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Human dipeptidyl peptidase III (hDPP III) is a zinc-exopeptidase of the family M49 involved in final steps of intracellular protein degradation and in cytoprotective pathway Keap1-Nrf2. Biochemical and structural properties of this enzyme have been extensively investigated, but the knowledge on its contacts with other proteins is scarce. Previously, polypeptide aprotinin was shown to be a competitive inhibitor of hDPP III hydrolytic activity. In this study, aprotinin was first investigated as a potential substrate of hDPP III, but no degradation products were demonstrated by MALDI-TOF mass spectrometry. Subsequently, molecular details of the protein-protein interaction between aprotinin and hDPP III were studied by molecular modeling. Docking and long molecular dynamics (MD) simulations have shown that aprotinin interacts by its canonical binding epitope with the substrate binding cleft of hDPP III. Thereby, free N-terminus of aprotinin is distant from the active-site zinc. Enzyme-inhibitor complex is stabilized by intermolecular hydrogen bonding network, electrostatic and hydrophobic interactions which mostly involve constituent amino acid residues of the hDPP III substrate binding subsites S1, S1', S2, S2' and S3'. This is the first study that gives insight into aprotinin binding to a metallopeptidase. Communicated by Ramaswamy H. Sarma.

A molecular modeling study has been performed on a series of 16 benzimidazole-based inhibitors of human dipeptidyl peptidase III (DPP III). Eight of these were novel compounds synthesized in excellent yields using green chemistry approach. This study aims at elucidating the structural features of benzimidazole derivatives required for the antagonism of human DPP III activity using Quantitative Structure-Activity Relationship (QSAR) analysis, and at understanding the mechanism of one of the most potent inhibitor bindings into the active site of this enzyme, namely by molecular dynamics (MD) simulations. The best model obtained includes S3K and RDF045m descriptors, which have explained 89.4 % of inhibitory activity. The depicted moiety for the strong inhibition activity matches the structure of the most potent compound. MD simulation has revealed the importance of imidazolinyl and phenyl groups in the mechanism of binding into the active site of human DPP III.

Aims We aimed to explore the impact of surgical 17β-estradiol (E2) deprivation/administration on the expression of antioxidant enzymes with an emphasis on the alteration of the NF-E2-related factor 2/Kelch-like ECH-associated protein 1 (Nrf2/Keap1) pathway under physiological conditions in the livers of CBA/H mice of both sexes. Main methods Hepatic oxidative stress markers were determined by measuring lipid peroxidation and DNA damage using the comet assay. The expression and activities of two isoforms of superoxide dismutase (Sod-1, Sod-2) and catalase (Cat) were studied using real-time PCR, Western blot and spectrophotometrical analyses. The effect of E2 on Nrf2/Keap1 protein levels and localization was assessed using cytosolic and nuclear fractions. Key findings We demonstrate the E2-mediated repression of the antioxidant enzymes Sod-1, Sod-2 and Cat in the livers of ovariectomized mice treated with E2 and its association with a decreased level of Nrf2/Keap1 proteins in the nucleus. We observed beneficial effects of long-term E2 administration on lipid peroxidation but not on DNA damage in the livers of ovariectomized mice. Significance The results of this study may additionally confirm the protective ability of E2 in prolonging the onset of age-related disease in females that ultimately contributes to their longer lifespan.

Flavonoids belong to the group of naturally occurring polyphenolic compounds ubiquitously found in plants. They are important components of human diet and have various biological activities. The ability of flavonoids to coordinate metal ions and to interact with peptidases whose catalytic activity depends on the metal cation is an important cause for their beneficial effects on human health. To date, numerous flavonoid compounds as inhibitors with pathophysiological significance in the regulation of human metalloprotease activity are known and are widely used for scientific and pharmaceutical studies. This review presents an overview of the investigations on the feasibility and application of flavonoids as natural inhibitors for well-known human metalloproteases: matrix metalloproteinases and angiotensin-converting enzyme.

The hydrogen deuterium exchange (HDX) mass spectrometry combined with molecular dynamics (MD) simulations was employed to investigate conformational dynamics and ligand binding within the M49 family (dipeptidyl peptidase III family). Six dipeptidyl peptidase III (DPP III) orthologues, human, yeast, three bacterial and one plant (moss) were studied. According to the results, all orthologues seem to be quite compact wherein DPP III from the thermophile Caldithrix abyssi seems to be the most compact. The protected regions are located within the two domains core and the overall flexibility profile consistent with semi-closed conformation as the dominant protein form in solution. Besides conservation of conformational dynamics within the M49 family, we also investigated the ligand, pentapeptide tynorphin, binding. By comparing HDX data obtained for unliganded protein with those obtained for its complex with tynorphin it was found that the ligand binding mode is conserved within the family. Tynorphin binds within inter-domain cleft, close to the lower domain β-core and induces its stabilization in all orthologues. Docking combined with MD simulations revealed details of the protein flexibility as well as of the enzyme– ligand interactions.

Dipeptidyl peptidase III (DPP III) isolated from the thermophilic bacteria Caldithrix abyssi (Ca) is a two-domain zinc exopeptidase, a member of the M49 family. Like other DPPs III, it cleaves dipeptides from the N-terminus of its substrates but differently from human, yeast and Bacteroides thetaiotaomicron (mesophile) orthologs, it has the pentapeptide zinc binding motif (HEISH) in the active site instead of the hexapeptide (HEXXGH). The aim of our study was to investigate structure, dynamics and activity of CaDPP III, as well as to find possible differences with already characterized DPPs III from mesophiles, especially B. thetaiotaomicron. The enzyme structure was determined by X-ray diffraction, while stability and flexibility were investigated using MD simulations. Using molecular modeling approach we determined the way of ligands binding into the enzyme active site and identified the possible reasons for the decreased substrate specificity compared to other DPPs III. The obtained results gave us possible explanation for higher stability, as well as higher temperature optimum of CaDPP III. The structural features explaining its altered substrate specificity are also given. The possible structural and catalytic significance of the HEISH motive, unique to CaDPP III, was studied computationally, comparing the results of long MD simulations of the wild type enzyme with those obtained for the HEISGH mutant. This study presents the first structural and biochemical characterization of DPP III from a thermophile.

Yeast dipeptidyl peptidase III (yDPP III) is a member of the metallopeptidase family M49 involved in intracellular protein catabolism. Elucidation of the yDPP III crystal structure has pinpointed the zinc-coordinating residues (two His from H(460)ELLGH(465) motif and the second Glu from E(516)ECRAE(521) motif), and several amino acid residues potentially important for catalytic activity whose roles have not been investigated. Here, three putative catalytic residues of the yDPP III, His578, Arg582 and Lys638 were substituted and the resultant single mutants characterized. The replacement of His578 with an asparagine significantly (122-fold) lowered the catalytic efficiency, kcat/Km, for Arg-Arg-2-naphthylamide (Arg2-2NA) hydrolysis, and affinity for hydroxamate inhibitor Tyr-Phe-NHOH (decline by 14-fold). The R582Q mutant exhibited an order of magnitude higher activity with all four dipeptide derivatives examined, compared to the wild type. The molecular dynamics simulations revealed the change in the H-bond networking in the R582Q variant active-site region. The mutation of Lys638, to Leu, slightly increased the specificity constant for Arg2-2NA hydrolysis. However, the affinity for Tyr-Phe-NHOH, and activity for the substrates with uncharged P2 side chains (Ala-Ala-, Ala-Arg- and Phe-Arg-2NA) were dramatically reduced, indicating the importance of the evolutionary conserved salt bridge Lys(638)-Glu(516) for the modulation of DPP III substrate specificity.

In a search for plant homologues of dipeptidyl peptidase III (DPP III) family, we found a predicted protein from the mossPhyscomitrella patens(UniProt entry: A9TLP4), which shared 61% sequence identity with theArabidopsis thalianauncharacterized protein, designated Nudix hydrolase 3. Both proteins contained all conserved regions of the DPP III family, but instead of the characteristic hexapeptide HEXXGH zinc-binding motif, they possessed a pentapeptide HEXXH, and at the N-terminus, a Nudix box, a hallmark of Nudix hydrolases, known to act upon a variety of nucleoside diphosphate derivatives. To investigate their biochemical properties, we expressed heterologously and purifiedPhyscomitrella(PpND) andArabidopsis(AtND) protein. Both hydrolyzed, with comparable catalytic efficiency, the isopentenyl diphosphate (IPP), a universal precursor for the biosynthesis of isoprenoid compounds. In addition, PpND dephosphorylated four purine nucleotides (ADP, dGDP, dGTP, and 8-oxo-dATP) with strong preference for oxidized dATP. Furthermore, PpND and AtND showed DPP III activity against dipeptidyl-2-arylamide substrates, which they cleaved with different specificity. This is the first report of a dual activity enzyme, highly conserved in land plants, which catalyzes the hydrolysis of a peptide bond and of a phosphate bond, acting both as a dipeptidyl peptidase III and an atypical Nudix hydrolase.

Dipeptidyl peptidase III (DPP III) is a cytosolic enzyme belonging to the metallopeptidase family M49, involved in the final steps of protein catabolism. More than a hundred missense mutations can be found in the coding region of the human DPP3 gene when searching cBioPortal for Cancer Genomics. The role of two highly conserved residues in the family M49, whose mutations G313W and R510W were detected in human cancer, was investigated using combined experimental and computational approaches (substrate docking and MD simulations). Several mutants of human DPP III were expressed and purified as recombinant proteins, and their biochemical properties were determined. The conservative substitution of Arg510 with lysine mildly decreased enzyme activity activity for Arg-Arg-2-naphtylamide substrate, while the substitutions of Arg510 with glutamine and Gly313 with alanine substantially decreased enzyme activity, and tryptophan substitutions found in cancer, G313W and R510W, almost abolished enzyme activity. MD simulations showed that substitution of Gly313, and especially Arg510 with tryptophan, significantly increases the enzyme flexibility, particularly that of the binding site including the H450ELLGH455 motif, and influences the substrate interactions with the catalytic His568. The results clearly indicate that, besides the enzyme structure, its dynamics properties also significantly influence the human DPP III activity.

Fifteen flavonoids were studied for their inhibitory activity against human dipeptidyl peptidase III (hDPP III) combining an in vitro assay with an in silico molecular modeling study. All analyzed flavonoids showed inhibitory effects against hDPP III with the IC50 values ranging from 22.0 to 437.2 μM. Our 3D QSAR studies indicate that the presence of hydrophilic regions at a flavonoid molecule increases its inhibitory activity while the higher percentage of hydrophobic surfaces have negative impact on enzyme inhibition. Furthermore, molecular dynamics (MD) simulations of the complex of hDPP III with one of the most potent inhibitors, luteolin, were performed and binding mode analysis revealed that the 3’ and 4’ hydroxyl group on B-ring as well as 5 and 7 hydroxyl group on A-ring helps luteolin to interact with the Asn391, Asn406, Tyr417, His450, Glu451, Val447, Glu512, Asn545, Gln566 and Arg572 residues. The MD results clearly provide valuable information explaining the importance of flavonoid hydroxyl groups in the mechanism for the binding pattern at the active site of hDPP III. This article is protected by copyright. All rights reserved.

Dipeptidyl peptidase III (DPP III), a member of the metallopeptidase family M49, was considered as an exclusively eukaryotic enzyme involved in intracellular peptide cata­bolism and pain modulation. In 2003, new data on genome sequences revealed the first prokaryotic orthologs, which showed low sequence similarity to eukaryotic ones and a cysteine (Cys) residue in the zinc-binding motif HEXXGH. Here we report the cloning and heterologous expression of DPP III from the human gut symbiontBacteroides thetaiotaomicron. The catalytic efficiency of bacterial DPP III for preferred synthetic substrate hydrolysis was very similar to that of the human host enzyme. Substitution of Cys450from the active-site motif by serine did not substantially change the enzymatic activity. However, this residue was wholly responsible for the inactivation effect of sulfhydryl reagents. Molecular modeling indicated seven basic amino acid residues in the local environment of Cys450as a possible cause for its high reactivity. Sequence analysis of 81 bacterial M49 peptidases showed conservation of the HECLGH motif in 68 primary structures with the majority of proteins lacking an active-site Cys originated from aerobic bacteria. Data obtained suggest that Cys450ofB. thetaiotaomicronDPP III is a regulatory residue for the enzyme activity.

Human dipeptidyl peptidase III (DPP III) is a zinc-exopeptidase with implied roles in protein catabolism, pain modulation and defense against oxidative stress. To understand the mode of ligand binding into its active site, we performed molecular modeling, site-directed mutagenesis and biochemical analyses. Using the recently determined crystal structure of the human DPP III we built complexes between both, the wild type protein and its mutant H568N with the preferred substrate Arg-Arg-2-naphthylamide (RRNA) and a competitive inhibitor Tyr-Phe-hydroxamate (Tyr-Phe-NHOH). The mutation of the conserved H1099-1352is568, structurally equivalent to catalytically important His231 in thermolysin, to Asn, resulted in a 1300-fold decrease of kcat for RRNA hydrolysis and in significantly lowered affinity for the inhibitor. Molecular dynamics (MD) simulations revealed the key protein ligand interactions as well as the ligand induced reorganization of the binding site and its partial closure. Simultaneously, the non catalytic domain was observed to stretch and the opening at the wide side of the inter-domain cleft became enhanced. The driving force for these changes was the formation of the hydrogen bond between Asp372 and the bound ligand. The structural and dynamical differences, found for the ligand binding to the wild-type enzyme and the H568N mutant, and the calculated binding free energies, agree well with the measured affinities. On the basis of the obtained results we suggest a possible reaction mechanism. In addition, this work provides a foundation for further site-directed mutagenesis experiments, as well as for modeling the reaction itself.

The role of the unique fully conserved tryptophan in metallopeptidase family M49 (dipeptidyl peptidase III family) was investigated by site-directed mutagenesis on human dipeptidyl peptidase III (DPP III) where Trp300 was subjected to two substitutions (W300F and W300L). The mutant enzymes showed thermal stability equal to the wild-type DPP III. Conservative substitution of the Trp300 with phenylalanine decreased enzyme activity 2–4 fold, but did not significantly change the Km values for two dipeptidyl 2-naphthylamide substrates. However, the Km for the W300L mutant was elevated 5-fold and the kcat value was reduced 16-fold with Arg-Arg-2-naphthylamide. Both substitutions had a negative effect on the binding of two competitive inhibitors designed to interact with S1 and S2 subsites. These results indicate the importance of the aromatic nature of W300 in DPP III ligand binding and catalysis, and contribution of this residue in maintaining the functional integrity of this enzyme’s S2 subsite.

The Streptomyces coelicolor A3(2) gene SCI11.14c was overexpressed and purified as a His-tagged protein from heterologous host, Streptomyces lividans. The purification procedure resulted in 34.1-fold increase in specific activity with an overall yield of 21.4%. Biochemical and physical properties of the purified enzyme were investigated and it was shown that it possesses (aryl)esterase and a true lipase activity. The enzyme was able to hydrolyze p-nitrophenyl-, alpha- and beta-naphthyl esters and poly(oxyethylene) sorbitan monoesters (Tween 20-80). It showed pronounced activity towards p-nitrophenyl and alpha- and beta-naphthyl esters of C(12)-C(16). Higher activity was observed with alpha-naphthyl esters. The enzyme hydrolyzed triolein (specific activity: 91.9U/mg) and a wide range of oils with a preference for those having higher content of linoleic or oleic acid (C18:2 ; C18:1, cis). The active-site serine specific inhibitor 3, 4-dichloroisocoumarin (DCI) strongly inhibited the enzyme, while tetrahydrofurane and 1, 4-dioxane significantly increased (2- and 4- fold, respectively) hydrolytic activity of lipase towards p-nitrophenyl caprylate. The enzyme exhibited relatively high temperature optimum (55 degrees C) and thermal stability. CD analysis revealed predominance of alpha-helical structure (54% alpha-helix, 21% beta-sheet) and a T(m) value at 66 degrees C. Systematic bioinformatic analysis of deduced amino acid sequence of S. coelicolor enzyme placed it to the SGNH-hydrolase family. Phylogenetic analysis of the predicted protein homologues to the S. coelicolor SGNH-hydrolase generated three distinct groups consisting of proteins from Actinomycetales, Ascomycota and nematodes. At present it seems that these enzymes are most conserved among soil inhabiting organisms.

Dipeptidyl-peptidases III (DPP III) are zinc-dependent enzymes that specifically cleave the first two amino acids from the N terminus of different length peptides. In mammals, DPP III is associated with important physiological functions and is a potential biomarker for certain types of cancer. Here, we present the 1.95-Å ; crystal structure of yeast DPP III representing the prototype for the M49 family of metallopeptidases. It shows a novel fold with two domains forming a wide cleft containing the catalytic metal ion. DPP III exhibits no overall similarity to other metallopeptidases, such as thermolysin and neprilysin, but zinc coordination and catalytically important residues are structurally conserved. Substrate recognition is accomplished by a binding site for the N terminus of the peptide at an appropriate distance from the metal center and by a series of conserved arginine residues anchoring the C termini of different length substrates.

Human dipeptidyl peptidase III (hDPP III), a zinc-metallopeptidase of the family M49, is an activator of the Keap1-Nrf2 cytoprotective pathway involved in defense against oxidative stress. Pathophysiological roles of DPP III have not been elucidated yet, partly due to the lack of specific inhibitors. We showed that substrate analog H-Tyr-Phe-NHOH is a strong competitive inhibitor of hDPP III, while H-Tyr-Gly-NHOH expresses much weaker inhibition. To investigate the effects of amino acid substitutions in inhibitor P1 position, we synthesized three new dipeptidyl hydroxamates and examined their influence on the activity of hDPP III and DPP III from the human gut symbiont Bacteroides thetaiotaomicron. The extent of inhibition of hDPP III, but not of bacterial enzyme, was dependent on the amino acid in P1. H-Phe-Phe-NHOH is recognized as one of the strongest inhibitors of hDPP III (Ki = 0.028 μM), and H-Phe-Leu-NHOH discriminated between human and bacterial ortholog of the M49 family.

A number of age-related diseases have a low incidence in females, which is attributed to a protective effect of sex hormones. For instance, the female sex hormone estrogen (E2) has a well established cytoprotective effect against oxidative stress, which strongly contributes to ageing. However, the mechanism by which E2 exerts its protective activity remains elusive. In this study we address the question whether the E2-induced protective effect against hyperoxia is mediated by the Nrf-2/Keap-1 signaling pathway. In particular, we investigate the E2-induced expression and cellular distribution of DPP III monozinc exopeptidase, a member of the Nrf-2/Keap-1 pathway, upon hyperoxia treatment. We find that DPP III accumulates in the nucleus in response to hyperoxia. Further, we show that combined induction of hyperoxia and E2 administration have an additive effect on the nuclear accumulation of DPP III. The level of nuclear accumulation of DPP III is comparable to nuclear accumulation of Nrf-2 in healthy female mice exposed to hyperoxia. In ovariectomized females exposed to hyperoxia, supplementation of E2 induced upregulation of DPP III, Ho-1, Sirt-1 and downregulation of Ppar-γ. While other cytoprotective mechanisms cannot be excluded, these findings demonstrate a prominent role of DPP III, along with Sirt-1, in the E2-mediated protection against hyperoxia., Graphical abstract fx1, Highlights • DPP III accumulates in the nucleus in response to hyperoxia. • Additive effect of hyperoxia and E2 on nuclear accumulation of DPP III is observed. • Protective effect of E2 is associated with increased DPP III, Ho-1 and Sirt-1.

Dipeptidyl peptidase III (DPP III) is a zinc dependant peptidase which catalyses hydrolysis of the second peptide bond from the N-termini of its substrates. DPP III is an enzyme of broad substrate specificity and it has been found in many organisms. It has been recognised in several processes of interest for the drug development like pain modulation and defence against oxidative stress. However, its fundamental physiological role is unknown and the specific inhibitors would be of significant help in identifying this role. In this work we combined experimental (UV/Vis, fluorimetry and microcalorimetry experiments) with molecular dynamic simulations to study binding of several newly designed and synthesised guanidiniocarbonyl-pyrrole -aryl conjugates to human DPP III. We found that new compounds bind with micromolar affinity to the enzyme and with various efficiency inhibit hydrolysis of Arg-Arg-2-naphthylamide, the standard synthetic substrate of DPP III. The molecular modelling study revealed multiple binding modes of the guanidiniocarbonyl-pyrrole -aryl conjugates into the active site of human DPP III. In order to elucidate which one is the most favourable we studied the molecular determinants for their binding to DPP III as well as their influence on protein structure. It seems that the main requirements for a good DPP III inhibitor is the bulky aryl-substituent and a linker of proper length and flexibility between it and guanidiniocarbonyl-pyrrole. The obtained results gave directions for future development and improvement of DPP III inhibitors.

Dipeptidyl peptidase III (DPP III), also known as enkephalinase B, is a zinc-hydrolase with an indicated role in the mammalian pain modulatory system. In order to find a potent antagonist of this enzyme, we synthesized and screened the effect of a small set of benzimidazole derivatives on its activity. To improve the inhibitory potential, a cyclobutane ring was introduced as rigid conformation support to the diamidino substituted dibenzimidazoles. Two such compounds ( 1 ′ and 4 ′) from the group of cyclobutane derivatives containing amidino-substituted benzimidazole moieties, obtained by photochemical cyclization in water and by respecting rules of the “green chemistry” approach, were found to be strong DPP III inhibitors, with IC 50 value below 5 μM. Compound 1 ′ displayed time-dependent inhibition towards human DPP III, characterized by the second-order rate constant of 6924 ± 549 M −1 min −1 ( K i = 0.20 μM). The peptide substrate valorphin protected the enzyme from inactivation by 1 ′.

In an attempt to identify glycolytic capacity of normal and neoplastic human ovary, total lactate dehydrogenase (LDH) activity was measured in tissue cytosol originating from 69 patients (18 with benign ovarian tumor, 34 with ovarian carcinoma, six with nonepithelial ovarian malignant tumors, and 11 with tumor metastatic to ovary) and compared to the LDH activity of normal ovarian tissues (n = 19). Median value of total LDH-specific activity expressed as U/mg protein was 0.546 in normal tissues, 0.584 in benign tumors, 1.071 in malignancies metastatic to ovaries, 0.872 in nonepithelial primary ovarian tumors, and 0.818 in primary carcinomas. A significant rise in LDH-specific activity was found in malignant primary and secondary tumors of epithelial and nonepithelial origin, but not in benign neoplasms, compared to the activity in normal tissue. Ovarian carcinomas of serous histologic type did not differ in LDH activity from mucinous tumors. However, poorly differentiated carcinomas (grade 3) showed significantly enhanced activity of this glycolytic enzyme when compared to its grade 1 counterpart. The subgroup of grade 1 tumors did not differ in LDH activity from normal and benign ovarian tissue. Obtained results suggest that direct correlation might exist between ovarian epithelial tumor grade and lactate dehydrogenase activity.

Objective Proteolytic enzymes have been implicated in the progression of various human malignancies, including ovarian cancer. The enhanced expression of dipeptidyl peptidase III (DPP III) was found in endometrial carcinomas of various histological types and grade. The aim of this study was to assess activity of DPP III in ovarian tissue specimens and to correlate it with clinico-pathological data. Methods DPP III hydrolytic activity toward Arg–Arg-2-naphthylamide was determined in 108 ovarian tissue cytosol specimens of 79 patients. The data obtained for 41 ovarian primary carcinoma specimens were stratified according to clinical stage, histological grade and type, and age of the patients. Results Median DPP III activity expressed as milliunits per milligram protein was 6 in normal ovarian tissues ( n = 29), 6.5 in benign ovarian tumors ( n = 19), 19.5 in primary ovarian carcinomas ( n = 41), 12.5 in nonepithelial primary ovarian tumors ( n = 7), and 22.1 in metastatic ovarian malignancies ( n = 12). A significant rise in median DPP III specific activity was observed in malignant ovarian tumors (of epithelial, nonepithelial, and metastatic origin), but not in benign ovarian tumors, compared to the activity in normal tissue. A significant difference of DPP III expression was found between the group of normal tissues and tumors of clinical stage I and II, of grade 2 and 3, of serous and mucinous histologic type. Conclusions DPP III activity of benign ovarian tumors equaled that in normal ovarian tissue. In malignant neoplasms of the ovary it increased with growing histologic grade.

Human dipeptidyl peptidase III (hDPP III) is a member of the M49 metallopeptidase family, which is involved in intracellular protein catabolism and oxidative stress response. To investigate the structural basis of hDPP III preference for diarginyl arylamide, using site-directed mutagenesis, we altered its S2 subsite to mimic the counterpart in yeast enzyme. Kinetic studies revealed that the single mutant D496G lost selectivity due to the increase of the K m value. The D496G, but not S504G, showed significantly decreased binding of peptides with N-terminal arginine, and of tynorphin. The results obtained identify Asp496 as an important determinant of human DPP III substrate specificity.

An extracellular lipase from Streptomyces rimosus R6-554W has been recently purified and biochemically characterized. In this report the cloning, sequencing and high-level expression of its gene is described. The cloned DNA contained an ORF of 804 bp encoding a 268-amino-acid polypeptide with 34 amino acid residues at the amino terminus of the sequence that were not found in the mature protein. The theoretical molecular mass (24.172 kDa) deduced from the amino acid sequence of the mature enzyme was experimentally confirmed. This lipase showed no overall amino acid sequence similarity to other lipases in the databases. However, two hypothetical proteins, i. e. putative hydrolases, derived from the genome sequencing data of Streptomyces coelicolor A3(2), showed 66 % and 33 % identity. In addition, a significant similarity to esterases from Streptomyces diastatochromogenes and Aspergillus terreus was found. Sequence analysis revealed that our novel S. rimosus lipase containing a GDS(L)-like consensus motif belongs to family II of lipolytic enzymes, previously unrecognized in Streptomyces. The lipase gene was expressed in a S. rimosus lipase-deficient strain harbouring the lipase gene on a high-copy number vector. A twenty two-fold higher lipase activity was obtained in comparison to the original strain.

Substrate specificity, regioselectivity and transesterification activity of purified extracellular lipase from Streptomyces rimosus were investigated. The enzyme showed pronounced lipolytic activity toward a number of triacylglycerols and oils of vegetable and animal origin. It hydrolyzed most efficiently medium chain length fatty acid glycerol esters (C8–C12). There was preference for the esters of C16 and C18 unsaturated fatty acids over C16 and C18 saturated fatty acid esters, as well as for triacylglycerol substrate with cis double bond (triolein) versus trans double bond (trielaidin). Streptomyces rimosus lipase hydrolyzed primary and secondary ester bonds in triacylglycerols (triolein and 2,3-dimercapto-1-propanol tributyrate). The lipase catalyzed the hydrolysis of poly(oxyethylene) sorbitan monoesters (Tween 20–80) with rate comparable for that determined with triacylglycerols and oils. Several water-miscible solvents enhanced the lipase activity. 1,4-Dioxane activated the enzyme in a broad concentration range, up to 4-fold. Lipase was stable in solvent mixtures containing 50% (v/v) ethanol, 1,4-dioxane, acetonitrile or acetone. Tetrahydrofuran and N,N -dimethylformamide (both 50%) inactivated the enzyme with t 1/2 of 5 min and t 1/2 of 2 h, respectively. Transesterification of racemic 1-phenyl ethanol with vinyl acetate, catalyzed by extracellular lipase from Streptomyces rimosus in n -hexane, proceeded with partial R -enantioselectivity.

The opioid peptide methionine-enkephalin (MENK) has significant immunomodulatory ability in addition to its neurotransmitter function. Since neutral endopeptidase (NEP, CD10, enkephalinase EC 3.4.24.11) cleaves opioid peptides, the presence and activity of NEP in neutrophils from different persons might be responsible for the diverse, neuropeptide-induced, responses of neutrophils from different donors [Ann. N. Y. Acad. Sci. 650 (1992) 146]. The results obtained showed statistically significant differences in NEP activity among donors (high, medium and low). A 10-fold higher NEP activity in neutrophils (160–280 nmol/10 6 cells/h) and in their corresponding membrane preparations (550 nmol/mg protein/min) in our study, as compared to literature data, was a result of high specificity and affinity of Suc-Ala-Ala-Phe–pNA as substrate. In control nontreated neutrophils, the number of CD10 positive cells were not correlated with NEP activity. However, in neutrophils treated with a physiological (10 −10 M) concentration of MENK, two main events occurred; not only did the number of CD10 positive cells correlate with NEP activity, but contrary to control samples, MENK upregulated the expression of CD10 marker as demonstrated by an increase of mean florescence intensity ( F -mean) in donors with low NEP activity. Taken together, these data add some clarity to the diverse activity of enkephalins in association with enzyme cleavage of those molecules.

Dipeptidyl peptidase III, a metallopeptidase of the M49 family, was first identified (in the pituitary) by its specific cleavage of diarginyl arylamides, which have been used as preferred assay substrates until now. Here we examined the activity of the yeast and human dipeptidyl peptidase III in parallel. The human enzyme preferred Arg2-β-naphthylamide and showed 620-fold higher k cat/K m for this substrate. In contrast, the yeast enzyme did not display a preference for any of the X-Arg-β-naphthylamide analyzed. The replacement of Gly505 with Asp, resulted in a less active, but more selective, yeast enzyme form. These results indicate diversity in cleavage specificity in the M49 family.

Opioid peptides are involved in various essential physiological processes, most notably nociception. Dipeptidyl peptidase III (DPP III) is one of the most important enkephalin-degrading enzymes associated with the mammalian pain modulatory system. Here we describe the X-ray structures of human DPP III and its complex with the opioid peptide tynorphin, which rationalize the enzyme's substrate specificity and reveal an exceptionally large domain motion upon ligand binding. Microcalorimetric analyses point at an entropy-dominated process, with the release of water molecules from the binding cleft (“entropy reservoir”) as the major thermodynamic driving force. Our results provide the basis for the design of specific inhibitors that enable the elucidation of the exact role of DPP III and the exploration of its potential as a target of pain intervention strategies.

Human dipeptidyl peptidase III (DPP III) is a member of the metallopeptidase family M49, involved in protein metabolism and oxidative stress response. DPP III crystal structure shows the two lobe-like domains separated by a wide cleft. The human enzyme has a total of six cysteines, three in the lower (Cys19, Cys147, and Cys176) and three in the upper (Cys509, Cys519, and Cys654), catalytic, domain containing the active-site zinc ion. To elucidate the molecular basis of this enzyme’s susceptibility to sulfhydryl reagents, biochemical analysis of a set of Cys to Ala mutants was used, supported by mass spectrometry. Cys176, a residue 44 Å apart from the catalytic center of the ligand-free enzyme, was found responsible for the inactivation with the submicromolar concentration of an organomercurial compound, and three additional cysteines contri\xadbuted to sensitivity to aromatic disulfides. Upon treatment with oxidized glutathione [glutathione disulfide (GSSG)], cysteine residues at positions 147, 176, and 654 were found glutathionylated. The mutational analysis confirmed the involvement of Cys176 and Cys654 in human DPP III inactivation by GSSG. Observation that Cys176, a residue quite distant from the active center, contributes to enzyme inactivation, indicates that the substrate-binding site of human DPP III comprises both lower and upper protein domain.

Metallopeptidase family M49 is characterized by five conserved sequence regions and the unique motif HEXXGH with two histidines - ligands of the active-site zinc ion. The crystal structure of the yeast ortholog represents a prototype for the whole family. To investigate the role of two invariant amino acid residues, a Glu(461) of the zinc-binding motif, and a Tyr(327), 21 angstrom from the catalytic zinc center, mutational analysis of the yeast enzyme was performed. The substitution of Glu(461) to glutamine decreased k(cat) for the substrate hydrolysis almost by 10 000-fold. The replacement of Tyr(327) by Phe or Ala reduced the catalytic efficiency (k(cat)/K-m) by two orders of magnitude. The affinity for the heptapeptide valorphin was siginificantly lowered in all mutants, indicating the contribution of both Glu(461) and Tyr(327) in substrate binding. Taken together, the effect of mutating Glu(461) is consistent with this residue being essential in M49 peptidase catalysis.

Enediyne-peptide conjugates were designed with the aim to inhibit aminopeptidase N, a widespread ectoenzyme with a variety of functions, like protein digestion, inactivation of cytokines in the immune system and endogenous opioid peptides in the central nervous system. Enediyne moiety was embedded within the 12-membered ring with hydrophobic amino acid alanine, valine, leucine or phenylalanine used as carriers. Aromatic part of the enediyne bridging unit and the amino acid side chains were considered as pharmacophores for the binding to the aminopeptidase N (APN) active site. Additionally, the fused enediyne-amino acid "heads" were bound through a flexible linker to the L-lysine, an amino group donor. The synthesis included building the aromatic enediyne core at the C-terminal of amino acids and subsequent intramolecular N-alkylation. APN inhibition test revealed that the alanine-based derivative 9a inhibits the APN with IC(50) of 34 ± 11 μM. Enediyne-alanine conjugate 12 missing the flexible linker was much less effective in the APN inhibition. These results show that enediyne-fused amino acids have potential as new pharmacophores in the design of APN inhibitors.

Human dipeptidyl peptidase III (DPP III) is a member of the zinc-metallopeptidase family M49 with a role in intracellular protein catabolism. Ligand-free crystal structure of yeast and human orthologues provided insight into the enzyme's active center and enabled some assumptions about the enzyme - substrate interactions. The molecular modeling performed for human and yeast DPP III indicated involvement of Asn406 and Asn415, respectively in ligand binding. To investigate further the role of this asparagine residue, conserved in all eukaryotic M49 peptidases, a site-directed mutagenesis of human DPP III was carried out. Replacement of Asn406 with Gln, but not with Ser, resulted in a large decrease in the enzyme's binding affinity for competitive peptide inhibitor and in catalytic efficiency. Molecular dynamics simulations performed for enzyme-substrate complexes, revealed changed coordination of the active- site zinc ion and the orientation of the catalytically important His568, in N406Q, but not in the N406S complexes.(doi: 10.5562/cca1808)

An interesting subclass of lipolytic enzymes that possesses a distinct GDSL sequence motif has multifunctional properties with potential for use in the hydrolysis and synthesis of important ester compounds of biotechnological interests. The sequencing of the genomes of several streptomycete species revealed that these bacteria have great potential for synthesis of a broad spectrum of lipases. In the last decade, our group has done intensive research on GDS(L) lipases from Streptomyces. Several genes encoding GDS(L) lipases have been cloned so far and the enzymes from S. rimosus (Q93MW7, SrL) and S. coelicolor (SCO1725, Sc1) were expressed and purified from heterologous and homologous host. Lipases were extensively biochemically characterized and the properties of these enzymes were compared. These enzymes might have significant biotechnological potential due to high working temperature ; stability in organic solvents, activity over a broad range of pH and temperature, and the ability to hydrolyze numerous classes of substrates. The most pronounced difference between SrL and Sc1 is in acyl chain length specificity, as SrL shows maximal activity toward substrates with chain lengths C8-C10, and Sc1 shows preference for substrates with longer acyl-chain lengths (C14). Further, enzymes are stable in several tested organic solvents, while some solvents even increase their activity (eg. dioxane). Although the structures of enzymes have not been solved, both enzymes are predominantly α-helical proteins, as shown by CD spectroscopy. The amino acid residues important for the catalytic activity were predicted, mutated and the activities of wild type enzyme and mutants were analyzed.

Lactate dehydrogenase (LDH) is essential for continuous glycolysis necessary for accelerated tumor growth. The aim of this study was to reconsider if assay of total tissue activity of this enzyme could be useful as marker for endometrial carcinoma (EC). Activity of LDH was measured spectrophotometrically in homogenate supernatants of uterine tissue samples of 40 patients (10 normal endometria, 27 normal myometria, and 33 EC), including 30 matched pairs. Data obtained were analyzed in relation to clinical and histopathologic findings and compared with our previously published results on the tissue levels of the same enzyme in ovarian cancer and on the proteolytic activity of dipeptidyl peptidase III (DPP III) in EC (suggested biochemical indicator of this malignancy). Significantly increased (1.8–3.0 times; P< 1 × 10−4) LDH activity was observed in EC samples if compared with normal uterine tissues. This rise was not related to the clinicopathologic findings, however. In contrast to previous results on LDH in ovarian carcinomas, a significant rise in LDH activity was found already in grade 1 EC. Using the cutoff value of 1.06 U/mg, diagnostic sensitivity of 82%, specificity of 100%, and accuracy of 91% for total tissue LDH assay have been calculated. A correlation of tissue's LDH and DPP III activities was found, and their combined assay for EC showed increased diagnostic sensitivity (94%) and accuracy (96%).

Human dipeptidyl peptidase III (DPP III) is a member of the metallopeptidase family M49 with an implied role in the pain-modulatory system and endogenous defense against oxidative stress. Apart from active site-zinc ligation, many details of the DPP III (M49 peptidase) mechanism are unknown. We report heterologous expression of human DPP III and the site-directed mutagenesis results which demonstrate a functional role for Tyr318 at this enzyme's active site . The substitution of Tyr318 to Phe decreased kcat by two orders of magnitude without altering the binding affinity of substrate, or of a competitive hydroxamate inhibitor designed to interact with S1 and S2 subsites. The results favor the involvement of the conserved tyrosine in transition state stabilization during the catalytic action of M49 peptidases. References: Salopek-Sondi, B., Vukelić, B., Špoljarić, J., Šimaga, Š., Vujaklija, D., Makarević, J., Jajčanin, N., Abramić, M. (2008): Functional tyrosine residue in the active center of human dipeptidyl peptidase III, Biol. Chem. 389: 163-167.

The co-localization of serotonin (5-hydroxytryptamine, 5HT) and neuroactive peptides in the same neuron points to the importance of interactions between serotonergic and peptidergic systems in maintaining body homeostasis. In this work, we used an original genetic rat model to search for possible interrelations between 5HT system functioning and the activities of aminopeptidases, i.e. enzymes which are the key regulators of (neuro)peptides level/function. The activities of three cytosolic exopeptidases: alanyl aminopeptidase (alanyl-AP), arginyl aminopeptidase (arginyl-AP) and dipeptidyl peptidase III (DPP III) were measured in brains and peripheral tissues of the sublines of rats with constitutionally upregulated/downregulated 5HT transporter activity. These rat sublines, termed as high-5HT and low-5HT subline, have been obtained previously by selective breeding for the extreme values of platelet 5HT level and velocity of 5HT uptake. Besides in the periphery they show marked alterations also in brain 5HT function, indicating the differences in central 5HT transmission/homeostasis. In this study, we have found that animals from the high-5HT subline have significantly lower activity of brain alanyl-AP (p

Dipeptidyl peptidase III (DPP III) is a zinc exopeptidase with an implied role in the mammalian pain-modulatory system owing to its high affinity for enkephalins and localisation in the superficial laminae of the spinal cord dorsal horn. Our study revealed that this human enzyme hydrolyses opioid peptides belonging to three new groups, endomorphins, hemorphins and exorphins. The enzymatic hydrolysis products of endomorphin-1 were separated and quantified by capillary electrophoresis and the kinetic parameters were determined for human DPP III and rat DPP IV. Both peptidases cleave endomorphin-1 at comparable rates, with liberation of the N-terminal Tyr-Pro. This is the first evidence of DPP III acting as an endomorphin-cleaving enzyme.

Recently, we detected that the lipase from Streptomyces rimosus belongs to a huge but poorly characterised family of SGNH hydrolases having the alpha/beta/alpha-fold. Our biochemical characterisation is related to the specific inhibition of an extracellular lipase from Streptomyces rimosus (SRL, 24.2 kDa, Q93MW7) by preincubation method with tetrahydrolipstatin (THL). In high molar excess, THL/SRL = 590 at 25 &ordm ; ; ; C, pH = 7.0, after 2 h of incubation in an aqueous system, 56 % of the enzyme inhibition was reached, whereas at the same conditions in the presence of 50 % (v/v) 2-propanol/water 71 % enzyme inhibition was obtained. Kinetics measurements are in agreement with pseudo-first-order kinetics. The nucleophilic attack of the catalytic serine 10 of SRL results by an opening of beta-lactam ring of tetrahydrolipstatin and formation of a covalent ester bond. The intact covalent complex of SRL-inhibitor was analysed by ESI and vacuum MALDI mass spectrometry and furthermore the exact covalent THL linkage was determined by vacuum MALDI high energy collision induced dissociation tandem mass spectrometric experiments.

Cloning, sequencing and high-level expression of the gene encoding extracellular lipase from Streptomyces rimosus R6-554W have been recently described, and primary structure of this gene product was deduced by bioinformatic approach. In this study, capillary electrophoresis-on-the-chip and mass spectrometry were used to characterize native and overexpressed extracellular lipase protein from Streptomyces rimosus. The exact molecular mass of the wild-type and the overexpressed lipase, determined by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry was in excellent agreement (Δ m = 0.11 Da and Δ m = 0.26 Da, respectively) with the value 24165.76 Da calculated from the structure deduced from nucleotide sequence, considering mature enzyme with all six cysteines forming disulfide bridges. The primary structure derived from nucleotide sequence was completely verified by means of a combination of tryptic digestion and formic acid cleavage of the protein followed by obtaining the peptide mass fingerprints. Selected peptides were further investigated by MALDI low energy collision induced dissociation hybrid tandem mass spectrometry, allowing the unambiguous determination of their predicted amino acid sequence. No post-translational modifications of mature Streptomyces rimosus lipase were detected. Comparison of the peptide mass fingerprints from the reduced and non-reduced overexpressed enzyme unequivocally revealed three intramolecular disulfide bonds with following linkages: C27-C52, C93-C101 and C151-C198.

A chemical modification approach combined with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry was used to identify the active site serine residue of an extracellular lipase from Streptomyces rimosus R6-554W. The lipase, purified from a high-level overexpressing strain, was covalently modified by incubation with 3,4-dichloroisocoumarin, a general mechanism-based serine protease inhibitor. MALDI time-of-flight (TOF) mass spectrometry was used to probe the nature of the intact inhibitor-modified lipase and to clarify the mechanism of lipase inhibition by 3,4-dichloroisocoumarin. The stoichiometry of the inhibition reaction revealed that specifically one molecule of inhibitor was bound to the lipase. The MALDI matrix 2,6-dihydroxyacetophenone facilitated the formation of highly abundant [M + 2H] 2+ ions with good resolution compared to other matrices in a linear TOF instrument. This allowed the detection of two different inhibitor-modified lipase species. Exact localization of the modified amino acid residue was accomplished by tryptic digestion followed by low-energy collision-induced dissociation peptide sequencing of the detected 2-(carboxychloromethyl)benzoylated peptide by means of a MALDI quadrupole ion trap reflectron TOF instrument. The high sequence coverage obtained by this approach allowed the confirmation of the site specificity of the inhibition reaction and the unambiguous identification of the serine at position 10 as the nucleophilic amino acid residue in the active site of the enzyme. This result is in agreement with the previously obtained data from multiple sequence alignment of S. rimosus lipase with different esterases, which indicated that this enzyme exhibits a characteristic Gly-Asp-Ser-(Leu) motif located close to the N-terminus and is harboring the catalytically active serine residue. Therefore, this study experimentally proves the classification of the S. rimosus lipase as GDS(L) lipolytic enzyme.

Dipeptidyl peptidase III (DPP III) is a cytosolic zinc-exopeptidase involved in the intracellular protein catabolism of eukaryotes. Although inhibition by thiol reagents is a general feature of DPP III originating from various species, the function of activity important sulfhydryl groups is still inadequately understood. The present study of the reactivity of these groups was undertaken in order to clarify their biological significance. The inactivation kinetics of human and rat DPP III by sulfhydryl reagent p -hydroxy-mercuribenzoate ( p HMB) was monitored by determination of the enzyme’s residual activity with fluorimetric detection. Inactivation of this human enzyme exhibited pseudo-first-order kinetics, suggesting that all reactive SH-groups have equivalent reactivity, and the second-order rate constant was calculated to be 3523±567 M −1 min −1 . Rat DPP III was hyperreactive to p HMB and showed biphasic kinetics indicating two classes of reactive SH-groups. The second-order rate constants of 3540 M −1 s −1 for slower reacting sulfhydryl, and 21,855 M −1 s −1 for faster reacting sulfhydryl were obtained from slopes of linear plots of pseudo-first-order constants versus reagent concentration. Peptide substrates protected both mammalian DPPs III from inactivation by p HMB. Physiological concentrations of biological thiols and H 2 O 2 inactivated the rat DPP III. Human enzyme was resistant to H 2 O 2 attack and less affected by reduced glutathione (GSH) than the rat homologue. A significantly lower DPP III level, determined by activity measurement and Western blotting, was found in the cytosols of highly oxygenated rat tissues. These results provide kinetic evidence that cysteine residues are involved in substrate binding of mammalian DPPs III.

In this study we examined surface expression of CD26 and the corresponding enzyme activity of dipeptidyl peptidase IV (DPPIV) on the cells of immature murine T-cell line, R1.1. The data obtained have shown that R1.1 cells express high density of surface CD26 as compared to normal thymus cells. This was associated with strong enzyme activity, which, based on substrates and inhibitor specificity, corresponded to DPPIV. The DPPIV enzyme activity of R1.1 cells was 10 times stronger than that found on normal murine thymus cells (V(max) = 39 micromol/min/10(6) cells, vs 3.7 micromol/min/10(6) cells, respectively). Upon activation with anti-CD3, up-regulation of both membrane CD26, as well as of DPPIV enzyme activity on R1.1 cells were observed. The finding of strong DPPIV on R1.1 cells makes them suitable model for testing putative substrates/inhibitors of the enzyme in its natural microenvironment. Since in addition to strong DPPIV, R1.1 cells also express kappa opioid receptors (KOR) [European Journal of Pharmacology 227 (1992) 257], we tested the effect of dynorphin-A(1-17), an endogenous opioid peptide with KOR selectivity, on DPPIV of R1.1 cells. Dynorphin-A(1-17) down-regulated DPPIV in a dose-dependent manner, with the potency similar to that of substance P, a known natural DPPIV substrate [Journal of Pharmacology and Experimental Therapeutics 260 (1992) 1257]. DPPIV down-regulation was resistant to bestatin and thiorphan, the inhibitors of two cell surface peptidases (APN and NEP, respectively) with potential of dynorphin-A(1-17) degradation, suggesting that the mechanism underlying the observed effect does not involve degradative products of dynorphin-A(1-17). DPPIV down-regulation was also resistent to KOR antagonist, NBI, suggesting that the mechanism underlying the observed phenomenon involves neither cointernalization of KOR and DPPIV. Collectively, cells of immature T cell line, R1.1 exert strong DPPIV enzyme activity, which could be down-regulated in the presence of dynorphin-A(1-17) by mechanism that presumably includes non-substrate inhibition. By down-regulating DPPIV, dynorphin-A(1-17) may indirectly affect activity and/or specificity of natural substrates of DPPIV, such as substance P, RANTES, and endomorphins.