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Fiorito S, Genovese S, Epifano F, Collevecchio C. Prolidase activity assays. A survey of the reported literature methodologies. Anal Biochem 2024; 689:115506. [PMID: 38460899 DOI: 10.1016/j.ab.2024.115506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Prolidase (EC.3.4.13.9) is a dipeptidase known nowadays to play a pivotal role in several physiological and pathological processes. More in particular, this enzyme is involved in the cleavage of proline- and hydroxyproline-containing dipeptides (imidodipeptides), thus finely regulating the homeostasis of free proline and hydroxyproline. Abnormally high or low levels of prolidase have been found in numerous acute and chronic syndromes affecting humans (chronic liver fibrosis, viral and acute hepatitis, cancer, neurological disorders, inflammation, skin diseases, intellectual disability, respiratory infection, and others) for which the content of proline is well recognized as a clinical marker. As a consequence, the accurate analytical determination of prolidase activity is of greatly significant importance in clinical diagnosis and therapy. Apart from the Chinard's assay, some other more sensitive and well validated methodologies have been published. These include colorimetric and spectrophotometric determinations of free proline produced by enzymatic reactions, capillary electrophoresis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, electrochemoluminescence, thin layer chromatography, and HPLC. The aim of this comprehensive review is to make a detailed survey of the in so far reported analytical techniques, highlighting their general features, as well as their advantages and possible drawbacks, providing in the meantime suggestions to stimulate further research in this intriguing field.
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Affiliation(s)
- Serena Fiorito
- Dipartimento di Farmacia, Università"Gabriele d'Annunzio" Chieti - Pescara, Via dei Vestini 31, 66100, Chieti Scalo, CH, Italy
| | - Salvatore Genovese
- Dipartimento di Farmacia, Università"Gabriele d'Annunzio" Chieti - Pescara, Via dei Vestini 31, 66100, Chieti Scalo, CH, Italy.
| | - Francesco Epifano
- Dipartimento di Farmacia, Università"Gabriele d'Annunzio" Chieti - Pescara, Via dei Vestini 31, 66100, Chieti Scalo, CH, Italy.
| | - Chiara Collevecchio
- Dipartimento di Farmacia, Università"Gabriele d'Annunzio" Chieti - Pescara, Via dei Vestini 31, 66100, Chieti Scalo, CH, Italy
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2
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Liu Z, Li K, Li J, Zhuang Z, Guo L, Bai L. Characterization and functional evidence for Orf2 of Streptomyces sp. 139 as a novel dipeptidase E. Appl Microbiol Biotechnol 2024; 108:326. [PMID: 38717487 PMCID: PMC11078827 DOI: 10.1007/s00253-024-13161-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 05/12/2024]
Abstract
Aspartyl dipeptidase (dipeptidase E) can hydrolyze Asp-X dipeptides (where X is any amino acid), and the enzyme plays a key role in the degradation of peptides as nutrient sources. Dipeptidase E remains uncharacterized in Streptomyces. Orf2 from Streptomyces sp. 139 is located in the exopolysaccharide biosynthesis gene cluster, which may be a novel dipeptidase E with "S134-H170-D198" catalytic triad by sequence and structure comparison. Herein, recombinant Orf2 was expressed in E. coli and characterized dipeptidase E activity using the Asp-ρNA substrate. The optimal pH and temperature for Orf2 are 7.5 and 40 ℃; Vmax and Km of Orf2 are 0.0787 mM·min-1 and 1.709 mM, respectively. Orf2 exhibits significant degradation activities to Asp-Gly-Gly, Asp-Leu, Asp-His, and isoAsp-Leu and minimal activities to Asp-Pro and Asp-Ala. Orf2 contains a Ser-His-Asp catalytic triad characterized by point mutation. In addition, the Asp147 residue of Orf2 is also proven to be critical for the enzyme's activity through molecular docking and point mutation. Transcriptome analysis reveals the upregulation of genes associated with ribosomes, amino acid biosynthesis, and aminoacyl-tRNA biosynthesis in the orf2 mutant strain. Compared with the orf2 mutant strain and WT, the yield of crude polysaccharide does not change significantly. However, crude polysaccharides from the orf2 mutant strain exhibit a wider range of molecular weight distribution. The results indicate that the Orf2 links nutrient stress to secondary metabolism as a novel dipeptidase E. KEY POINTS: • A novel dipeptidase E with a Ser-His-Asp catalytic triad was characterized from Streptomyces sp. 139. • Orf2 was involved in peptide metabolism both in vitro and in vivo. • Orf2 linked nutrient stress to mycelia formation and secondary metabolism in Streptomyces.
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Affiliation(s)
- Zhe Liu
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Kemeng Li
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Jialin Li
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Zhuochen Zhuang
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Lianhong Guo
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Liping Bai
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
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Chmielewska K, Vittorio S, Gervasoni S, Dzierzbicka K, Inkielewicz-Stepniak I, Vistoli G. Human carnosinases: A brief history, medicinal relevance, and in silico analyses. Drug Discov Today 2024; 29:103860. [PMID: 38128717 DOI: 10.1016/j.drudis.2023.103860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/03/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
Carnosine, an endogenous dipeptide, has been found to have a plethora of medicinal properties, such as antioxidant, antiageing, and chelating effects, but with one downside: a short half-life. Carnosinases and two hydrolytic enzymes, which remain enigmatic, are responsible for these features. Hence, here we emphasize why research is valuable for better understanding crucial concepts like ageing, neurodegradation, and cancerogenesis, given that inhibition of carnosinases might significantly prolong carnosine bioavailability and allow its further use in medicine. Herein, we explore the literature regarding carnosinases and present a short in silico analysis aimed at elucidating the possible recognition pattern between CN1 and its ligands.
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Affiliation(s)
- Klaudia Chmielewska
- Department of Organic Chemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Serena Vittorio
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy
| | - Silvia Gervasoni
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy; Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Krystyna Dzierzbicka
- Department of Organic Chemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
| | | | - Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy.
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Pandya VK, Shankar SS, Sonwane BP, Rajesh S, Rathore R, Kumaran S, Kulkarni MJ. Mechanistic insights on anserine hydrolyzing activities of human carnosinases. Biochim Biophys Acta Gen Subj 2023; 1867:130290. [PMID: 36529243 DOI: 10.1016/j.bbagen.2022.130290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 11/16/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Anserine and carnosine represent histidine-containing dipeptides that exert a pluripotent protective effect on human physiology. Anserine is known to protect against oxidative stress in diabetes and cardiovascular diseases. Human carnosinases (CN1 and CN2) are dipeptidases involved in the homeostasis of carnosine. In poikilothermic vertebrates, the anserinase enzyme is responsible for hydrolyzing anserine. However, there is no specific anserine hydrolyzing enzyme present in humans. In this study, we have systematically investigated the anserine hydrolyzing activity of human CN1 and CN2. A targeted multiple reaction monitoring (MRM) based approach was employed for studying the enzyme kinetics of CN1 and CN2 using carnosine and anserine as substrates. Surprisingly, both CN1 and CN2 can hydrolyze anserine effectively. The observed catalytic turnover rate (Vmax/[E]t) was 21.6 s-1 and 2.8 s-1 for CN1 and CN2, respectively. CN1 is almost eight-fold more efficient in hydrolyzing anserine compared to CN2, which is comparable to the efficiency of the carnosine hydrolyzing activity of CN2. The Michaelis constant (Km) value for CN1 (1.96 mM) is almost three-fold lower compared to CN2 (6.33 mM), representing higher substrate affinity for anserine-CN1 interactions. Molecular docking studies showed that anserine binds at the catalytic site of the carnosinases with an affinity similar to carnosine. Overall, the present study elucidated the inherent promiscuity of human carnosinases in hydrolyzing anserine using a sensitive LC-MS/MS approach.
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Affiliation(s)
- Vaibhav Kumar Pandya
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India.
| | - S Shiva Shankar
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Babasaheb P Sonwane
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - S Rajesh
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Rajeshwari Rathore
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sangaralingam Kumaran
- CSIR-Institute of Microbial Technology, Chandigarh 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mahesh J Kulkarni
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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5
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Kölpin M, Hellwig M. Quantitation of Methionine Sulfoxide in Milk and Milk-Based Beverages-Minimizing Artificial Oxidation by Anaerobic Enzymatic Hydrolysis. J Agric Food Chem 2019; 67:8967-8976. [PMID: 31334650 DOI: 10.1021/acs.jafc.9b03605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein oxidation in milk products may entail flavor changes through reactions at methionine residues. However, little is known about the extent of methionine oxidation in milk and milk products. In the present study, a method for quantitation of methionine, methionine sulfoxide, and methionine sulfone by a stable isotope dilution assay using HILIC-ESI-MS/MS was established. For the quantitation of protein-bound analytes, anaerobic enzymatic hydrolysis was optimized to suppress artificial methionine oxidation. Moreover, the method allowed for monitoring of artificial oxidation by coincubation of the labeled probe [2H8]methionine. The percentage of oxidized methionine was low in UHT milk (up to 1.6%) and evaporated milk (up to 8.8%), but higher in beverages such as cocoa milk drinks (up to 19.0%) and coffee milk drinks (up to 32.8%), resulting in methionine sulfoxide concentrations of up to 6.7 g/kg protein in the latter. These products are important dietary sources of methionine sulfoxide. Model studies revealed that methionine residues can be oxidized strongly in the presence of phenolic compounds such as catechin, caffeic acid, and gallic acid, which are present in cocoa and coffee and may account for the high extent of oxidation in commercial samples.
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Affiliation(s)
- Martin Kölpin
- Chair of Food Chemistry , Technische Universität Dresden , D-01062 Dresden , Germany
| | - Michael Hellwig
- Chair of Food Chemistry , Technische Universität Dresden , D-01062 Dresden , Germany
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Wang TF, Lo HF, Chi MC, Lai KL, Lin MG, Lin LL. Affinity Immobilization of a Bacterial Prolidase onto Metal-Ion-Chelated Magnetic Nanoparticles for the Hydrolysis of Organophosphorus Compounds. Int J Mol Sci 2019; 20:E3625. [PMID: 31344929 PMCID: PMC6696040 DOI: 10.3390/ijms20153625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/10/2019] [Accepted: 07/22/2019] [Indexed: 12/23/2022] Open
Abstract
In this study, silica-coated magnetic nanoparticles (SiMNPs) with isocyanatopropyltriethoxysilane as a metal-chelating ligand were prepared for the immobilization of His6-tagged Escherichia coli prolidase (His6-EcPepQ). Under one-hour coupling, the enzyme-loading capacity for the Ni2+-functionalized SiMNPs (NiNTASiMNPs) was 1.5 mg/mg support, corresponding to about 58.6% recovery of the initial activity. Native and enzyme-bound NiNTASiMNPs were subsequently characterized by transmission electron microscopy (TEM), superparamagnetic analysis, X-ray diffraction, and Fourier transform infrared (FTIR) spectroscopy. As compared to free enzyme, His6-EcPepQ@NiNTASiMNPs had significantly higher activity at 70 °C and pH ranges of 5.5 to 10, and exhibited a greater stability during a storage period of 60 days and could be recycled 20 times with approximately 80% retention of the initial activity. The immobilized enzyme was further applied in the hydrolysis of two different organophosphorus compounds, dimethyl p-nitrophenyl phosphate (methyl paraoxon) and diethyl p-nitrophenyl phosphate (ethyl paraoxon). The experimental results showed that methyl paraoxon was a preferred substrate for His6-EcPepQ and the kinetic behavior of free and immobilized enzymes towards this substance was obviously different. Taken together, the immobilization strategy surely provides an efficient means to deposit active enzymes onto NiNTASiMNPs for His6-EcPepQ-mediated biocatalysis.
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Affiliation(s)
- Tzu-Fan Wang
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City 60004, Taiwan
| | - Huei-Fen Lo
- Department of Food Science and Technology, Hungkuang University, 1018 Taiwan Boulevard, Shalu District, Taichung City 43302, Taiwan.
| | - Meng-Chun Chi
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City 60004, Taiwan
| | - Kuan-Ling Lai
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City 60004, Taiwan
- Department of Food Science and Technology, Hungkuang University, 1018 Taiwan Boulevard, Shalu District, Taichung City 43302, Taiwan
| | - Min-Guan Lin
- Institute of Molecular Biology, Academia Sinica, Nangang District, Taipei City 11529, Taiwan
| | - Long-Liu Lin
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City 60004, Taiwan.
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7
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Pirone L, Di Gaetano S, Rizzarelli E, Bellia F, Pedone E. Focusing on the functional characterization of the anserinase from Oreochromis niloticus. Int J Biol Macromol 2019; 130:158-165. [PMID: 30797810 DOI: 10.1016/j.ijbiomac.2019.02.118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 12/24/2022]
Abstract
Carnosine, anserine and homocarnosine are the three most representative compounds of the histidine dipeptides family, widely distributed in mammals in different amounts depending on the species and the tissue considered. Histidine dipeptides are mainly degraded by two different carnosinase homologues: a highly specific metal-ion dependent carnosinase (CN1) located in serum and brain and a non-specific cytosolic form (CN2). The hydrolysis of such dipeptides in prokaryotes and eukaryotes is also catalyzed by the anserinase (ANSN). Such naturally occurring dipeptides represent an interesting topic because they seem to have numerous biological roles such as potential neuroprotective and neurotransmitter functions in the brain and therefore ANSN results to be a very interesting target of study. We here report, for the first time, cloning, expression of ANSN from the fish Oreochromis niloticus both in a mammalian and in a prokaryotic system, in order to perform deep functional studies by enzymatic assays in the presence of different metals and substrates. Furthermore, by means of a mass spectrometry-based proteomic approach, we analysed protein sequence and the potential presence of post-translational modifications in the mammalian recombinant protein. Finally, a preliminary structural characterization was carried out on ANSN produced in Escherichia coli.
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Affiliation(s)
- L Pirone
- Institute of Biostructure and Bioimaging, CNR, Napoli, Italy
| | - S Di Gaetano
- Institute of Biostructure and Bioimaging, CNR, Napoli, Italy
| | - E Rizzarelli
- Institute of Biostructure and Bioimaging, CNR, Catania, Italy; Department of Chemical Sciences, University of Catania, Catania, Italy
| | - F Bellia
- Institute of Biostructure and Bioimaging, CNR, Catania, Italy.
| | - E Pedone
- Institute of Biostructure and Bioimaging, CNR, Napoli, Italy.
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Abstract
Prolidases, metalloproteases that catalyze the cleavage of Xaa-Pro dipeptides, are conserved enzymes found in prokaryotes and eukaryotes. In humans, prolidase is crucial for the recycling of collagen. To further characterize the essential elements of this enzyme, we utilized the Escherichia coli prolidase, PepQ, which shares striking similarity with eukaryotic prolidases. Through structural and bioinformatic insights, we have extended previous characterizations of the prolidase active site, uncovering a key component for substrate specificity. Here we report the structure of E. coli PepQ, solved at 2.0 Å resolution. The structure shows an antiparallel, dimeric protein, with each subunit containing N-terminal and C-terminal domains. The C-terminal domain is formed by the pita-bread fold typical for this family of metalloproteases, with two Mg(II) ions coordinated by five amino-acid ligands. Comparison of the E. coli PepQ structure and sequence with homologous structures and sequences from a diversity of organisms reveals distinctions between prolidases from Gram-positive eubacteria and archaea, and those from Gram-negative eubacteria, including the presence of loop regions in the E. coli protein that are conserved in eukaryotes. One such loop contains a completely conserved arginine near the catalytic site. This conserved arginine is predicted by docking simulations to interact with the C-terminus of the substrate dipeptide. Kinetic analysis using both a charge-neutralized substrate and a charge-reversed variant of PepQ support this conclusion, and allow for the designation of a new role for this key region of the enzyme active site.
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Affiliation(s)
- Jeremy Weaver
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Tylan Watts
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Pingwei Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Hays S. Rye
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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Kumar A, Are VN, Ghosh B, Agrawal U, Jamdar SN, Makde RD, Sharma SM. Crystallization and preliminary X-ray diffraction analysis of Xaa-Pro dipeptidase from Xanthomonas campestris. Acta Crystallogr F Struct Biol Commun 2014; 70:1268-71. [PMID: 25195907 PMCID: PMC4157434 DOI: 10.1107/s2053230x14017324] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 07/28/2014] [Indexed: 10/10/2023] Open
Abstract
Xaa-Pro dipeptidase (XPD; prolidase; EC 3.4.13.9) specifically hydrolyzes dipeptides with a prolyl residue at the carboxy-terminus. Xanthomonas spp. possess two different isoforms of XPD (48 and 43 kDa) which share ∼24% sequence identity. The XPD of 43 kDa in size (XPD43) from Xanthomonas spp. is unusual as it lacks the strictly conserved tyrosine residue (equivalent to Tyr387 in Escherichia coli aminopeptidase P) that is suggested to be important in the proton-shuttle transfer required for catalysis in the M24B (MEROPS) family. Here, the crystallization and preliminary X-ray analysis of XPD43 from X. campestris (GenBank accession No. NP_637763) are reported. Recombinant XPD43 was crystallized using the microbatch-under-oil technique. Diffraction data were collected on the recently commissioned protein crystallography beamline (PX-BL21) at the Indian synchrotron (Indus-2, 2.5 GeV) to 1.83 Å resolution with 100% completeness. The crystal belonged to space group P212121, with unit-cell parameters a = 84.32, b = 105.51, c = 111.35 Å. Two monomers are expected to be present in the asymmetric unit of the crystal, corresponding to a solvent content of 58%. Structural analysis of XPD43 will provide new insights into the role of the conserved residues in catalysis in the M24B family.
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Affiliation(s)
- Ashwani Kumar
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400 085, India
| | - Venkata Narayana Are
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400 085, India
| | - Biplab Ghosh
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400 085, India
| | - Utsavi Agrawal
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400 085, India
| | - Sahayog N. Jamdar
- Food Technology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400 085, India
| | - Ravindra D. Makde
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400 085, India
| | - Surinder M. Sharma
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400 085, India
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10
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Abstract
Carnosinases are Xaa-His dipeptidases that play diverse functions throughout all kingdoms of life. Human isoforms of carnosinase (CN1 and CN2) under appropriate conditions catalyze the hydrolysis of the dipeptides carnosine (β-alanyl-l-histidine) and homocarnosine (γ-aminobutyryl-l-histidine). Alterations of serum carnosinase (CN1) activity has been associated with several pathological conditions, such as neurological disorders, chronic diseases and cancer. For this reason the use of carnosinase levels as a biomarker in cerebrospinal fluid (CSF) has been questioned. The hydrolysis of imidazole-related dipeptides in prokaryotes and eukaryotes is also catalyzed by aminoacyl-histidine dipeptidases like PepD (EC 3.4.13.3), PepV (EC 3.4.13.19) and anserinase (EC 3.4.13.5). The review deals with the structure and function of this class of enzymes in physiological and pathological conditions. The main substrates of these enzymes, i.e., carnosine, homocarnosine and anserine (β-alanyl-3-methyl-l-histidine) will also be described.
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Affiliation(s)
- Francesco Bellia
- Institute of Biostructure and Bioimaging, CNR, viale A. Doria 6, 95125 Catania, Italy.
| | - Graziella Vecchio
- Department of Chemical Sciences, University of Catania, viale A. Doria 6, 95125 Catania, Italy.
| | - Enrico Rizzarelli
- Institute of Biostructure and Bioimaging, CNR, viale A. Doria 6, 95125 Catania, Italy.
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Štěpánková A, Dušková J, Skálová T, Hašek J, Koval’ T, Østergaard LH, Dohnálek J. Organophosphorus acid anhydrolase from Alteromonas macleodii: structural study and functional relationship to prolidases. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:346-54. [PMID: 23545636 PMCID: PMC3614155 DOI: 10.1107/s1744309113002674] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 01/27/2013] [Indexed: 11/10/2022]
Abstract
The bacterial enzyme organophosphorus acid anhydrolase (OPAA) is able to catalyze the hydrolysis of both proline dipeptides (Xaa-Pro) and several types of organophosphate (OP) compounds. The full three-dimensional structure of the manganese-dependent OPAA enzyme is presented for the first time. This enzyme, which was originally isolated from the marine bacterium Alteromonas macleodii, was prepared recombinantly in Escherichia coli. The crystal structure was determined at 1.8 Å resolution in space group C2, with unit-cell parameters a = 133.8, b = 49.2, c = 97.3 Å, β = 125.0°. The enzyme forms dimers and their existence in solution was confirmed by dynamic light scattering and size-exclusion chromatography. The enzyme shares the pita-bread fold of its C-terminal domain with related prolidases. The binuclear manganese centre is located in the active site within the pita-bread domain. Moreover, an Ni(2+) ion from purification was localized according to anomalous signal. This study presents the full structure of this enzyme with complete surroundings of the active site and provides a critical analysis of its relationship to prolidases.
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Affiliation(s)
- Andrea Štěpánková
- Institute of Macromolecular Chemistry, AS CR, v.v.i., Heyrovsky sq. 2, 162 06 Prague 6, Czech Republic
- Faculty of Nuclear Sciences and Physical Engineering, CTU in Prague, Trojanova 13, 120 00 Prague 2, Czech Republic
| | - Jarmila Dušková
- Institute of Macromolecular Chemistry, AS CR, v.v.i., Heyrovsky sq. 2, 162 06 Prague 6, Czech Republic
| | - Tereza Skálová
- Institute of Macromolecular Chemistry, AS CR, v.v.i., Heyrovsky sq. 2, 162 06 Prague 6, Czech Republic
| | - Jindřich Hašek
- Institute of Macromolecular Chemistry, AS CR, v.v.i., Heyrovsky sq. 2, 162 06 Prague 6, Czech Republic
| | - Tomáš Koval’
- Institute of Macromolecular Chemistry, AS CR, v.v.i., Heyrovsky sq. 2, 162 06 Prague 6, Czech Republic
| | | | - Jan Dohnálek
- Institute of Macromolecular Chemistry, AS CR, v.v.i., Heyrovsky sq. 2, 162 06 Prague 6, Czech Republic
- Institute of Physics, AS CR, v.v.i., Na Slovance 2, 182 21 Prague 8, Czech Republic
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12
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Besio R, Gioia R, Cossu F, Monzani E, Nicolis S, Cucca L, Profumo A, Casella L, Tenni R, Bolognesi M, Rossi A, Forlino A. Kinetic and structural evidences on human prolidase pathological mutants suggest strategies for enzyme functional rescue. PLoS One 2013; 8:e58792. [PMID: 23516557 PMCID: PMC3596340 DOI: 10.1371/journal.pone.0058792] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 02/06/2013] [Indexed: 12/17/2022] Open
Abstract
Prolidase is the only human enzyme responsible for the digestion of iminodipeptides containing proline or hydroxyproline at their C-terminal end, being a key player in extracellular matrix remodeling. Prolidase deficiency (PD) is an intractable loss of function disease, characterized by mutations in the prolidase gene. The exact causes of activity impairment in mutant prolidase are still unknown. We generated three recombinant prolidase forms, hRecProl-231delY, hRecProl-E412K and hRecProl-G448R, reproducing three mutations identified in homozygous PD patients. The enzymes showed very low catalytic efficiency, thermal instability and changes in protein conformation. No variation of Mn(II) cofactor affinity was detected for hRecProl-E412K; a compromised ability to bind the cofactor was found in hRecProl-231delY and Mn(II) was totally absent in hRecProl-G448R. Furthermore, local structure perturbations for all three mutants were predicted by in silico analysis. Our biochemical investigation of the three causative alleles identified in perturbed folding/instability, and in consequent partial prolidase degradation, the main reasons for enzyme inactivity. Based on the above considerations we were able to rescue part of the prolidase activity in patients’ fibroblasts through the induction of Heath Shock Proteins expression, hinting at new promising avenues for PD treatment.
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Affiliation(s)
- Roberta Besio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Roberta Gioia
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Federica Cossu
- Department of BioSciences, CNR-IBF and CIMAINA, University of Milano, Milano, Italy
| | - Enrico Monzani
- Department of Chemistry, University of Pavia, Pavia, Italy
| | | | - Lucia Cucca
- Department of Chemistry, University of Pavia, Pavia, Italy
| | | | - Luigi Casella
- Department of Chemistry, University of Pavia, Pavia, Italy
| | - Ruggero Tenni
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Martino Bolognesi
- Department of BioSciences, CNR-IBF and CIMAINA, University of Milano, Milano, Italy
| | - Antonio Rossi
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Antonella Forlino
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
- * E-mail:
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13
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Trofimov AA, Slutskaya EA, Polyakov KM, Dorovatovskii PV, Gumerov VM, Popov VO. Influence of intermolecular contacts on the structure of recombinant prolidase from Thermococcus sibiricus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1275-8. [PMID: 23143231 PMCID: PMC3515363 DOI: 10.1107/s174430911203761x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 08/31/2012] [Indexed: 11/10/2022]
Abstract
Prolidases are peptidases that are specific for dipeptides with proline as the second residue. The structure of recombinant prolidase from the hyperthermophilic archaeon Thermococcus sibiricus (Tsprol) was determined at 2.6 Å resolution. The homodimer of Tsprol is characterized by a complete lack of interactions between the N- and C-terminal domains of the two subunits and hence can be considered to be the most open structure when compared with previously structurally studied prolidases. This structure exists owing to intermolecular coordination bonds between cadmium ions derived from the crystallization solution and histidine residues of a His tag and aspartate and glutamate residues, which link the dimers to each other. This linking leads to the formation of a crystal with a loose packing of protein molecules and low resistance to mechanical influence and temperature increase.
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Affiliation(s)
- A A Trofimov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russian Federation.
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14
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Girish TS, Gopal B. Crystal structure of Staphylococcus aureus metallopeptidase (Sapep) reveals large domain motions between the manganese-bound and apo-states. J Biol Chem 2010; 285:29406-15. [PMID: 20610394 PMCID: PMC2937973 DOI: 10.1074/jbc.m110.147579] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Revised: 06/26/2010] [Indexed: 11/06/2022] Open
Abstract
Proteases belonging to the M20 family are characterized by diverse substrate specificity and participate in several metabolic pathways. The Staphylococcus aureus metallopeptidase, Sapep, is a member of the aminoacylase-I/M20 protein family. This protein is a Mn(2+)-dependent dipeptidase. The crystal structure of this protein in the Mn(2+)-bound form and in the open, metal-free state suggests that large interdomain movements could potentially regulate the activity of this enzyme. We note that the extended inactive conformation is stabilized by a disulfide bond in the vicinity of the active site. Although these cysteines, Cys(155) and Cys(178), are not active site residues, the reduced form of this enzyme is substantially more active as a dipeptidase. These findings acquire further relevance given a recent observation that this enzyme is only active in methicillin-resistant S. aureus. The structural and biochemical features of this enzyme provide a template for the design of novel methicillin-resistant S. aureus-specific therapeutics.
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Affiliation(s)
- Tavarekere S. Girish
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Balasubramanian Gopal
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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15
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Abstract
Point mutations resulting in the substitution of a single amino acid can cause severe functional consequences, but can also be completely harmless. Understanding what determines the phenotypical impact is important both for planning targeted mutation experiments in the laboratory and for analyzing naturally occurring mutations found in patients. Common wisdom suggests using the extent of evolutionary conservation of a residue or a sequence motif as an indicator of its functional importance and thus vulnerability in case of mutation. In this work, we put forward the hypothesis that in addition to conservation, co-evolution of residues in a protein influences the likelihood of a residue to be functionally important and thus associated with disease. While the basic idea of a relation between co-evolution and functional sites has been explored before, we have conducted the first systematic and comprehensive analysis of point mutations causing disease in humans with respect to correlated mutations. We included 14,211 distinct positions with known disease-causing point mutations in 1,153 human proteins in our analysis. Our data show that (1) correlated positions are significantly more likely to be disease-associated than expected by chance, and that (2) this signal cannot be explained by conservation patterns of individual sequence positions. Although correlated residues have primarily been used to predict contact sites, our data are in agreement with previous observations that (3) many such correlations do not relate to physical contacts between amino acid residues. Access to our analysis results are provided at http://webclu.bio.wzw.tum.de/~pagel/supplements/correlated-positions/. Point mutations (i.e., changes of a single sequence element) can have a severe impact on protein function. Many diseases are caused by such minute defects. On the other hand, the majority of such mutations does not lead to noticeable effects. Although previous research has revealed important aspects that influence or predict the chance of a mutation to cause disease, much remains to be learned before we fully understand this complex problem. In our work, we use the observation that sometimes certain positions in a protein mutate in an apparently correlated fashion and analyze this correlation with respect to mutation vulnerability. Our results show that positions exhibiting evolutionary correlation are significantly more likely to be vulnerable to mutation than average positions. On one hand, our data further support the concept of correlated positions to not only be associated with protein contacts but also functional sites and/or disease positions (as introduced by others). On the other hand, this could be useful to further improve the understanding and prediction of the consequences of mutations. Our work is the first to attempt a large-scale quantitation of this relationship.
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Affiliation(s)
- Andreas Kowarsch
- Lehrstuhl für Genomorientierte Bioinformatik, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany
- Institut für Bioinformatik und Systembiologie/MIPS, Helmholtz Zentrum München – Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Angelika Fuchs
- Lehrstuhl für Genomorientierte Bioinformatik, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany
| | - Dmitrij Frishman
- Lehrstuhl für Genomorientierte Bioinformatik, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany
- Institut für Bioinformatik und Systembiologie/MIPS, Helmholtz Zentrum München – Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Philipp Pagel
- Lehrstuhl für Genomorientierte Bioinformatik, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany
- Institut für Bioinformatik und Systembiologie/MIPS, Helmholtz Zentrum München – Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
- * E-mail:
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16
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Cantor JR, Stone EM, Chantranupong L, Georgiou G. The human asparaginase-like protein 1 hASRGL1 is an Ntn hydrolase with beta-aspartyl peptidase activity. Biochemistry 2009; 48:11026-31. [PMID: 19839645 PMCID: PMC2782781 DOI: 10.1021/bi901397h] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein we report the bacterial expression, purification, and enzymatic characterization of the human asparaginase-like protein 1 (hASRGL1). We present evidence that hASRGL1 exhibits beta-aspartyl peptidase activity consistent with enzymes designated as plant-type asparaginases, which had thus far been found in only plants and bacteria. Similar to nonmammalian plant-type asparaginases, hASRGL1 is shown to be an Ntn hydrolase for which Thr168 serves as the essential N-terminal nucleophile for intramolecular processing and catalysis, corroborated in part by abolishment of both activities through the Thr168Ala point mutation. In light of the activity profile reported here, ASRGL1s may act synergistically with protein l-isoaspartyl methyl transferase to relieve accumulation of potentially toxic isoaspartyl peptides in mammalian brain and other tissues.
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Affiliation(s)
- Jason R. Cantor
- Department of Chemical Engineering, University of Texas, Austin, Texas 78712, USA
| | - Everett M. Stone
- Department of Chemical Engineering, University of Texas, Austin, Texas 78712, USA
| | | | - George Georgiou
- Department of Chemical Engineering, University of Texas, Austin, Texas 78712, USA
- Institute for Cell and Molecular Biology, University of Texas, Austin, Texas 78712, USA
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17
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Garner AE, Smith DA, Hooper NM. Sphingomyelin chain length influences the distribution of GPI-anchored proteins in rafts in supported lipid bilayers. Mol Membr Biol 2009; 24:233-42. [PMID: 17520480 DOI: 10.1080/09687860601127770] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Glycosyl-phosphatidylinositol (GPI)-anchored proteins are enriched in cholesterol- and sphingolipid-rich lipid rafts within the membrane. Rafts are known to have roles in cellular organization and function, but little is understood about the factors controlling the distribution of proteins in rafts. We have used atomic force microscopy to directly visualize proteins in supported lipid bilayers composed of equimolar sphingomyelin, dioleoyl-sn-glycero-3-phosphocholine and cholesterol. The transmembrane anchored angiotensin converting enzyme (TM-ACE) was excluded from the liquid ordered raft domains. Replacement of the transmembrane and cytoplasmic domains of TM-ACE with a GPI anchor (GPI-ACE) promoted the association of the protein with rafts in the bilayers formed with brain sphingomyelin (mainly C18:0). Association with the rafts did not occur if the shorter chain egg sphingomyelin (mainly C16:0) was used. The distribution of GPI-anchored proteins in supported lipid bilayers was investigated further using membrane dipeptidase (MDP) whose GPI anchor contains distearoyl phosphatidylinositol. MDP was also excluded from rafts when egg sphingomyelin was used but associated with raft domains formed using brain sphingomyelin. The effect of sphingomyelin chain length on the distribution of GPI-anchored proteins in rafts was verified using synthetic palmitoyl or stearoyl sphingomyelin. Both GPI-ACE and MDP only associated with the longer chain stearoyl sphingomyelin rafts. These data obtained using supported lipid bilayers provide the first direct evidence that the nature of the membrane-anchoring domain influences the association of a protein with lipid rafts and that acyl chain length hydrophobic mismatch influences the distribution of GPI-anchored proteins in rafts.
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Affiliation(s)
- Ashley E Garner
- Proteolysis Research Group, Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, and Leeds Institute of Genetics, Health and Therapeutics, University of Leeds, Leeds, UK
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18
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Karna E, Trojan S, Pałka JA. The mechanism of butyrate-induced collagen biosynthesis in cultured fibroblasts. Acta Pol Pharm 2009; 66:129-134. [PMID: 19719045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The data showing that butyrate may play an important role in cellular metabolism led us to study its effect on collagen biosynthesis in cultured fibroblasts. Since insulin-like growth factor-I (IGF-I) is the most potent stimulator of collagen biosynthesis in fibroblasts, the effect of butyrate on IGF-I receptor (IGF-IR) expression was evaluated. Confluent human dermal fibroblasts were treated with millimolar concentrations of sodium butyrate (NaB) for 48 hours. It was found that butyrate induced collagen biosynthesis and prolidase activity. It was found that the exposure of the cells to 4 mM butyrate contributed to a distinct increase in IGF-IR. It was accompanied by a parallel increase in the expression of SOS protein and MAP-kinases (ERK1, ERK2). It was found that the MEK inhibitor decreased collagen biosynthesis and expression of MAP-kinases (ERK1, ERK2), while NaB counteracted the process. The data suggest that butyrate-dependent stimulation of collagen biosynthesis in cultured human skin fibroblasts undergoes through IGF-IR signaling.
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Affiliation(s)
- Ewa Karna
- Department of Medicinal Chemistry, Medical University in Białystok, Kilińskiego 1, 15-089 Białystok, Poland.
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19
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Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Structure 2008; 16:1668-77. [PMID: 19000819 PMCID: PMC2714228 DOI: 10.1016/j.str.2008.08.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Revised: 08/14/2008] [Accepted: 08/19/2008] [Indexed: 11/28/2022]
Abstract
We have developed a computational approach to aid the assignment of enzymatic function for uncharacterized proteins that uses homology modeling to predict the structure of the binding site and in silico docking to identify potential substrates. We apply this method to proteins in the functionally diverse enolase superfamily that are homologous to the characterized L-Ala-D/L-Glu epimerase from Bacillus subtilis. In particular, a protein from Thermotoga martima was predicted to have different substrate specificity, which suggests that it has a different, but as yet unknown, biological function. This prediction was experimentally confirmed, resulting in the assignment of epimerase activity for L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His, whereas the enzyme is annotated incorrectly in GenBank as muconate cycloisomerase. Subsequently, crystal structures of the enzyme were determined in complex with three substrates, showing close agreement with the computational models and revealing the structural basis for the observed substrate selectivity.
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Affiliation(s)
- Chakrapani Kalyanaraman
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, 600 16 Street, San Francisco, CA 94158, USA
| | - Heidi J. Imker
- Departments of Biochemistry and Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Alexander A. Fedorov
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Elena V. Fedorov
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Margaret E. Glasner
- Department of Biopharmaceutical Sciences, School of Pharmacy, University of California, 1700 4 Street, San Francisco, CA 94158, USA
| | - Patricia C. Babbitt
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, 600 16 Street, San Francisco, CA 94158, USA
- Department of Biopharmaceutical Sciences, School of Pharmacy, University of California, 1700 4 Street, San Francisco, CA 94158, USA
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - John A. Gerlt
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Matthew P. Jacobson
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, 600 16 Street, San Francisco, CA 94158, USA
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20
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Emter R, Natsch A. The sequential action of a dipeptidase and a beta-lyase is required for the release of the human body odorant 3-methyl-3-sulfanylhexan-1-ol from a secreted Cys-Gly-(S) conjugate by Corynebacteria. J Biol Chem 2008; 283:20645-52. [PMID: 18515361 PMCID: PMC3258934 DOI: 10.1074/jbc.m800730200] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Revised: 05/09/2008] [Indexed: 11/06/2022] Open
Abstract
Human axillary odor is formed by the action of Corynebacteria on odorless axilla secretions. Sulfanylalkanols, 3-methyl-3-sulfanylhexan-1-ol in particular, form one key class of the odoriferous compounds. A conjugate with the dipeptide Cys-Gly has been reported as the secreted precursor for 3-methyl-3-sulfanylhexan-1-ol. Here, we confirm the Cys-Gly-(S) conjugate as the major precursor of this odorant, with lower levels of the Cys-(S) conjugate being present in axilla secretions. The enzymatic release of 3-methyl-3-sulfanylhexan-1-ol from the Cys-Gly-(S) conjugate by the axilla isolate Corynebacterium Ax20 was thus investigated. Cellular extracts of Ax20 released 3-methyl-3-sulfanylhexan-1-ol from the Cys-Gly-(S) conjugate and from the Cys-(S) conjugate, whereas the previously isolated C-S lyase of this bacterial strain was only able to cleave the Cys-(S) conjugate. o-Phenanthroline blocked the release from the Cys-Gly-(S) conjugate but did not affect cleavage of the Cys-(S) conjugate, indicating that in a first step, a metal-dependent dipeptidase hydrolyzes the Cys-Gly bond. This enzyme was purified by four chromatographic steps and gel electrophoresis, and the partial amino acid sequence was determined. The corresponding gene was cloned and expressed in Escherichia coli. It codes for a novel dipeptidase with a high affinity toward the Cys-Gly-(S) conjugate of 3-methyl-3-sulfanylhexan-1-ol. Co-incubating either the synthetic Cys-Gly-(S) conjugate or fresh axilla secretions with both the C-S lyase and the novel dipeptidase did release 3-methyl-3-sulfanylhexan-1-ol, proving that the sequential action of these two enzymes from the skin bacterium Corynebacterium Ax20 does release the odorant from the key secreted precursor.
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Affiliation(s)
| | - Andreas Natsch
- Bioscience Departement, Givaudan Schweiz AG, CH-8600 Duebendorf,
Switzerland
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21
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Shi Q, Meroueh SO, Fisher JF, Mobashery S. Investigation of the mechanism of the cell wall DD-carboxypeptidase reaction of penicillin-binding protein 5 of Escherichia coli by quantum mechanics/molecular mechanics calculations. J Am Chem Soc 2008; 130:9293-303. [PMID: 18576637 PMCID: PMC6993461 DOI: 10.1021/ja801727k] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Penicillin-binding protein 5 (PBP 5) of Escherichia coli hydrolyzes the terminal D-Ala-D-Ala peptide bond of the stem peptides of the cell wall peptidoglycan. The mechanism of PBP 5 catalysis of amide bond hydrolysis is initial acylation of an active site serine by the peptide substrate, followed by hydrolytic deacylation of this acyl-enzyme intermediate to complete the turnover. The microscopic events of both the acylation and deacylation half-reactions have not been studied. This absence is addressed here by the use of explicit-solvent molecular dynamics simulations and ONIOM quantum mechanics/molecular mechanics (QM/MM) calculations. The potential-energy surface for the acylation reaction, based on MP2/6-31+G(d) calculations, reveals that Lys47 acts as the general base for proton abstraction from Ser44 in the serine acylation step. A discrete potential-energy minimum for the tetrahedral species is not found. The absence of such a minimum implies a conformational change in the transition state, concomitant with serine addition to the amide carbonyl, so as to enable the nitrogen atom of the scissile bond to accept the proton that is necessary for progression to the acyl-enzyme intermediate. Molecular dynamics simulations indicate that transiently protonated Lys47 is the proton donor in tetrahedral intermediate collapse to the acyl-enzyme species. Two pathways for this proton transfer are observed. One is the direct migration of a proton from Lys47. The second pathway is proton transfer via an intermediary water molecule. Although the energy barriers for the two pathways are similar, more conformers sample the latter pathway. The same water molecule that mediates the Lys47 proton transfer to the nitrogen of the departing D-Ala is well positioned, with respect to the Lys47 amine, to act as the hydrolytic water in the deacylation step. Deacylation occurs with the formation of a tetrahedral intermediate over a 24 kcal x mol(-1) barrier. This barrier is approximately 2 kcal x mol(-1) greater than the barrier (22 kcal x mol(-1)) for the formation of the tetrahedral species in acylation. The potential-energy surface for the collapse of the deacylation tetrahedral species gives a 24 kcal x mol(-1) higher energy species for the product, signifying that the complex would readily reorganize and pave the way for the expulsion of the product of the reaction from the active site and the regeneration of the catalyst. These computational data dovetail with the knowledge on the reaction from experimental approaches.
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Affiliation(s)
- Qicun Shi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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22
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Chu L, Lai Y, Xu X, Eddy S, Yang S, Song L, Kolodrubetz D. A 52-kDa leucyl aminopeptidase from treponema denticola is a cysteinylglycinase that mediates the second step of glutathione metabolism. J Biol Chem 2008; 283:19351-8. [PMID: 18482986 PMCID: PMC2443665 DOI: 10.1074/jbc.m801034200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Revised: 04/28/2008] [Indexed: 11/06/2022] Open
Abstract
The metabolism of glutathione by the periodontal pathogen Treponema denticola produces hydrogen sulfide, which may play a role in the host tissue destruction seen in periodontitis. H2S production in this organism has been proposed to occur via a three enzyme pathway, gamma-glutamyltransferase, cysteinylglycinase (CGase), and cystalysin. In this study, we describe the purification and characterization of T. denticola CGase. Standard approaches were used to purify a 52-kDa CGase activity from T. denticola, and high pressure liquid chromatography electrospray ionization tandem mass spectrometry analysis of this molecule showed that it matches the amino acid sequence of a predicted 52-kDa protein in the T. denticola genome data base. A recombinant version of this protein was overexpressed in and purified from Escherichia coli and shown to catalyze the hydrolysis of cysteinylglycine (Cys-Gly) with the same kinetics as the native protein. Surprisingly, because sequence homology indicates that this protein is a member of a family of metalloproteases called M17 leucine aminopeptidases, the preferred substrate for the T. denticola protein is Cys-Gly (k cat/Km of 8.2 microm(-1) min(-1)) not l-Leu-p-NA (k cat/Km of 1.1 microm(-1) min(-1)). The activity of CGase for Cys-Gly is optimum at pH 7.3 and is enhanced by Mn2+, Co2+, or Mg2+ but not by Zn2+ or Ca2+. Importantly, in combination with the two other previously purified T. denticola enzymes, gamma-glutamyltransferase and cystalysin, CGase mediates the in vitro degradation of glutathione into the expected end products, including H2S. These results prove that T. denticola contains the entire three-step pathway to produce H2S from glutathione, which may be important for pathogenesis.
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Affiliation(s)
- Lianrui Chu
- Department of Orthodontics, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA.
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23
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Weber KC, da Silva ABF. A chemometric study of the 5-HT1A receptor affinities presented by arylpiperazine compounds. Eur J Med Chem 2008; 43:364-72. [PMID: 17562349 DOI: 10.1016/j.ejmech.2007.03.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 03/28/2007] [Accepted: 03/29/2007] [Indexed: 11/24/2022]
Abstract
Arylpiperazine compounds are promising 5-HT(1A) receptor ligands that can contribute for accelerating the onset of therapeutic effect of selective serotonin reuptake inhibitors. In the present work, the chemometric methods HCA, PCA, KNN, SIMCA and PLS were employed in order to obtain SAR and QSAR models relating the structures of arylpiperazine compounds to their 5-HT(1A) receptor affinities. A training set of 52 compounds was used to construct the models and the best ones were obtained with nine topological descriptors. The classification and regression models were externally validated by means of predictions for a test set of 14 compounds and have presented good quality, as verified by the correctness of classifications, in the case of pattern recognition studies, and by the high correlation coefficients (q(2)=0.76, r(2)=0.83) and small prediction errors for the PLS regression. Since the results are in good agreement with previous SAR studies, we can suggest that these findings can help in the search for 5-HT(1A) receptor ligands that are able to improve antidepressant treatment.
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Affiliation(s)
- Karen C Weber
- Instituto de Química de São Carlos, Universidade de São Paulo, P.O. Box 780, 13566-590 São Carlos, SP, Brazil
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24
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Liu G, Nakayama K, Awata S, Tang S, Kitaoka N, Manabe M, Kodama H. Prolidase isoenzymes in the rat: their organ distribution, developmental change and specific inhibitors. Pediatr Res 2007; 62:54-9. [PMID: 17515839 DOI: 10.1203/pdr.0b013e3180676d05] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Lack of prolidase I (PD I) leads to prolidase deficiency, a disease characterized by intractable skin lesions, recurrent respiratory infections, and mental retardation. The present study was undertaken to characterize and determine the physiologic roles of different prolidase isoenzymes. Two isoforms of prolidase were isolated from rat kidney. PD I showed higher activity against seryl-proline and alanyl-proline, whereas PD II was active especially against methionyl-proline. PD I was highly concentrated in the small intestine and kidney, whereas PD II was shown not to vary in the organs examined. Expression of PD I and PD II in the small intestine were maximal within 1 wk of birth, and then rapidly declined. The changes of prolidase in the kidney and heart were found to differ slightly. N-benzyloxycarbonyl-l-proline and captopril inhibited PD I dose-dependently, but showed no inhibition of PD II at low concentrations. NiCl2 inhibited PD II much more effectively than PD I. Our findings suggest that PD I functions by way of an intestinal peptide carrier, which may also be regulated by the uptake of various iminodipeptides. Similarly, age-related alterations of prolidase isoenzymes suggest that intestinal PD II also participates in absorption of proline and other amino acids early in life.
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Affiliation(s)
- Gang Liu
- Department of Anesthesiology and Critical Care Medicine, Kochi Medical School, Oko, Kochi 783-8505, Japan
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25
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Abstract
Lysosomal dipeptidase catalyzes the hydrolysis of dipeptides with unsubstituted terminals. It is a homodimer and binds zinc. Dimerization is an important issue in understanding the enzyme's function. In this study, we investigated the influence of the propeptide on the folding and dimerization of recombinant lysosomal dipeptidase. For this purpose, we separately cloned and overexpressed the mature protein and the proenzyme. The overexpressed proteins were localized exclusively to insoluble inclusion bodies. Refolding of the urea-solubilized inclusion bodies showed that only dipeptidase lacking the propeptide was dimeric. The soluble renatured proenzyme was a monomer, although circular dichroism and fluorescence spectra of the proenzyme indicated the formation of secondary and tertiary structure. The propeptide thus controls dimerization, as well as activation, of lysosomal dipeptidase.
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Affiliation(s)
- Iztok Dolenc
- Department of Biochemistry and Molecular Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
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26
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Abstract
Dipeptidyl peptidase 4 (DP4) inhibitors are currently under intensive investigation in late-stage clinical trials as a treatment for type II diabetes. Lack of selectivity toward the related enzymes DP8 and DP9 has recently emerged as a possible source of drug-induced toxicity. Unlike DP4, X-ray structures of DP8 and DP9 are not yet available. As an aid to understanding the structural basis for selectivity, the authors have constructed homology models of DP8 and DP9 based on the X-ray coordinates of DP4. Accurate sequence alignment reveals common structural features indicative for a well-preserved overall fold comprising two domains, namely, a hydrolase domain and a so-called beta-propeller, which together form the active site deeply buried within the protein. The conformation of two loops inside this deep cavity is particularly relevant for the active sites. The authors used a published protocol for loop prediction based on conformational sampling and energy analysis to generate plausible solutions for these two loops. The predictive power of the approach was successfully evaluated for the template protein DP4 and two additional known structures from the same protein family, namely, FAP and DPX. The authors also show that inclusion of the covalent ligand NVP-728 greatly enhances the refinement. Based on the established evaluation protocol, the corresponding loops of DP8 and DP9 were predicted and the resulting active sites were compared with DP4. In particular, the authors conclude that differences in the P2-pocket are relevant for the design of selective DP4 inhibitors. The loss of key interactions in DP8 and DP9 as predicted from their models is consistent with the selectivity profile of the DP4 clinical candidate MK-431.
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Affiliation(s)
- Christian Rummey
- Santhera Pharmaceuticals (Switzerland) Ltd., Hammerstrasse 47, 4410 Liestal, Switzerland.
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Gorrell MD, Wang XM, Park J, Ajami K, Yu DMT, Knott H, Seth D, McCaughan GW. Structure and Function in Dipeptidyl Peptidase IV and Related Proteins. Advances in Experimental Medicine and Biology 2006; 575:45-54. [PMID: 16700507 DOI: 10.1007/0-387-32824-6_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Mark D Gorrell
- A. W. Morrow Gastroenterology and Liver Centre at Royal Prince Alfred Hospital, Centenary Institute of Cancer Medicine and Cell Biology and The Discipline of Medicine, University of Sydney, Sydney, New South Wales, Australia
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28
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Lee HJ, Chen YS, Chou CY, Chien CH, Lin CH, Chang GG, Chen X. Investigation of the dimer interface and substrate specificity of prolyl dipeptidase DPP8. J Biol Chem 2006; 281:38653-62. [PMID: 17040910 DOI: 10.1074/jbc.m603895200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
DPP8 belongs to the family of prolyl dipeptidases, which are capable of cleaving the peptide bond after a penultimate proline residue. Unlike DPP-IV, a drug target for type II diabetes, no information is available on the crystal structure of DPP8, the regulation of its enzymatic activity, or its substrate specificity. In this study, using analytical ultracentrifugation and native gel electrophoresis, we show that the DPP8 protein is predominantly dimeric when purified or in the cell extracts. Four conserved residues in the C-terminal loop of DPP8 (Phe(822), Val(833), Tyr(844), and His(859)), corresponding to those located at the dimer interface of DPP-IV, were individually mutated to Ala. Surprisingly, unlike DPP-IV, these single-site mutations abolished the enzymatic activity of DPP8 without disrupting its quaternary structure, indicating that dimerization itself is not sufficient for the optimal enzymatic activity of DPP8. Moreover, these mutations not only decreased k(cat), as did the corresponding DPP-IV mutations, but also dramatically increased K(m). We further show that the K(m) effect is independent of the substrate assayed. Finally, we identified the distinctive and strict substrate selectivity of DPP8 for hydrophobic or basic residues at the P2 site, which is in sharp contrast to the much less discriminative substrate specificity of DPP-IV. Our study has identified the residues absolutely required for the optimal activity of DPP8 and its unique substrate specificity. This study extends the functional importance of the C-terminal loop to the whole family of prolyl dipeptidases.
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Affiliation(s)
- Hong-Jen Lee
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhu Nan Town, Miaoli Co., Taiwan 350, Republic of China
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29
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Mori S, Miyamoto M, Kaneko S, Nirasawa S, Komba S, Kasumi T. Characterization and kinetic analysis of enzyme-substrate recognition by three recombinant lactococcal PepVs. Arch Biochem Biophys 2006; 454:137-45. [PMID: 16962986 DOI: 10.1016/j.abb.2006.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2006] [Revised: 07/31/2006] [Accepted: 08/01/2006] [Indexed: 11/18/2022]
Abstract
The dipeptidases (PepVs) from three typical lactococcal strains, Lactococcus lactis subsp. lactis (L9), L. lactis subsp. cremoris (L6) and L. lactis subsp. hordniae (hT) were cloned and characterized. The metal-binding, catalytic, and substrate-binding sites are highly conserved among of them. A computer-generated three-dimensional model suggested that the amino acid differences between these PepVs were mostly located away from the active center. L9 PepV does not hydrolyze dipeptides bearing Pro or D-amino acid at the C-terminal amino acid. Unlike PepV from Lactobacillus delbrueckii, L9 PepV does not cleave beta-Asp-His, and has little ability to cleave dipeptides containing a beta-alanine. In addition, L9 PepV has a much higher kcat for dipeptides with an N-terminal Ala but a significantly higher Km when the N-terminal amino acid is Gly. The substrate recognition profile of PepV is further discussed on the basis of the kinetic analysis and the structural model.
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Affiliation(s)
- Sumiko Mori
- Biological Function Division, National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
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Yamashita T, Unno H, Ujita S, Otani H, Okumura N, Hashida-Okumura A, Nagai K, Kusunoki M. Crystallization and preliminary crystallographic study of carnosinase CN2 from mice. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:996-8. [PMID: 17012794 PMCID: PMC2225185 DOI: 10.1107/s1744309106034701] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Accepted: 08/29/2006] [Indexed: 11/10/2022]
Abstract
Mammalian tissues contain several histidine-containing dipeptides, of which L-carnosine is the best characterized and is found in various tissues including the brain and skeletal muscles. However, the mechanism for its biosynthesis and degradation have not yet been fully elucidated. Crystallographic study of carnosinase CN2 from mouse has been undertaken in order to understand its enzymatic mechanism from a structural viewpoint. CN2 was crystallized by the hanging-drop vapour-diffusion technique using PEG 3350 as a precipitant. Crystals were obtained in complex with either Mn(2+) or Zn(2+). Both crystals of CN2 belong to the monoclinic space group P2(1) and have almost identical unit-cell parameters (a = 54.41, b = 199.77, c = 55.49 A, beta = 118.52 degrees for the Zn(2+) complex crystals). Diffraction data were collected to 1.7 and 2.3 A for Zn(2+) and Mn(2+) complex crystals, respectively, using synchrotron radiation. Structure determination is ongoing using the multiple-wavelength anomalous diffraction (MAD) method.
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Affiliation(s)
- Tetsuo Yamashita
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Hideaki Unno
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Sayuri Ujita
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Hiroto Otani
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Nobuaki Okumura
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Akiko Hashida-Okumura
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Katsuya Nagai
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Masami Kusunoki
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
- Correspondence e-mail:
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31
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Bjelke J, Christensen J, Nielsen P, Branner S, Kanstrup A, Wagtmann N, Rasmussen H. Dipeptidyl peptidases 8 and 9: specificity and molecular characterization compared with dipeptidyl peptidase IV. Biochem J 2006; 396:391-9. [PMID: 16475979 PMCID: PMC1462722 DOI: 10.1042/bj20060079] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Dipeptidyl peptidases 8 and 9 have been identified as gene members of the S9b family of dipeptidyl peptidases. In the present paper, we report the characterization of recombinant dipeptidyl peptidases 8 and 9 using the baculovirus expression system. We have found that only the full-length variants of the two proteins can be expressed as active peptidases, which are 882 and 892 amino acids in length for dipeptidyl peptidase 8 and 9 respectively. We show further that the purified proteins are active dimers and that they show similar Michaelis-Menten kinetics and substrate specificity. Both cleave the peptide hormones glucagon-like peptide-1, glucagon-like peptide-2, neuropeptide Y and peptide YY with marked kinetic differences compared with dipeptidyl peptidase IV. Inhibition of dipeptidyl peptidases IV, 8 and 9 using the well-known dipeptidyl peptidase IV inhibitor valine pyrrolidide resulted in similar K(i) values, indicating that this inhibitor is non-selective for any of the three dipeptidyl peptidases.
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Affiliation(s)
- Jais R. Bjelke
- *Protein Structure and Biophysics, Novo Nordisk A/S, Novo Allé, 2880 Bagsvaerd, Denmark
| | - Jesper Christensen
- †Biotech Research Innovation Center, Fruebjergvej, 2100 Copenhagen Ø, Denmark
| | - Per F. Nielsen
- ‡Protein Science, Novo Nordisk A/S, Novo Allé, 2880 Bagsvaerd, Denmark
| | - Sven Branner
- ‡Protein Science, Novo Nordisk A/S, Novo Allé, 2880 Bagsvaerd, Denmark
| | - Anders B. Kanstrup
- §Medicinal Chemistry, Novo Nordisk A/S, Novo Allé, 2880 Bagsvaerd, Denmark
| | - Nicolai Wagtmann
- ∥Cancer and Immunobiology, Novo Nordisk A/S, Novo Allé, 2880 Bagsvaerd, Denmark
| | - Hanne B. Rasmussen
- *Protein Structure and Biophysics, Novo Nordisk A/S, Novo Allé, 2880 Bagsvaerd, Denmark
- To whom correspondence should be addressed (email )
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32
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Longenecker KL, Stewart KD, Madar DJ, Jakob CG, Fry EH, Wilk S, Lin CW, Ballaron SJ, Stashko MA, Lubben TH, Yong H, Pireh D, Pei Z, Basha F, Wiedeman PE, von Geldern TW, Trevillyan JM, Stoll VS. Crystal Structures of DPP-IV (CD26) from Rat Kidney Exhibit Flexible Accommodation of Peptidase-Selective Inhibitors. Biochemistry 2006; 45:7474-82. [PMID: 16768443 DOI: 10.1021/bi060184f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Dipeptidyl peptidase IV (DPP-IV) belongs to a family of serine peptidases, and due to its indirect regulatory role in plasma glucose modulation, DPP-IV has become an attractive pharmaceutical target for diabetes therapy. DPP-IV inactivates the glucagon-like peptide (GLP-1) and several other naturally produced bioactive peptides that contain preferentially a proline or alanine residue in the second amino acid sequence position by cleaving the N-terminal dipeptide. To elucidate the details of the active site for structure-based drug design, we crystallized a natural source preparation of DPP-IV isolated from rat kidney and determined its three-dimensional structure using X-ray diffraction techniques. With a high degree of similarity to structures of human DPP-IV, the active site architecture provides important details for the design of inhibitory compounds, and structures of inhibitor-protein complexes offer detailed insight into three-dimensional structure-activity relationships that include a conformational change of Tyr548. Such accommodation is exemplified by the response to chemical substitution on 2-cyanopyrrolidine inhibitors at the 5 position, which conveys inhibitory selectivity for DPP-IV over closely related homologues. A similar conformational change is also observed in the complex with an unrelated synthetic inhibitor containing a xanthine core that is also selective for DPP-IV. These results suggest the conformational flexibility of Tyr548 is unique among protein family members and may be utilized in drug design to achieve peptidase selectivity.
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Affiliation(s)
- Kenton L Longenecker
- Department of Structural Biology, Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064-6098, USA.
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33
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Vistoli G, Pedretti A, Cattaneo M, Aldini G, Testa B. Homology Modeling of Human Serum Carnosinase, a Potential Medicinal Target, and MD Simulations of Its Allosteric Activation by Citrate. J Med Chem 2006; 49:3269-77. [PMID: 16722645 DOI: 10.1021/jm0602099] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent biochemical and clinical evidence implicates human serum carnosinase in a variety of pathological conditions, such as neurological disorders and diabetic nephropathy, suggesting that this enzyme is of potential interest as a novel medicinal target. The present study was undertaken with a view to model the serum carnosinase and its catalytic site and to unravel the molecular mechanism by which citrate ions increase the catalytic efficiency of serum carnosinase. A homology model of the enzyme was obtained on the basis of beta-alanine synthetase, and its active center was found to bind known substrates carnosine, homocarnosine, and anserine in a binding mode conducive to catalysis. Citrate ions were shown to bind at only three well-defined sites involving both ion pairs and hydrogen bonds. Molecular dynamics simulations evidenced that citrate binding had a remarkable conformational influence on the 3D structure of carnosinase, increasing the binding affinity (i.e., binding score) of carnosine to the catalytic site. This is one of the first reports documenting the molecular mechanism of an allosteric enzyme activator using MD simulations.
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Affiliation(s)
- Giulio Vistoli
- Istituto di Chimica Farmaceutica, Facoltà di Farmacia, Università di Milano, Viale Abruzzi 42, I-20131 Milano, Italy.
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Abstract
Prolidase [E.C. 3.4.13.9], a member of the matrix metalloproteinase (MMP) family, is a manganese-dependent cytosolic exopeptidase that cleaves imidodipeptides containing C-terminal proline or hydroxyproline. It plays an important role in collagen metabolism, matrix remodeling and cell growth. Nitric oxide (NO), a versatile signaling molecule, regulates many processes including collagen synthesis and matrix remodeling and, thereby, may modulate angiogenesis, tumor invasiveness, and metastasis. Thus, we considered that prolidase may be an important target of NO regulation. In our study, SIN I and DETA/NO were used as NO donors. Both donors increased prolidase activity in a time-dependent and dose-dependent manner. Prolidase activity increased not only with NO donors but also with endogenous NO in cells transfected with iNOS. The effect of iNOS was abolished by treatment with S-methylisothiourea (SMT), a selective inhibitor of iNOS. However, with either exogenous or endogenous sources of NO, the increase in prolidase activity was not accompanied by increased prolidase expression. Therefore, we suspected phosphorylation of prolidase as a potential mechanism regulating enzyme activation. We observed increased serine/threonine phosphorylation on prolidase protein in cells treated with NO donors and in cells transfected with iNOS. To determinate the pathways that may mediate prolidase induction by NO, we first used 8-Br-cGMP, a cGMP agonist, and found that 8-Br-cGMP strongly and rapidly stimulated prolidase activity accompanied by increased phosphorylation. Rp-8-Br-pCPT-cGMP, an inhibitor of cGMP, reduced NO donor-stimulated prolidase activity to control levels. To test whether the MAPK pathway is involved in this NO-dependent activation, we used an ERK1/2 inhibitor and found that it had no effect on prolidase activity increased by NO donors. These results demonstrate that NO stimulates prolidase activity by increasing serine/threonine phosphorylation through PKG-cGMP pathway, but independent of MAPK and suggest an interaction between inflammatory signaling pathways and regulation of the terminal step of matrix degradation.
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Affiliation(s)
- Arkadiusz Surazynski
- Metabolism and Cancer Susceptibility Section, Laboratory of Comparative Carcinogenesis, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
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Abstract
AIM To investigate the role of a novel dipeptidyl peptidase 8 transcript variant (DPP8-v3) gene in testis development and/or spermatogenesis. METHODS A human testis cDNA microarray was hybridized with mRNA of human adult and fetal testes. Differentially expressed clones were sequenced and characterized and their expression was analyzed by real-time reverse transcription polymerase chain reaction (RT-PCR) and Southern-blot analysis. RESULTS A new transcript variant of the human dipeptidyl peptidase (DPP8), exhibiting a 5-fold higher expression level in human adult than that in fetal testes, was cloned and was named DPP8 variant 3 (DPP8-v3). The full-length sequence of DPP8-v3 was 3,030 bp, encoding a protein of 898 amino acids. CONCLUSION DPP8-v3 is a novel human DPP8 transcript variant highly expressed in the adult testis. Similar to DPPIV, DPP8-v3 may play a key role in the immunoregulation of testes and accordingly may influence spermatogenesis and male fertility.
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Affiliation(s)
- Hui Zhu
- Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China
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36
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Du X, Tove S, Kast-Hutcheson K, Grunden AM. Characterization of the dinuclear metal center ofPyrococcus furiosusprolidase by analysis of targeted mutants. FEBS Lett 2005; 579:6140-6. [PMID: 16243319 DOI: 10.1016/j.febslet.2005.09.086] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 09/27/2005] [Accepted: 09/28/2005] [Indexed: 11/24/2022]
Abstract
Prolidases are dipeptidases specific for cleavage of Xaa-Pro dipeptides. Pyrococcus furiosus prolidase is a homodimer having one Co-bound dinuclear metal cluster per monomer with one tightly bound Co(II) site and the other loosely bound (Kd 0.24 mM). To identify which Co site is tight-binding and which is loose-binding, site-directed mutagenesis was used to modify amino acid residues that participate in binding the Co1 (E-313 and H-284), the Co2 site (D-209) or the bidentate ligand (E-327). Metal-content, enzyme activity and CD-spectra analyses of D209A-, H284L-, and E327L-prolidase mutants show that Co1 is the tight-binding and Co2 the loose-binding metal center.
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Affiliation(s)
- Xuelian Du
- Department of Microbiology, North Carolina State University, Box 7615, Raleigh, NC 27695, USA
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Sheng Y, Li S, Gou X, Kong X, Wang X, Sun Y, Zhang J. The hybrid enzymes from α-aspartyl dipeptidase and l-aspartase. Biochem Biophys Res Commun 2005; 331:107-12. [PMID: 15845365 DOI: 10.1016/j.bbrc.2005.03.140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2005] [Indexed: 10/25/2022]
Abstract
With combinative functionalities as well as the improved activity and stability, the novel hybrid enzymes (HEs) from the heterogeneous enzymes of alpha-aspartyl dipeptidase (PepE, monomer) and l-aspartase (l-AspA, tetramer) were constructed successfully by gene random deletion strategy. The wild-type hybrid enzyme (WHE) and the evolved hybrid enzyme (EHE) were selected, respectively, upon the phenotype and the enzyme activity. The relative activity of the WHE tested was about 110% of the wild-type PepE and 26% of the wild-type l-AspA, whilst the activity of EHE was about 340% of the PepE and 87% of the l-AspA. In comparison to its individual wild-type enzymes, the EHE exhibited an improved thermostability, when examined at the enzyme concentration of 10(-7)mol/L, but the WHE showed a reduced thermostability. The activity of the EHE was about 3-fold compared to that of the WHE. The current results give a good example that the hybridization of enzymes could be attained between the monomer and multimer enzymes. In addition, they also indicate that construction hybrid enzyme from evolved enzymes is feasible.
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Affiliation(s)
- Yongjie Sheng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, PR China
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Martí-Arbona R, Fresquet V, Thoden JB, Davis ML, Holden HM, Raushel FM. Mechanism of the Reaction Catalyzed by Isoaspartyl Dipeptidase from Escherichia coli,. Biochemistry 2005; 44:7115-24. [PMID: 15882050 DOI: 10.1021/bi050008r] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isoaspartyl dipeptidase (IAD) is a member of the amidohydrolase superfamily and catalyzes the hydrolytic cleavage of beta-aspartyl dipeptides. Structural studies of the wild-type enzyme have demonstrated that the active site consists of a binuclear metal center positioned at the C-terminal end of a (beta/alpha)(8)-barrel domain. Steady-state kinetic parameters for the hydrolysis of beta-aspartyl dipeptides were obtained at pH 8.1. The pH-rate profiles for the hydrolysis of beta-Asp-Leu were obtained for the Zn/Zn-, Co/Co-, Ni/Ni-, and Cd/Cd-substituted forms of IAD. Bell-shaped profiles were observed for k(cat) and k(cat)/K(m) as a function of pH for all four metal-substituted forms. The pK(a) of the group that must be unprotonated for catalytic activity varied according to the specific metal ion bound in the active site, whereas the pK(a) of the group that must be protonated for catalytic activity was relatively independent of the specific metal ion present. The identity of the group that must be unprotonated for catalytic activity was consistent with the hydroxide that bridges the two divalent cations of the binuclear metal center. The identity of the group that must be protonated for activity was consistent with the free alpha-amino group of the dipeptide substrate. Kinetic constants were obtained for the mutant enzymes at conserved residues Glu77, Tyr137, Arg169, Arg233, Asp285, and Ser289. The catalytic properties of the wild-type and mutant enzymes, coupled with the X-ray crystal structure of the D285N mutant complexed with beta-Asp-His, are consistent with a chemical reaction mechanism for the hydrolysis of dipeptides that is initiated by the polarization of the amide bond via complexation to the beta-metal ion of the binuclear metal center. Nucleophilic attack by the bridging hydroxide is facilitated by abstraction of its proton by the side chain carboxylate of Asp285. Collapse of the tetrahedral intermediate and cleavage of the carbon-nitrogen bond occur with donation of a proton from the protonated form of Asp285.
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Affiliation(s)
- Ricardo Martí-Arbona
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012, USA
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39
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Wang SH, Zhi QW, Sun MJ. Purification and characterization of recombinant human liver prolidase expressed in Saccharomyces cerevisiae. Arch Toxicol 2005; 79:253-9. [PMID: 15902422 DOI: 10.1007/s00204-004-0634-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Accepted: 12/22/2004] [Indexed: 12/01/2022]
Abstract
The recombinant human liver prolidase (rh-prolidase, EC 3.4.13.9) from the lysate supernatant of engineering yeast Saccharomyces cerevisiae was purified in two steps employing anion-exchange gradient chromatography (DEAE-Sepharose fast flow) and gel filtration chromatography (Sephacryl S-200 high resolution). The purified recombinant protein furnished a single band with a molecular weight of 56 kD. Intensity scanning of the SDS-PAGE gel revealed that the prolidase accounted for more than 90% of total protein. The optimum pH of the catalytic reaction was 8.0. The enzyme was stimulated by Mn2+, but strongly inhibited by Cu2+ and Zn2+. The rh-prolidase expressed in S. cerevisiae had both dipeptidase and organophosphorus acid anhydrolase activity. It catalyzed the hydrolysis of soman and the dipeptide Gly -Pro. In a detoxification test in vitro, purified rh-prolidase was remarkably efficient at eliminating the toxicity of a lethal dose of soman, with the result that mice survived injection of such a dose.
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Affiliation(s)
- Shu-Hao Wang
- Department of Biochemical Pharmacology, Beijing Institute of Pharmacology and Toxicology, Tai-Ping Road 27, Beijing, 100850, China
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Mori S, Mori K, Suzuki I, Kasumi T. Phylogenetic analysis of Lactococcus lactis subspecies based on decoding the sequence of the pepT tripeptidase gene, the pepV dipeptidase gene and 16S rRNA. Syst Appl Microbiol 2004; 27:414-22. [PMID: 15368846 DOI: 10.1078/0723202041438400] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Tripeptidase (PepT) and dipeptidase (PepV), the enzymes located in the final stage of the intracellular proteolytic system, were demonstrated to be distributed widely in lactic acid bacteria, especially in lactococci. Both the tripeptidase genes (pepT) and dipeptidase genes (pepV) of 15 lactococcal strains consisting of the type and domestic strains were cloned and sequenced using normal and TAIL PCR methods. Amino acid sequences of these enzymes were highly conserved among strains. Evolutionary distance trees based on the sequence of 1239 nucleotides of pepT and 1416 nucleotide of pepV showed a similar cluster as that obtained from the 1499 fragment of the 16S rRNA. Based on this profile, the species Lactococcus lactis is reasonably divided into three subspecies groups, subsp. lactis, cremoris, and hordniae, as in the current classification. Figure of trees from pepT and pepV were essentially identical to each other and slightly more intricate than that from 16S rRNA. The K nuc values obtained from pepT and pepV genes were approximately ten times as high as that from 16S rRNA. Considering these results, phylogenetic analysis based on pepT and pepV genes may aid in a more precise index of classification of L. lactis subspecies. PepT and PepV seem to have evolved in similar directions in lactococci.
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Affiliation(s)
- Sumiko Mori
- National Food Research Institute, Tsukuba, Japan
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41
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Prahl A, Pazgier M, Hejazi M, Lockau W, Lubkowski J. Structure of the isoaspartyl peptidase withL-asparaginase activity fromEscherichia coli. Acta Crystallogr D Biol Crystallogr 2004; 60:1173-6. [PMID: 15159592 DOI: 10.1107/s0907444904003403] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2003] [Accepted: 02/12/2004] [Indexed: 11/10/2022]
Abstract
The crystal structure of the Escherichia coli enzyme (EcAIII) with isoaspartyl dipeptidase and L-asparaginase activity has been solved and refined to a resolution of 1.65 angstroms, with crystallographic R-factor and Rfree values of 0.178 and 0.209, respectively. EcAIII belongs to the family of N-terminal hydrolases. The amino-acid sequence of EcAIII is homologous to those of putative asparaginases from plants. The structure of EcAIII is similar to the structures of glycosylasparaginases. The mature and catalytically active form of EcAIII is a heterotetramer consisting of two alpha-subunits and two beta-subunits. Both of the equivalent active sites present in the EcAIII tetramer is assisted by a metal-binding site. The metal cations, modelled here as Na+, have not previously been observed in glycosylasparaginases. This reported structure helps to explain the inability of EcAIII and other plant-type asparaginases to hydrolyze N4-(beta-N-acetylglucosaminyl)-L-asparagine, the substrate of glycosylasparaginases.
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Affiliation(s)
- Adam Prahl
- Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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42
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Baek DH, Song JJ, Kwon SJ, Park C, Jung CM, Sung MH. Characteristics of a new enantioselective thermostable dipeptidase from Brevibacillus borstelensis BCS-1 and its application to synthesis of a D-amino-acid-containing dipeptide. Appl Environ Microbiol 2004; 70:1570-5. [PMID: 15006780 PMCID: PMC368365 DOI: 10.1128/aem.70.3.1570-1575.2004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new thermostable dipeptidase gene was cloned from the thermophile Brevibacillus borstelensis BCS-1 by genetic complementation of the D-Glu auxotroph Escherichia coli WM335 on a plate containing D-Ala-D-Glu. Nucleotide sequence analysis revealed that the gene included an open reading frame coding for a 307-amino-acid sequence with an M(r) of 35,000. The deduced amino acid sequence of the dipeptidase exhibited 52% similarity with the dipeptidase from Listeria monocytogenes. The enzyme was purified to homogeneity from recombinant E. coli WM335 harboring the dipeptidase gene from B. borstelensis BCS-1. Investigation of the enantioselectivity (E) to the P(1) and P(1)' site of Ala-Ala revealed that the ratio of the specificity constant (k(cat)/K(m)) for L-enantioselectivity to the P(1) site of Ala-Ala was 23.4 +/- 2.2 [E = (k(cat)/K(m))(L,D)/(k(cat)/K(m))(D,D)], while the D-enantioselectivity to the P(1)' site of Ala-Ala was 16.4 +/- 0.5 [E = (k(cat)/K(m))(L,D)/(k(cat)/K(m))(L,L)] at 55 degrees C. The enzyme was stable up to 55 degrees C, and the optimal pH and temperature were 8.5 and 65 degrees C, respectively. The enzyme was able to hydrolyze L-Asp-D-Ala, L-Asp-D-AlaOMe, Z-D-Ala-D-AlaOBzl, and Z-L-Asp-D-AlaOBzl, yet it could not hydrolyze D-Ala-L-Asp, D-Ala-L-Ala, D-AlaNH(2), and L-AlaNH(2.) The enzyme also exhibited beta-lactamase activity similar to that of a human renal dipeptidase. The dipeptidase successfully synthesized the precursor of the dipeptide sweetener Z-L-Asp-D-AlaOBzl.
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Affiliation(s)
- Dae Heoun Baek
- Laboratory of Microbial Function, Korea Research Institute of Bioscience and Biotechnology, Yusong-Gu. BioLeaders Corporation, Joong-Gu, Daejeon, South Korea
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Cappiello M, Lazzarotti A, Buono F, Scaloni A, D'Ambrosio C, Amodeo P, Méndez BL, Pelosi P, Del Corso A, Mura U. New role for leucyl aminopeptidase in glutathione turnover. Biochem J 2004; 378:35-44. [PMID: 14583094 PMCID: PMC1223929 DOI: 10.1042/bj20031336] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2003] [Revised: 10/22/2003] [Accepted: 10/29/2003] [Indexed: 11/17/2022]
Abstract
A manganese-dependent cysteinyl-glycine hydrolysing activity has been purified to electrophoretic homogeneity from bovine lens. The characterization of the purified enzyme (molecular mass of the native protein, molecular mass of the subunit and extensive primary structure analysis) allowed the unequivocal attribution of the cysteinyl-glycine hydrolysing activity, which is usually associated with alanyl aminopeptidase (EC 3.4.11.2) or membrane-bound dipeptidase (EC 3.4.13.19), to LAP (leucyl aminopeptidase; EC 3.4.11.1). Analysis of the pH dependence of Cys-Gly hydrolysis catalysed by LAP, supported by a molecular modelling approach to the enzyme-substrate conformation, gave insights into the ability of the enzyme to recognize Cys-Gly as a substrate. Due to the effectiveness of LAP in hydrolysing Cys-Gly (K(m)=0.57 mM, kcat=6.0x10(3) min(-1) at pH 7.4 and 25 degrees C) with respect to other dipeptide substrates, a new role for this enzyme in glutathione turnover is proposed.
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Affiliation(s)
- Mario Cappiello
- Dipartimento di Fisiologia e Biochimica, Università di Pisa, via S. Maria 55, 56126 Pisa, Italy
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44
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Abstract
The structure of prolidase from the hyperthermophilic archaeon Pyrococcus furiosus (Pfprol) has been solved and refined at 2.0 A resolution. This is the first structure of a prolidase, i.e., a peptidase specific for dipeptides having proline as the second residue. The asymmetric unit of the crystals contains a homodimer of the enzyme. Each of the two protein subunits has two domains. The C-terminal domain includes the catalytic site, which is centered on a dinuclear metal cluster. In the as-isolated form of Pfprol, the active-site metal atoms are Co(II) [Ghosh, M., et al. (1998) J. Bacteriol. 180, 4781-9]. An unexpected finding is that in the crystalline enzyme the active-site metal atoms are Zn(II), presumably as a result of metal exchange during crystallization. Both of the Zn(II) atoms are five-coordinate. The ligands include a bridging water molecule or hydroxide ion, which is likely to act as a nucleophile in the catalytic reaction. The two-domain polypeptide fold of Pfprol is similar to the folds of two functionally related enzymes, aminopeptidase P (APPro) and creatinase. In addition, the catalytic C-terminal domain of Pfprol has a polypeptide fold resembling that of the sole domain of a fourth enzyme, methionine aminopeptidase (MetAP). The active sites of APPro and MetAP, like that of Pfprol, include a dinuclear metal center. The metal ligands in the three enzymes are homologous. Comparisons with the molecular structures of APPro and MetAP suggest how Pfprol discriminates against oligopeptides and in favor of Xaa-Pro substrates. The crystal structure of Pfprol was solved by multiple-wavelength anomalous dispersion. The crystals yielded diffraction data of relatively high quality and resolution, despite the fact that one of the two protein subunits in the asymmetric unit was found to be significantly disordered. The final R and R(free) values are 0.24 and 0.28, respectively.
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Affiliation(s)
- Megan J Maher
- School of Molecular and Microbial Biosciences, University of Sydney, New South Wales 2006, Australia
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Abstract
Peptidase-catalyzed formation of macrocyclic lactams on solid phase identifies ring systems that are favorably bound in the enzyme active site. We evaluated several cyclic peptide motifs linked by ester bonds between the P2 and P1' or the P1 and P2' side chains. The depsipeptide represented by structure 5 was readily generated by a variety of peptidases from precursor omega-amino acids or omega-amino esters. This strategy for identifying ring systems for potential macrocyclic transition state analogues was demonstrated with the serine peptidases trypsin and chymotrypsin, with the aspartic peptidase pepsin, and with the zinc peptidase thermolysin.
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Affiliation(s)
- Kristina K Hansen
- Center for New Directions in Organic Synthesis Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
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Jozic D, Kaiser JT, Huber R, Bode W, Maskos K. X-ray structure of isoaspartyl dipeptidase from E.coli: a dinuclear zinc peptidase evolved from amidohydrolases. J Mol Biol 2003; 332:243-56. [PMID: 12946361 DOI: 10.1016/s0022-2836(03)00845-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
L-aspartyl and L-asparaginyl residues in proteins spontaneously undergo intra-residue rearrangements forming isoaspartyl/beta-aspartyl residues linked through their side-chain beta-carboxyl group with the following amino acid. In order to avoid accumulation of isoaspartyl dipeptides left over from protein degradation, some bacteria have developed specialized isoaspartyl/beta-aspartyl zinc dipeptidases sequentially unrelated to other peptidases, which also poorly degrade alpha-aspartyl dipeptides. We have expressed and crystallized the 390 amino acid residue isoaspartyl dipeptidase (IadA) from E.coli, and have determined its crystal structure in the absence and presence of the phosphinic inhibitor Asp-Psi[PO(2)CH(2)]-LeuOH. This structure reveals an octameric particle of 422 symmetry, with each polypeptide chain organized in a (alphabeta)(8) TIM-like barrel catalytic domain attached to a U-shaped beta-sandwich domain. At the C termini of the beta-strands of the beta-barrel, the two catalytic zinc ions are surrounded by four His, a bridging carbamylated Lys and an Asp residue, which seems to act as a proton shuttle. A large beta-hairpin loop protruding from the (alphabeta)(8) barrel is disordered in the free peptidase, but forms a flap that stoppers the barrel entrance to the active center upon binding of the dipeptide mimic. This isoaspartyl dipeptidase shows strong topological homology with the alpha-subunit of the binickel-containing ureases, the dinuclear zinc dihydroorotases, hydantoinases and phosphotriesterases, and the mononuclear adenosine and cytosine deaminases, which all are catalyzing hydrolytic reactions at carbon or phosphorous centers. Thus, nature has adapted an existing fold with catalytic tools suitable for hydrolysis of amide bonds to the binding requirements of a peptidase.
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Affiliation(s)
- Daniela Jozic
- Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried, Germany
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Walmsley AR, Hooper NM. Glycosylation efficiency of Asn-Xaa-Thr sequons is independent of distance from the C-terminus in membrane dipeptidase. Glycobiology 2003; 13:641-6. [PMID: 12773476 DOI: 10.1093/glycob/cwg080] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In vitro transcription/translation studies with model proteins have shown that glycosylation of Asn-Xaa-Thr sequons is reduced when the sequon is within 60 residues of the C-terminus of the protein. We have previously shown that in living cells N-glycosylation of the prion protein (PrP) is also abolished when its Asn-Ile-Thr and Asn-Phe-Thr sequons are less than 60 residues from the C-terminus (Walmsley and Hooper [2003] Biochemical Journal, 370, 351-355). To investigate whether sequon distance to the C-terminus is a general determinant of N-glycosylation in living cells, Asn-Ile/Phe-Thr sequons were introduced into another glycosylphosphatidylinositol (GPI) anchored protein, membrane dipeptidase (MDP), at similar distances from the C-terminus as those in PrP. When expressed in the human neuroblastoma SH-SY5Y cell line, the introduced sequons were fully N-glycosylated even when they were less than 60 residues from the C-terminus in both GPI-anchored and secreted forms of MDP. These data demonstrate that the utilization of sequons in some proteins is independent of their distance from the C-terminus.
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Affiliation(s)
- Adrian R Walmsley
- School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
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Abstract
Much attention has recently been given to a class of proteases that cleave proteins and peptides after proline residues. This class includes dipeptidyl peptidase IV (DPP IV; also termed CD26), fibroblast activation protein alpha (FAP; seprase), DPP7 (DPP II; quiescent cell proline dipeptidase), DPP8, DPP9, and prolyl carboxypeptidase (PCP; angiotensinase C). More distant members include prolyl oligopeptidase (POP; post proline cleaving enzyme) and acylaminoacylpeptidase (AAP; acylpeptide hydrolase). The DPPs and related proteins contain both membrane-bound and soluble members and span a broad range of expression patterns, tissue distributions and compartmentalization. These proteins have important roles in regulation of signaling by peptide hormones, and are emerging targets for diabetes, oncology and other indications.
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Anissimova M, Yaouancq L, Noor F, Badet-Denisot MA, Badet B. New chromogenic dipeptide substrate for continuous assay of the D-alanyl-D-alanine dipeptidase VanX required for high-level vancomycin resistance. J Pept Res 2003; 62:88-95. [PMID: 12823621 DOI: 10.1034/j.1399-3011.2003.00072.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A direct continuous UV-Vis spectrophotometric assay has been developed for VanX, a D-alanyl-D-alanine aminodipeptidase necessary for vancomycin resistance. This method is based on the hydrolysis of the alternative substrate D-alanyl-alpha-(R)-phenylthio-glycine D-Ala-D-Gly(S-Ph)-OH (H-DAla-DPsg-OH, 5a). Spontaneous decomposition of the released phenylthioglycine generates thiophenol, which is quantified using Ellman's reagent. The dipeptide behaved as an excellent substrate of VanX, exhibiting Michaelis-Menten kinetics with a kcat of 76 +/- 5/s and a KM of 0.83 +/- 0.08 mm (kcat = 46 +/- 3/s and KM = 0.11 +/- 0.01 mm for D-Ala-D-Ala). Determination of the kinetic parameters of the previously reported mechanism-based inhibitor D-Ala-D-Gly(SPhip-CHF2)-OH (H-D-Ala-DPfg-OH, 5c) [Araoz, R., Anhalt, E., René, L., Badet-Denisot, M.-A., Courvalin, P. & Badet, B. (2000) Biochemistry 39, 15971-15979] using the substrate reported in the present study yielded values of Kirr of 22 +/- 1 microM and kinact of 9.3 +/- 0.4/min in good agreement with values previously obtained in our laboratory (Kirr = 30 +/- 1 mm; kinact = 7.3 +/- 0.3/min). In addition, inhibition by the competing substrate D-Ala-D-Ala resulted in determination of a Ki = 70 +/- 6 microM close to the previously reported KM value. These results demonstrate that the present assay is a convenient, rapid and sensitive tool in the search for VanX inhibitors.
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Affiliation(s)
- M Anissimova
- Institut de Chimie des Substances Naturelles, CNRS-UPR 2301, 91198 Gif-sur-Yvette, France
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50
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Abstract
Isoaspartyl dipeptidase from Escherichia coli functions in protein degradation by catalyzing the hydrolysis of beta-L-isoaspartyl linkages in dipeptides. The best substrate for the enzyme reported thus far is iso-Asp-Leu. Here we report the X-ray analysis of the enzyme in its resting state and complexed with aspartate to 1.65 and 2.1 A resolution, respectively. The quaternary structure of the enzyme is octameric and can be aptly described as a tetramer of dimers. Each subunit folds into two distinct domains: the N-terminal region containing eight strands of mixed beta-sheet and the C-terminal motif that is dominated by a (beta,alpha)(8)-barrel. A binuclear zinc center is located in each subunit at the C-terminal end of the (beta,alpha)(8)-barrel. Ligands to the binuclear metal center include His 68, His 70, His 201, His 230, and Asp 285. The two zincs are bridged by a carboxylated lysine residue (Lys 162) and a solvent molecule, most likely a hydroxide ion. The product of the reaction, aspartate, binds to the enzyme by displacing the bridging solvent with its side chain functional group. From this investigation it is proposed that the reaction mechanism of the enzyme proceeds through a tetrahedral intermediate and that the bridging solvent attacks the re face of the carbonyl carbon of the scissile peptide bond. This structural analysis confirms the placement of isoaspartyl dipeptidase into the urease-related amidohydrolase superfamily.
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Affiliation(s)
- James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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