigatus as in pathogenic fungi but the mechanism of regulation and its key components are not identified. The present study focuses on the molecular modeling and in silico characterization of the main player of this regulation, the NmrA of A. fumigatus. Physiochemical and structural characterization using various sequence and structure based predictors and quality assessment of the proposed two- and three-dimensional models were carried out. The characteristic motifs such as glycine-rich NAD(P)-binding motif (GxxGxxG) and altered active site motif (HxxxK) were located in NmrA along with DNA-binding residues (T11, R39, D40 and A45). The results obtained using bioinformatics tools indicated that the protein was hydrophilic in nature, stable in vitro and had very low disorder probability. Based on the quality score, the proposed secondary and tertiary structures were correct and extremely good to represent NmrA of A. fumigatus. Phylogenetic analysis signified its close relation with NMR regulatory protein of opportunistic human pathogens A. lentulus and A. novofumigatus.

Thermodynamic Considerations for Optimizing Selective CO2 Reduction by Molecular Catalysts.

Energetically efficient electrocatalysts with high product selectivity are desirable targets for sustainable chemical fuel generation using renewable electricity. Recycling CO2 by reduction to more energy dense products would support a carbon-neutral cycle that mitigates the intermittency of renewable energy sources. Conversion of CO2 to more saturated products typically requires proton equivalents. Complications with product selectivity stem from competitive reactions between H+ or CO2 at shared intermediates. We describe generalized catalytic cycles for H2, CO, and HCO2– formation that are commonly proposed in inorganic molecular catalysts. Thermodynamic considerations and trends for the reactions of H+ or CO2 at key intermediates are outlined. A quantitative understanding of intermediate catalytic steps is key to designing systems that display high selectivity while promoting energetically efficient catalysis by minimizing the overall energy landscape. For CO2 reduction to CO, we describe how an enzymatic active site motif facilitates efficient and selective catalysis and highlight relevant examples from synthetic systems.

The b′ domain of protein disulfide isomerase cooperates with the a and a′ domains to functionally interact with platelets

Essentials Protein disulfide isomerase (PDI) interacts with the αIIbβ3 integrin on platelets We generated PDI domain fragments and full-length PDI containing point mutations PDI interacts with αIIbβ3 through the b' domain, with the a and a' domains contributing This is the first report demonstrating PDI binding to a native protein on intact cells SUMMARY: Background Protein disulfide isomerase (PDI) is an oxidoreductase consisting of four domains arranged in the order a-b-b'-a' with an x-linker between the b' and a' domains. PDI binds to αIIb β3 integrin on activated platelets, and potentiates activation of this integrin through the C-terminal CGHC active-site motif. How PDI binds to platelet αIIb β3 is unknown. Objective and methods We used PDI domain fragments and full-length PDI containing point mutations to study inhibition of Alexa488-labeled PDI binding to thrombin-activated platelets. The effect of the PDI variants on platelet aggregation was tested. Results Only PDI fragments containing the b' domain bound to activated platelets. A double mutant of the b' domain had decreased binding, confirming the essential role of the b' domain. Addition of mutations in the a and a' domains further decreased binding, suggesting that these domains contribute to the interaction of PDI with platelets. The ability of the b' domain to interact directly with αIIb β3 was demonstrated with surface plasmon resonance, with contributions from the a and a' domains. The abb'x PDI fragment that binds to platelets but lacks the critical C-terminal active site inhibited platelet aggregation and invivo thrombosis. Moreover, site mutations in the a, b' and a' domains that resulted in partial binding to platelets partially recovered aggregation of PDI-null platelets. PDI mutants that did not bind showed no recovery. Conclusion PDI functionally interacts with αIIb β3 on platelets through the substrate-binding b' domain, with the a and a' domains contributing to efficient binding.

Redox-tuning of oxidizing disulfide oxidoreductase generates a potent disulfide isomerase

Oxidative folding of extracellular proteins is pivotal for the biogenesis of bacterial virulence factors. Escherichia coli DsbA catalyzes disulfide bond formation in extracellular proteins and in multicomponent architectures on the cell surface. The present study assessed the significance of the redox properties of DsbA by exploiting the plaque-forming ability of bacteriophage M13, which specifically recognizes F-pili during infection of the host cell. A library of mutant dsbA genes was constructed by randomizing the dipeptide XX sequence in the active-site redox motif CXXC and then screened for mutants that altered plaque yield and appearance. In total, 24 dsbA mutant alleles produced substantially different degrees of complementation, and one mutant dsbA gene that encodes a CDIC sequence produced over 40-fold more clear plaques than wild type dsbA. The redox potential of purified DsbA [CDIC] was −172 mV, representing a less-oxidizing catalysis than the wild type DsbA (−122 mV), but one that is closer to yeast protein disulfide isomerase (−175 mV). DsbA [CDIC] exhibited a greater ability to refold fully denatured glutathionylated ribonuclease A than the wild type enzyme and a DsbA [CRIC] mutant, which has the same redox potential of −172 mV. Homology modeling and molecular dynamics simulation suggest that the CDIC mutant may have an enlarged substrate-binding cleft near the redox center, which confers kinetic advantages when acting on protein substrates.

Methods to identify the substrates of thiol-disulfide oxidoreductases.

The formation of a disulfide bond is a critical step in the folding of numerous secretory and membrane proteins and catalyzed in vivo. A variety of mechanisms and protein structures have evolved to catalyze oxidative protein folding. Those enzymes that directly interact with a folding protein to accelerate its oxidative folding are mostly thiol-disulfide oxidoreductases that belong to the thioredoxin superfamily. The enzymes of this class often use a CXXC active-site motif embedded in their thioredoxin-like fold to promote formation, isomerization, and reduction of a disulfide bond in their target proteins. Over the past decade or so, an increasing number of substrates of the thiol-disulfide oxidoreductases that are present in the ER of mammalian cells have been discovered, revealing that the enzymes play unexpectedly diverse physiological functions. However, functions of some of these enzymes still remain unclear due to the lack of information on their substrates. Here, we review the methods used by researchers to identify the substrates of these enzymes and provide data that show the importance of using trichloroacetic acid in sample preparation for the substrate identification, hoping to aid future studies. We particularly focus on successful studies that have uncovered physiological substrates and functions of the enzymes in the periplasm of Gram-negative bacteria and the endoplasmic reticulum of mammalian cells. Similar approaches should be applicable to enzymes in other cellular compartments or in other organisms.

Structural and mechanistic analysis of the arsenate respiratory reductase provides insight into environmental arsenic transformations

Arsenate respiration by bacteria was discovered over two decades ago and is catalyzed by diverse organisms using the well-conserved Arr enzyme complex. Until now, the mechanisms underpinning this metabolism have been relatively opaque. Here, we report the structure of an Arr complex (solved by X-ray crystallography to 1.6-Å resolution), which was enabled by an improved Arr expression method in the genetically tractable arsenate respirer Shewanella sp. ANA-3. We also obtained structures bound with the substrate arsenate (1.8 Å), the product arsenite (1.8 Å), and the natural inhibitor phosphate (1.7 Å). The structures reveal a conserved active-site motif that distinguishes Arr [(R/K)GRY] from the closely related arsenite respiratory oxidase (Arx) complex (XGRGWG). Arr activity assays using methyl viologen as the electron donor and arsenate as the electron acceptor display two-site ping-pong kinetics. A Mo(V) species was detected with EPR spectroscopy, which is typical for proteins with a pyranopterin guanine dinucleotide cofactor. Arr is an extraordinarily fast enzyme that approaches the diffusion limit (Km = 44.6 ± 1.6 μM, kcat = 9,810 ± 220 seconds-1), and phosphate is a competitive inhibitor of arsenate reduction (Ki = 325 ± 12 μM). These observations, combined with knowledge of typical sedimentary arsenate and phosphate concentrations and known rates of arsenate desorption from minerals in the presence of phosphate, suggest that (i) arsenate desorption limits microbiologically induced arsenate reductive mobilization and (ii) phosphate enhances arsenic mobility by stimulating arsenate desorption rather than by inhibiting it at the enzymatic level.

A126 in the active site and TI167/168 in the TI loop are essential determinants of the substrate specificity of PTEN

PTEN prevents tumor genesis by antagonizing the PI3 kinase/Akt pathway through D3 site phosphatase activity toward PI(3,4)P2 and PI(3,4,5)P3. The structural determinants of this important specificity remain unknown. Interestingly, PTEN shares remarkable homology to voltage-sensitive phosphatases (VSPs) that dephosphorylate D5 and D3 sites of PI(4,5)P2, PI(3,4)P2, and PI(3,4,5)P3. Since the catalytic center of PTEN and VSPs differ markedly only in TI/gating loop and active site motif, we wondered whether these differences explained the variation of their substrate specificity. Therefore, we introduced mutations into PTEN to mimic corresponding sequences of VSPs and studied phosphatase activity in living cells utilizing engineered, voltage switchable PTENCiV, a Ci-VSP/PTEN chimera that retains D3 site activity of the native enzyme. Substrate specificity of this enzyme was analyzed with whole-cell patch clamp in combination with total internal reflection fluorescence microscopy and genetically encoded phosphoinositide sensors. In PTENCiV, mutating TI167/168 in the TI loop into the corresponding ET pair of VSPs induced VSP-like D5 phosphatase activity toward PI(3,4,5)P3, but not toward PI(4,5)P2. Combining TI/ET mutations with an A126G exchange in the active site removed major sequence variations between PTEN and VSPs and resulted in D5 activity toward PI(4,5)P2 and PI(3,4,5)P3 of PTENCiV. This PTEN mutant thus fully reproduced the substrate specificity of native VSPs. Importantly, the same combination of mutations also induced D5 activity toward PI(3,4,5)P3 in native PTEN demonstrating that the same residues determine the substrate specificity of the tumor suppressor in living cells. Reciprocal mutations in VSPs did not alter their substrate specificity, but reduced phosphatase activity. In summary, A126 in the active site and TI167/168 in the TI loop are essential determinants of PTEN’s substrate specificity, whereas additional features might contribute to the enzymatic activity of VSPs.

Crystal structure of human anterior gradient protein 3.

Oxidative protein folding in the endoplasmic reticulum is catalyzed by the protein disulfide isomerase family of proteins. Of the 20 recognized human family members, the structures of eight have been deposited in the PDB along with domains from six more. Three members of this family, ERp18, anterior gradient protein 2 (AGR2) and anterior gradient protein 3 (AGR3), are single-domain proteins which share sequence similarity. While ERp18 has a canonical active-site motif and is involved in native disulfide-bond formation, AGR2 and AGR3 lack elements of the active-site motif found in other family members and may both interact with mucins. In order to better define its function, the structure of AGR3 is required. Here, the recombinant expression, purification, crystallization and crystal structure of human AGR3 are described.

BadGluc, a β-glucosidase from Bjerkandera adusta with anthocyanase properties.

A glycosidase of the basidiomycete Bjerkandera adusta (BadGluc) was found in screenings to possess a strong decolorizing ability towards malvidin-3-galactoside, an anthocyanin abundant in various berry fruits. The BadGluc was purified from the culture supernatant via FPLC, and the corresponding gene was identified which showed low similarity to other characterized glucosidases. Scanning the primary sequence with PROSITE no active site motif was detected. Eventually, a specific 18 aa consensus pattern was identified manually. The active site motif possessed an undescribed sequence which was only found in a few hypothetical proteins. The corresponding gene was cloned and expressed in Pichia pastoris GS115 yielding activities up to 100 U/L using 4-nitrophenyl-β-d-glucopyranoside (pNPG) as substrate. The enzyme possessed a good temperature (70% after 1 h at 50°C) and pH stability (70% between pH 2 and 7.5), and preferably catalysed the hydrolysis of delphinidin-3-glucoside and cyanidin-3-glucoside, regardless of the position of the terminal Hexa-His tag. This novel glucosidase worked in aqueous solution as well as on pre-stained fabrics making it the first known candidate anthocyanase for applications in the detergent and food industries.

Molecular and biological characterization of gamma-interferon-inducible lysosomal thiol reductase in silver carp (Hypophthalmichthys molitrix)

Gamma-interferon-inducible lysosomal thiol reductase (GILT) plays an important role in the processing of major histocompatibility complex (MHC) class II-restricted antigens by catalyzing disulfide bonds reduction. Herein, a GILT homolog (ScGILT) was identified from silver carp. Its open reading frame covers 771 base pairs, encoding a protein of 256 amino acids that possesses GILT signature sequence CQHGX2ECX2NX4C, active-site CXXC motif, and two potential N-linked glycosylation sites. The predicted tertiary structures of ScGILT and other GILTs were quite similar in shape and positional arrangement of the key motifs. ScGILT mRNA was constitutively expressed in all detected tissues, with high-level expression in fish immune organs, spleen and head kidney. After stimulation with lipopolysaccharide, the expression of ScGILT mRNA significantly increased in spleen and head kidney cells, and ScGILT protein translocated to late endosomes and lysosomes in HeLa cells. Recombinant ScGILT fused with a His6 tag was expressed and purified, and could reduce the interchain disulfide bonds of IgG at pH 4.5. These results suggested that ScGILT was capable of catalyzing disulfide bonds reduction, and then might play an important role in the processing of MHC class II-restricted antigens in silver carp.

Probing and Engineering Key Residues for Bis-C-glycosylation and Promiscuity of a C-Glycosyltransferase

C-Glycosyltransferases (CGTs) are powerful tools for the C-glycosylation of natural and unnatural products. However, CGTs able to catalyze bis-C-glycosylation are very rare and the key amino acids of which have not been uncovered. Here, we discovered a C-glycosyltransferase MiCGTb from Mangifera indica that has the capacity for bis-C-glycosylation. Further studies on active-site motifs revealed that I152 of MiCGTb was the critical amino acid residue for the second C-glycosylation and its S60/V100/T104 residues were pivotal for bis-C-glycosylation activity. Moreover, we developed a panel of variants with acceptor and donor promiscuity by site-directed mutagenesis. Among these variants, a mutant MiCGT-E152L displayed a broader acceptor scope for bis-C-glycosylation, and three mutants of MiCGTb exhibited sugar donor promiscuity toward structurally varied α-d- and β-l-glycosyl donors. Our work provides insights into the pivotal amino acid residues of CGTs for bis-C-glycosylation and biocatalytic tools to effi...

Characterization of an A-Site Selective Protein Disulfide Isomerase A1 Inhibitor.

Protein disulfide isomerase A1 (PDIA1) is an endoplasmic reticulum (ER)-localized thiol-disulfide oxidoreductase that is an important folding catalyst for secretory pathway proteins. PDIA1 contains two active-site domains (a and a'), each containing a Cys-Gly-His-Cys (CGHC) active-site motif. The two active-site domains share 37% sequence identity and function independently to perform disulfide-bond reduction, oxidation, and isomerization. Numerous inhibitors for PDIA1 have been reported, yet the selectivity of these inhibitors toward the a and a' sites is poorly characterized. Here, we identify a potent and selective PDIA1 inhibitor, KSC-34, with 30-fold selectivity for the a site over the a' site. KSC-34 displays time-dependent inhibition of PDIA1 reductase activity in vitro with a kinact/ KI of 9.66 × 103 M-1 s-1 and is selective for PDIA1 over other members of the PDI family, and other cellular cysteine-containing proteins. We provide the first cellular characterization of an a-site selective PDIA1 inhibitor and demonstrate that KSC-34 has minimal sustained effects on the cellular unfolded protein response, indicating that a-site inhibition does not induce global protein folding-associated ER stress. KSC-34 treatment significantly decreases the rate of secretion of a destabilized, amyloidogenic antibody light chain, thereby minimizing pathogenic amyloidogenic extracellular proteins that rely on high PDIA1 activity for proper folding and secretion. Given the poor understanding of the contribution of each PDIA1 active site to the (patho)physiological functions of PDIA1, site selective inhibitors like KSC-34 provide useful tools for delineating the pathological role and therapeutic potential of PDIA1.

Structure and function of the cytochrome P450 peroxygenase enzymes

The cytochromes P450 (P450s or CYPs) constitute a large heme enzyme superfamily, members of which catalyze the oxidative transformation of a wide range of organic substrates, and whose functions are crucial to xenobiotic metabolism and steroid transformation in humans and other organisms. The P450 peroxygenases are a subgroup of the P450s that have evolved in microbes to catalyze the oxidative metabolism of fatty acids, using hydrogen peroxide as an oxidant rather than NAD(P)H-driven redox partner systems typical of the vast majority of other characterized P450 enzymes. Early members of the peroxygenase (CYP152) family were shown to catalyze hydroxylation at the α and β carbons of medium-to-long-chain fatty acids. However, more recent studies on other CYP152 family P450s revealed the ability to oxidatively decarboxylate fatty acids, generating terminal alkenes with potential applications as drop-in biofuels. Other research has revealed their capacity to decarboxylate and to desaturate hydroxylated fatty acids to form novel products. Structural data have revealed a common active site motif for the binding of the substrate carboxylate group in the peroxygenases, and mechanistic and transient kinetic analyses have demonstrated the formation of reactive iron-oxo species (compounds I and II) that are ultimately responsible for hydroxylation and decarboxylation of fatty acids, respectively. This short review will focus on the biochemical properties of the P450 peroxygenases and on their biotechnological applications with respect to production of volatile alkenes as biofuels, as well as other fine chemicals.

Crystal structure of a UDP-GlcNAc epimerase for surface polysaccharide biosynthesis in Acinetobacter baumannii.

With new strains of Acinetobacter baumannii undergoing genomic analysis, it has been possible to define regions of genomic plasticity (RGPs), encoding specific adaptive elements. For a selected RGP from a community-derived isolate of A. baumannii, we outline sequences compatible with biosynthetic machinery of surface polysaccharides, specifically enzymes utilized in the dehydration and conversion of UDP-N-acetyl-D-glucosamine (UDP-D-GlcNAc). We have determined the crystal structure of one of these, the epimerase Ab-WbjB. This dehydratase belongs to the ‘extended’ short-chain dehydrogenase/reductase (SDR) family, related in fold to previously characterised enzymes CapE and FlaA1. Our 2.65Å resolution structure of Ab-WbjB shows a hexamer, organised into a trimer of chain pairs, with coenzyme NADP+ occupying each chain. Specific active-site interactions between each coenzyme and a lysine quaternary group of a neighbouring chain interconnect adjacent dimers, so stabilising the hexameric form. We show UDP-GlcNAc to be a specific substrate for Ab-WbjB, with binding evident by ITC (Ka = 0.23 μmol-1). The sequence of Ab-WbjB shows variation from the consensus active-site motifs of many SDR enzymes, demonstrating a likely catalytic role for a specific threonine sidechain (as an alternative to tyrosine) in the canonical active site chemistry of these epimerases.

Performance of Density Functional Theory for Predicting Methane-to-Methanol Conversion by a Tri-Copper Complex

Efficient, low-temperature, and catalytic methane-to-methanol conversion (MMC) is of great interest, as methanol can be used as a liquid fuel and is a value-adding intermediate in the petrochemical industry. MMC can be achieved through direct C–H activation or via oxidation in strongly acidic media using noble metal catalysts. However, these processes are expensive and generally have low selectivity for methanol. In contrast, copper-exchanged zeolites can facilitate methane oxidation stoichiometrically under mild conditions with high selectivities for methanol. Approaches for achieving catalytic MMC on copper-exchanged zeolites have recently been developed. A better understanding of this process is required in order to facilitate the design of more efficient catalysts. In this work, we benchmark the performance of density functional theory (DFT) for modeling the MMC pathway by a tri-copper complex, [Cu3O3(H2O)6]2+. This complex is reminiscent of [Cu3O3]2+ proposed as the active-site motif in the zeolite m...

Cation-exchanged zeolites for the selective oxidation of methane to methanol

Development of an ideal methane activation catalyst presents a trade-off between stability and reactivity of the active site that can be achieved by tuning the transition metal cation, active site motif and the zeolite topology.

DFT exploration of active site motifs in methane hydroxylation by Ni-ZSM-5 zeolite

DFT calculations suggest [Ni2(μ-O)2]2+ and [Ni3(μ-O)3]2+ species as two possible active sites in methane hydroxylation by Ni-ZSM-5 zeolite. Both of them are predicted to activate methane and desorb the formed methanol with low activation and desorption energies.