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Gaonkar SK, Alvares JJ, Furtado IJ. Recent advances in the production, properties and applications of haloextremozymes protease and lipase from haloarchaea. World J Microbiol Biotechnol 2023; 39:322. [PMID: 37755613 DOI: 10.1007/s11274-023-03779-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 09/22/2023] [Indexed: 09/28/2023]
Abstract
Proteases and lipases are significant groups of enzymes for commercialization at the global level. Earlier, the industries depended on mesophilic proteases and lipases, which remain nonfunctional under extreme conditions. The discovery of extremophilic microorganisms, especially those belonging to haloarchaea, paved a new reserve of industrially competent extremozymes. Haloarchaea or halophilic archaea are polyextremophiles of domain Archaea that grow at high salinity, elevated temperature, pH range (pH 6-12), and low aw. Interestingly, haloarchaeal proteolytic and lipolytic enzymes also perform their catalytic function in the presence of 4-5 M NaCl in vivo and in vitro. Also, they are of great interest to study due to their capacity to function and are active at elevated temperatures, tolerance to pH extremes, and in non-aqueous media. In recent years, advances have been achieved in various aspects of genomic/molecular expression methods involving homologous and heterologous processes for the overproduction of these extremozymes and their characterization from haloarchaea. A few protease and lipase extremozymes have been successfully expressed in prokaryotic systems, especially E.coli, and enzyme modification techniques have improved the catalytic properties of the recombinant enzymes. Further, in-silico methods are currently applied to elucidate the structural and functional features of salt-stable protease and lipase in haloarchaea. In this review, the production and purification methods, catalytic and biochemical properties and biotechnological applications of haloextremozymes proteases and lipases are summarized along with recent advancements in overproduction and characterization of these enzymes, concluding with the directions for further in-depth research on proteases and lipases from haloarchaea.
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Affiliation(s)
- Sanket K Gaonkar
- Microbiology Programme, School of Biological Sciences and Biotechnology, Goa University, Taleigao Plateau, Goa, 403206, India.
- Department of Microbiology, P.E.S's R.S.N College of Arts and Science, Farmagudi, Ponda-Goa, 403401, India.
| | - Jyothi Judith Alvares
- Microbiology Programme, School of Biological Sciences and Biotechnology, Goa University, Taleigao Plateau, Goa, 403206, India
| | - Irene J Furtado
- Microbiology Programme, School of Biological Sciences and Biotechnology, Goa University, Taleigao Plateau, Goa, 403206, India
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2
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Dutoit R, Brandt N, Van Gompel T, Van Elder D, Van Dyck J, Sobott F, Droogmans L. M42 aminopeptidase catalytic site: the structural and functional role of a strictly conserved aspartate residue. Proteins 2020; 88:1639-1647. [PMID: 32673419 DOI: 10.1002/prot.25982] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/06/2020] [Accepted: 07/02/2020] [Indexed: 11/08/2022]
Abstract
The M42 aminopeptidases are a family of dinuclear aminopeptidases widely distributed in Prokaryotes. They are potentially associated to the proteasome, achieving complete peptide destruction. Their most peculiar characteristic is their quaternary structure, a tetrahedron-shaped particle made of twelve subunits. The catalytic site of M42 aminopeptidases is defined by seven conserved residues. Five of them are involved in metal ion binding which is important to maintain both the activity and the oligomeric state. The sixth conserved residue, a glutamate, is the catalytic base deprotonating the water molecule during peptide bond hydrolysis. The seventh residue is an aspartate whose function remains poorly understood. This aspartate residue, however, must have a critical role as it is strictly conserved in all MH clan enzymes. It forms some kind of catalytic triad with the histidine residue and the metal ion of the M2 binding site. We assess its role in TmPep1050, an M42 aminopeptidase of Thermotoga maritima, through a mutational approach. Asp-62 was substituted with alanine, asparagine, or glutamate residue. The Asp-62 substitutions completely abolished TmPep1050 activity and impeded dodecamer formation. They also interfered with metal ion binding as only one cobalt ion is bound per subunit instead of two. The structure of Asp62Ala variant was solved at 1.5 Å showing how the substitution has an impact on the active site fold. We propose a structural role for Asp-62, helping to stabilize a crucial loop in the active site and to position correctly the catalytic base and a metal ion ligand of the M1 site.
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Affiliation(s)
- Raphaël Dutoit
- Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, Brussels, Belgium.,Labiris Institut de Recherche, Brussels, Belgium
| | | | - Tom Van Gompel
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, Universiteit van Antwerpen, Antwerpen, Belgium
| | - Dany Van Elder
- Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, Brussels, Belgium
| | - Jeroen Van Dyck
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, Universiteit van Antwerpen, Antwerpen, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, Universiteit van Antwerpen, Antwerpen, Belgium.,Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - Louis Droogmans
- Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, Brussels, Belgium
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3
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P1' Residue-Oriented Virtual Screening for Potent and Selective Phosphinic (Dehydro) Dipeptide Inhibitors of Metallo-Aminopeptidases. Biomolecules 2020; 10:biom10040659. [PMID: 32344658 PMCID: PMC7225938 DOI: 10.3390/biom10040659] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/17/2020] [Accepted: 04/20/2020] [Indexed: 01/01/2023] Open
Abstract
Designing side chain substituents complementary to enzyme binding pockets is of great importance in the construction of potent and selective phosphinic dipeptide inhibitors of metallo-aminopeptidases. Proper structure selection makes inhibitor construction more economic, as the development process typically consists of multiple iterative preparation/bioassay steps. On the basis of these principles, using noncomplex computation and modeling methodologies, we comprehensively screened 900 commercial precursors of the P1′ residues of phosphinic dipeptide and dehydrodipeptide analogs to identify the most promising ligands of 52 metallo-dependent aminopeptidases with known crystal structures. The results revealed several nonproteinogenic residues with an improved energy of binding compared with the best known inhibitors. The data are discussed taking into account the selectivity and stereochemical implications of the enzymes. Using this approach, we were able to identify nontrivial structural elements substituting the recognized phosphinic peptidomimetic scaffold of metallo-aminopeptidase inhibitors.
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4
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Ma L, Zhao Y, Meng L, Wang X, Yi Y, Shan Y, Liu B, Zhou Y, Lü X. Isolation of Thermostable Lignocellulosic Bacteria From Chicken Manure Compost and a M42 Family Endocellulase Cloning From Geobacillus thermodenitrificans Y7. Front Microbiol 2020; 11:281. [PMID: 32174898 PMCID: PMC7054444 DOI: 10.3389/fmicb.2020.00281] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/07/2020] [Indexed: 01/01/2023] Open
Abstract
The composting ecosystem provides a potential resource for finding new microorganisms with the capability for cellulose degradation. In the present study, Congo red method was used for the isolating of thermostable lignocellulose-degrading bacteria from chicken manure compost. A thermophilic strain named as Geobacillus thermodenitrificans Y7 with acid-resident property was successfully isolated and employed to degrade raw switchgrass at 60°C for 5 days, which resulted in the final degradation rates of cellulose, xylan, and acid-insoluble lignin as 18.64, 12.96, and 17.21%, respectively. In addition, GC-MS analysis about aromatic degradation affirm the degradation of lignin by G. thermodenitrificans Y7. Moreover, an endocellulase gene belong to M42 family was successfully cloned from G. thermodenitrificans Y7 and expressed in Escherichia coli BL21. Recombinant enzyme Cel-9 was purified by Ni-NTA column based the His-tag, and the molecular weight determined as 40.4 kDa by SDA-PAGE. The characterization of the enzyme Cel-9 indicated that the maximum enzyme activity was realized at 50°C and pH 8.6 and, Mn2+ could greatly improve the CMCase enzyme activity of Cel-9 at 10 mM, which was followed by Fe2+ and Co2+. Besides, it also found that the β-1,3-1,4, β-1,3, β-1,4, and β-1,6 glucan linkages all could be hydrolyzed by enzyme Cel-9. Finally, during the application of enzyme Cel-9 to switchgrass, the saccharification rates achieved to 1.81 ± 0.04% and 2.65 ± 0.03% for 50 and 100% crude enzyme, respectively. All these results indicated that both the strain G. thermodenitrificans Y7 and the recombinant endocellulase Cel-9 have the potential to be applied to the biomass industry.
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Affiliation(s)
- Lingling Ma
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yuchun Zhao
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Limin Meng
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Xin Wang
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yanglei Yi
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yuanyuan Shan
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Bianfang Liu
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yuan Zhou
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Xin Lü
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
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5
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Bhat SY, Qureshi IA. Mutations of key substrate binding residues of leishmanial peptidase T alter its functional and structural dynamics. Biochim Biophys Acta Gen Subj 2020; 1864:129465. [DOI: 10.1016/j.bbagen.2019.129465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 10/15/2019] [Accepted: 10/24/2019] [Indexed: 11/27/2022]
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6
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Medvedev KE, Kinch LN, Schaeffer RD, Grishin NV. Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways. PLoS Comput Biol 2019; 15:e1007569. [PMID: 31869345 PMCID: PMC6957218 DOI: 10.1371/journal.pcbi.1007569] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 01/13/2020] [Accepted: 11/26/2019] [Indexed: 12/18/2022] Open
Abstract
Rossmann folds are ancient, frequently diverged domains found in many biological reaction pathways where they have adapted for different functions. Consequently, discernment and classification of their homologous relations and function can be complicated. We define a minimal Rossmann-like structure motif (RLM) that corresponds for the common core of known Rossmann domains and use this motif to identify all RLM domains in the Protein Data Bank (PDB), thus finding they constitute about 20% of all known 3D structures. The Evolutionary Classification of protein structure Domains (ECOD) classifies RLM domains in a number of groups that lack evidence for homology (X-groups), which suggests that they could have evolved independently multiple times. Closely related, homologous RLM enzyme families can diverge to bind different ligands using similar binding sites and to catalyze different reactions. Conversely, non-homologous RLM domains can converge to catalyze the same reactions or to bind the same ligand with alternate binding modes. We discuss a special case of such convergent evolution that is relevant to the polypharmacology paradigm, wherein the same drug (methotrexate) binds to multiple non-homologous RLM drug targets with different topologies. Finally, assigning proteins with RLM domain to the Enzyme Commission classification suggest that RLM enzymes function mainly in metabolism (and comprise 38% of reference metabolic pathways) and are overrepresented in extant pathways that represent ancient biosynthetic routes such as nucleotide metabolism, energy metabolism, and metabolism of amino acids. In fact, RLM enzymes take part in five out of eight enzymatic reactions of the Wood-Ljungdahl metabolic pathway thought to be used by the last universal common ancestor (LUCA). The prevalence of RLM domains in this ancient metabolism might explain their wide distribution among enzymes.
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Affiliation(s)
- Kirill E. Medvedev
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Lisa N. Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - R. Dustin Schaeffer
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nick V. Grishin
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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7
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Dutoit R, Van Gompel T, Brandt N, Van Elder D, Van Dyck J, Sobott F, Droogmans L. How metal cofactors drive dimer-dodecamer transition of the M42 aminopeptidase TmPep1050 of Thermotoga maritima. J Biol Chem 2019; 294:17777-17789. [PMID: 31611236 DOI: 10.1074/jbc.ra119.009281] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/24/2019] [Indexed: 11/06/2022] Open
Abstract
The M42 aminopeptidases are dinuclear aminopeptidases displaying a peculiar tetrahedron-shaped structure with 12 subunits. Their quaternary structure results from the self-assembly of six dimers controlled by their divalent metal ion cofactors. The oligomeric-state transition remains debated despite the structural characterization of several archaeal M42 aminopeptidases. The main bottleneck is the lack of dimer structures, hindering the understanding of structural changes occurring during the oligomerization process. We present the first dimer structure of an M42 aminopeptidase, TmPep1050 of Thermotoga maritima, along with the dodecamer structure. The comparison of both structures has allowed us to describe how the metal ion cofactors modulate the active-site fold and, subsequently, affect the interaction interface between dimers. A mutational study shows that the M1 site strictly controls dodecamer formation. The dodecamer structure of TmPep1050 also reveals that a part of the dimerization domain delimits the catalytic pocket and could participate in substrate binding.
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Affiliation(s)
- Raphaël Dutoit
- Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, B6041 Charleroi, Belgium .,Labiris Institut de Recherche, avenue Emile Gryzon 1, B1070 Brussels, Belgium
| | - Tom Van Gompel
- Biomolecular and Analytical Mass Spectrometry, Department of Chemistry, Universiteit van Antwerpen, Groenenborgerlaan 171, B2020 Antwerpen, Belgium
| | - Nathalie Brandt
- Labiris Institut de Recherche, avenue Emile Gryzon 1, B1070 Brussels, Belgium
| | - Dany Van Elder
- Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, B6041 Charleroi, Belgium
| | - Jeroen Van Dyck
- Biomolecular and Analytical Mass Spectrometry, Department of Chemistry, Universiteit van Antwerpen, Groenenborgerlaan 171, B2020 Antwerpen, Belgium
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry, Department of Chemistry, Universiteit van Antwerpen, Groenenborgerlaan 171, B2020 Antwerpen, Belgium.,Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Louis Droogmans
- Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, B6041 Charleroi, Belgium
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8
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Proteolytic systems of archaea: slicing, dicing, and mincing in the extreme. Emerg Top Life Sci 2018; 2:561-580. [PMID: 32953999 DOI: 10.1042/etls20180025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Archaea are phylogenetically distinct from bacteria, and some of their proteolytic systems reflect this distinction. Here, the current knowledge of archaeal proteolysis is reviewed as it relates to protein metabolism, protein homeostasis, and cellular regulation including targeted proteolysis by proteasomes associated with AAA-ATPase networks and ubiquitin-like modification. Proteases and peptidases that facilitate the recycling of peptides to amino acids as well as membrane-associated and integral membrane proteases are also reviewed.
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9
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Characterization of a Glycyl-Specific TET Aminopeptidase Complex from Pyrococcus horikoshii. J Bacteriol 2018; 200:JB.00059-18. [PMID: 29866801 DOI: 10.1128/jb.00059-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/29/2018] [Indexed: 01/03/2023] Open
Abstract
The TET peptidases are large self-compartmentalized complexes that form dodecameric particles. These metallopeptidases, members of the M42 family, are widely distributed in prokaryotes. Three different versions of TET complexes, with different substrate specificities, were found to coexist in the cytosol of the hyperthermophilic archaeon Pyrococcus horikoshii In the present work, we identified a novel type of TET complex that we named PhTET4. The recombinant PhTET4 enzyme was found to self-assemble as a tetrahedral edifice similar to other TET complexes. We determined PhTET4 substrate specificity using a broad range of monoacyl chromogenic and fluorogenic compounds. High-performance liquid chromatographic peptide degradation assays were also performed. These experiments demonstrated that PhTET4 is a strict glycyl aminopeptidase, devoid of amidolytic activity toward other types of amino acids. The catalytic efficiency of PhTET4 was studied under various conditions. The protein was found to be a hyperthermophilic alkaline aminopeptidase. Interestingly, unlike other peptidases from the same family, it was activated only by nickel ions.IMPORTANCE We describe here the first known peptidase displaying exclusive activity toward N-terminal glycine residues. This work indicates a specific role for intracellular glycyl peptidases in deep sea hyperthermophilic archaeal metabolism. These observations also provide critical evidence for the use of these archaeal extremozymes for biotechnological applications.
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Appolaire A, Colombo M, Basbous H, Gabel F, Girard E, Franzetti B. TET peptidases: A family of tetrahedral complexes conserved in prokaryotes. Biochimie 2015; 122:188-96. [PMID: 26546839 DOI: 10.1016/j.biochi.2015.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 11/02/2015] [Indexed: 11/26/2022]
Abstract
The TET peptidases are large polypeptide destruction machines present among prokaryotes. They form 12-subunits hollow tetrahedral particles, and belong to the family of M42 metallo-peptidases. Structural characterization of various archaeal and bacterial complexes has revealed a unique mechanism of internal compartmentalization and peptide trafficking that distinguishes them from the other oligomeric peptidases. Different versions of the TET complex often co-exist in the cytosol of microorganisms. In depth enzymatic studies have revealed that they are non-processive cobalt-activated aminopeptidases and display contrasting substrate specificities based on the properties of the catalytic chambers. Recent studies have shed light on the assembly mechanism of homo and hetero-dodecameric TET complexes and shown that the activity of TET aminopeptidase towards polypeptides is coupled with its assembly process. These findings suggested a functional regulation based on oligomerization control in vivo. This review describes a current knowledge on M42 TET peptidases biochemistry and discuss their possible physiological roles. This article is a part of the Special Issue entitled: «A potpourri of proteases and inhibitors: from molecular toolboxes to signalling scissors».
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Affiliation(s)
- Alexandre Appolaire
- CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - Matteo Colombo
- CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - Hind Basbous
- CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - Frank Gabel
- CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - E Girard
- CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - Bruno Franzetti
- CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France.
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11
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Slutskaya E, Artemova N, Kleymenov S, Petrova T, Popov V. Heat-induced conformational changes of TET peptidase from crenarchaeon Desulfurococcus kamchatkensis. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015. [PMID: 26219412 DOI: 10.1007/s00249-015-1064-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The effects of heating on the structure and stability of multimeric TET aminopeptidase (APDkam589) were studied by differential scanning calorimetry, tryptophan fluorescence quenching, and dynamic light scattering. Thermally induced structural changes in APDkam589 were found to occur in two phases: local conformational changes, which occur below 70 °C and are not associated with thermal denaturation of the protein, and global structural changes (above 70 °C) induced by irreversible thermal unfolding of the protein accompanied by its spontaneous aggregation. These results may explain the bell-shaped temperature dependence with a maximum at ~70 °C previously observed for enzymatic activity of APDkam589. Interestingly, the thermal unfolding of APDkam589 at about 81.2 °C is accompanied by a so-called blue-shift of about 10 nm-a shift of the Trp fluorescence spectrum toward shorter wavelength. From this point of view, APDkam589 is quite different from most proteins, which are characterized by a long wavelength shift of the spectrum ("red-shift") upon denaturation. The blue-shift of the Trp fluorescence spectrum reflects the changes in the environment of Trp residues, which becomes more hydrophobic upon denaturation. The molecular structure of APDkam589 was determined by X-ray diffraction. The monomer of APDkam589 has six Trp residues, five of which are on the external surface of the dodecamer. Therefore, the blue-shift of the Trp fluorescence spectrum can be explained, at least partly, by aggregation of APDkam589, which occurs simultaneously with its thermal denaturation and probably makes the environment of these Trp residues more hydrophobic.
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Affiliation(s)
- Elvira Slutskaya
- A.N. Bakh Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russian Federation.
| | - Natalia Artemova
- A.N. Bakh Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russian Federation
| | - Sergey Kleymenov
- A.N. Bakh Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russian Federation.,N.K. Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova str. 26, Moscow, 119334, Russian Federation
| | - Tatiana Petrova
- Institute of Mathematical Problems of Biology, RAS, Institutskaja str., 4, Pushchino, 142290, Russian Federation
| | - Vladimir Popov
- A.N. Bakh Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russian Federation.,Russian National Research Centre "Kurchatov Institute", Akademika Kurchatova sq. 1, Moscow, 123182, Russian Federation
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12
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Petrova TE, Slutskaya ES, Boyko KM, Sokolova OS, Rakitina TV, Korzhenevskiy DA, Gorbacheva MA, Bezsudnova EY, Popov VO. Structure of the dodecamer of the aminopeptidase APDkam598 from the archaeon Desulfurococcus kamchatkensis. Acta Crystallogr F Struct Biol Commun 2015; 71:277-85. [PMID: 25760701 PMCID: PMC4356302 DOI: 10.1107/s2053230x15000783] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 01/14/2015] [Indexed: 11/10/2022] Open
Abstract
The crystal structure of the aminopeptidase APDkam589 from the thermophilic crenarchaeon Desulfurococcus kamchatkensis was determined at a resolution of 3.0 Å. In the crystal, the monomer of APDkam589 and its symmetry-related monomers are densely packed to form a 12-subunit complex. Single-particle electron-microscopy analysis confirms that APDkam589 is present as a compact dodecamer in solution. The APDkam589 molecule is built similarly to the molecules of the PhTET peptidases, which have the highest sequence identity to APDkam589 among known structures and were isolated from the more thermostable archaeon Pyrococcus horikoshii. A comparison of the interactions of the subunits in APDkam589 with those in PhTET1, PhTET2 and PhTET3 reveals that APDkam589 has a much lower total number of salt bridges, which correlates with the lower thermostability of APDkam589. The monomer of APDkam589 has six Trp residues, five of which are on the external surface of the dodecamer. A superposition of the structure of APDkam589 with those having a high sequence similarity to APDkam589 reveals that, although the positions of Trp45, Trp252 and Trp358 are not conserved in the sequences, the spatial locations of the Trp residues in these models are similar.
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Affiliation(s)
- T. E. Petrova
- A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation
- Institute of Mathematical Problems of Biology, RAS, Institutskaja str. 4, Pushchino 142290, Russian Federation
| | - E. S. Slutskaya
- A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation
| | - K. M. Boyko
- A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation
- NRC ‘Kurchatov Institute’, Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation
| | - O. S. Sokolova
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/73, Moscow 119991, Russian Federation
| | - T. V. Rakitina
- NRC ‘Kurchatov Institute’, Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation
- Institute of Bioorganic Chemistry, RAS, Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - D. A. Korzhenevskiy
- NRC ‘Kurchatov Institute’, Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation
| | - M. A. Gorbacheva
- NRC ‘Kurchatov Institute’, Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation
| | - E. Y. Bezsudnova
- A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation
| | - V. O. Popov
- A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation
- NRC ‘Kurchatov Institute’, Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation
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13
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Appolaire A, Girard E, Colombo M, Durá MA, Moulin M, Härtlein M, Franzetti B, Gabel F. Small-angle neutron scattering reveals the assembly mode and oligomeric architecture of TET, a large, dodecameric aminopeptidase. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2983-93. [PMID: 25372688 PMCID: PMC4220976 DOI: 10.1107/s1399004714018446] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 08/13/2014] [Indexed: 01/10/2023]
Abstract
The specific self-association of proteins into oligomeric complexes is a common phenomenon in biological systems to optimize and regulate their function. However, de novo structure determination of these important complexes is often very challenging for atomic-resolution techniques. Furthermore, in the case of homo-oligomeric complexes, or complexes with very similar building blocks, the respective positions of subunits and their assembly pathways are difficult to determine using many structural biology techniques. Here, an elegant and powerful approach based on small-angle neutron scattering is applied, in combination with deuterium labelling and contrast variation, to elucidate the oligomeric organization of the quaternary structure and the assembly pathways of 468 kDa, hetero-oligomeric and symmetric Pyrococcus horikoshii TET2-TET3 aminopeptidase complexes. The results reveal that the topology of the PhTET2 and PhTET3 dimeric building blocks within the complexes is not casual but rather suggests that their quaternary arrangement optimizes the catalytic efficiency towards peptide substrates. This approach bears important potential for the determination of quaternary structures and assembly pathways of large oligomeric and symmetric complexes in biological systems.
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Affiliation(s)
- Alexandre Appolaire
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
| | - Eric Girard
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
| | - Matteo Colombo
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
| | - M. Asunción Durá
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
| | - Martine Moulin
- Life Sciences Group, Institut Laue–Langevin, 38042 Grenoble CEDEX 9, France
| | - Michael Härtlein
- Life Sciences Group, Institut Laue–Langevin, 38042 Grenoble CEDEX 9, France
| | - Bruno Franzetti
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
| | - Frank Gabel
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
- Large Scale Structures Group, Institut Laue–Langevin, 38042 Grenoble CEDEX 9, France
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14
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Appolaire A, Durá MA, Ferruit M, Andrieu JP, Godfroy A, Gribaldo S, Franzetti B. The TET2 and TET3 aminopeptidases fromPyrococcus horikoshiiform a hetero-subunit peptidasome with enhanced peptide destruction properties. Mol Microbiol 2014; 94:803-14. [DOI: 10.1111/mmi.12775] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Alexandre Appolaire
- Univ. Grenoble Alpes; Institut de Biologie Structurale (IBS); F-38027 Grenoble France
- CNRS, IBS; F-38027 Grenoble France
- CEA, DSV, IBS; F-38027 Grenoble France
| | - M. Asunción Durá
- Univ. Grenoble Alpes; Institut de Biologie Structurale (IBS); F-38027 Grenoble France
- CNRS, IBS; F-38027 Grenoble France
- CEA, DSV, IBS; F-38027 Grenoble France
| | - Mylène Ferruit
- Univ. Grenoble Alpes; Institut de Biologie Structurale (IBS); F-38027 Grenoble France
- CNRS, IBS; F-38027 Grenoble France
- CEA, DSV, IBS; F-38027 Grenoble France
| | - Jean-Pierre Andrieu
- Univ. Grenoble Alpes; Institut de Biologie Structurale (IBS); F-38027 Grenoble France
- CNRS, IBS; F-38027 Grenoble France
- CEA, DSV, IBS; F-38027 Grenoble France
| | - Anne Godfroy
- Ifremer, UMR6197; Laboratoire de Microbiologie des Environnements Extrêmes; 29280 Plouzané France
| | - Simonetta Gribaldo
- Institut Pasteur; Unité Biologie Moléculaire du Gène chez les Extremophiles; Département de Microbiologie; 75724 Paris Cedex 15 France
| | - Bruno Franzetti
- Univ. Grenoble Alpes; Institut de Biologie Structurale (IBS); F-38027 Grenoble France
- CNRS, IBS; F-38027 Grenoble France
- CEA, DSV, IBS; F-38027 Grenoble France
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15
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Biochemical Characterization of Deblocking Aminopeptidases from the Hyperthermophilic ArchaeonThermococcus kodakarensisKOD1. Biosci Biotechnol Biochem 2014; 75:1160-6. [DOI: 10.1271/bbb.110114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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Appolaire A, Rosenbaum E, Durá MA, Colombo M, Marty V, Savoye MN, Godfroy A, Schoehn G, Girard E, Gabel F, Franzetti B. Pyrococcus horikoshii TET2 peptidase assembling process and associated functional regulation. J Biol Chem 2013; 288:22542-54. [PMID: 23696647 PMCID: PMC3829341 DOI: 10.1074/jbc.m113.450189] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 05/13/2013] [Indexed: 11/06/2022] Open
Abstract
Tetrahedral (TET) aminopeptidases are large polypeptide destruction machines present in prokaryotes and eukaryotes. Here, the rules governing their assembly into hollow 12-subunit tetrahedrons are addressed by using TET2 from Pyrococcus horikoshii (PhTET2) as a model. Point mutations allowed the capture of a stable, catalytically active precursor. Small angle x-ray scattering revealed that it is a dimer whose architecture in solution is identical to that determined by x-ray crystallography within the fully assembled TET particle. Small angle x-ray scattering also showed that the reconstituted PhTET2 dodecameric particle displayed the same quaternary structure and thermal stability as the wild-type complex. The PhTET2 assembly intermediates were characterized by analytical ultracentrifugation, native gel electrophoresis, and electron microscopy. They revealed that PhTET2 assembling is a highly ordered process in which hexamers represent the main intermediate. Peptide degradation assays demonstrated that oligomerization triggers the activity of the TET enzyme toward large polypeptidic substrates. Fractionation experiments in Pyrococcus and Halobacterium cells revealed that, in vivo, the dimeric precursor co-exists together with assembled TET complexes. Taken together, our observations explain the biological significance of TET oligomerization and suggest the existence of a functional regulation of the dimer-dodecamer equilibrium in vivo.
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Affiliation(s)
- Alexandre Appolaire
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Eva Rosenbaum
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - M. Asunción Durá
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Matteo Colombo
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Vincent Marty
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Marjolaine Noirclerc Savoye
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Anne Godfroy
- the Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Guy Schoehn
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Eric Girard
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Frank Gabel
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Bruno Franzetti
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
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Dutoit R, Brandt N, Legrain C, Bauvois C. Functional characterization of two M42 aminopeptidases erroneously annotated as cellulases. PLoS One 2012; 7:e50639. [PMID: 23226342 PMCID: PMC3511314 DOI: 10.1371/journal.pone.0050639] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 10/23/2012] [Indexed: 11/18/2022] Open
Abstract
Several aminopeptidases of the M42 family have been described as tetrahedral-shaped dodecameric (TET) aminopeptidases. A current hypothesis suggests that these enzymes are involved, along with the tricorn peptidase, in degrading peptides produced by the proteasome. Yet the M42 family remains ill defined, as some members have been annotated as cellulases because of their homology with CelM, formerly described as an endoglucanase of Clostridium thermocellum. Here we describe the catalytic functions and substrate profiles CelM and of TmPep1050, the latter having been annotated as an endoglucanase of Thermotoga maritima. Both enzymes were shown to catalyze hydrolysis of nonpolar aliphatic L-amino acid-pNA substrates, the L-leucine derivative appearing as the best substrate. No significant endoglucanase activity was measured, either for TmPep1050 or CelM. Addition of cobalt ions enhanced the activity of both enzymes significantly, while both the chelating agent EDTA and bestatin, a specific inhibitor of metalloaminopeptidases, proved inhibitory. Our results strongly suggest that one should avoid annotating members of the M42 aminopeptidase family as cellulases. In an updated assessment of the distribution of M42 aminopeptidases, we found TET aminopeptidases to be distributed widely amongst archaea and bacteria. We additionally observed that several phyla lack both TET and tricorn. This suggests that other complexes may act downstream from the proteasome.
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Affiliation(s)
- Raphaël Dutoit
- Institut de Recherches Microbiologiques JM Wiame, Brussels, Belgium.
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18
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Chaikuad A, Pilka ES, De Riso A, von Delft F, Kavanagh KL, Vénien-Bryan C, Oppermann U, Yue WW. Structure of human aspartyl aminopeptidase complexed with substrate analogue: insight into catalytic mechanism, substrate specificity and M18 peptidase family. BMC STRUCTURAL BIOLOGY 2012; 12:14. [PMID: 22720794 PMCID: PMC3472314 DOI: 10.1186/1472-6807-12-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/29/2012] [Indexed: 11/13/2022]
Abstract
Backround Aspartyl aminopeptidase (DNPEP), with specificity towards an acidic amino acid at the N-terminus, is the only mammalian member among the poorly understood M18 peptidases. DNPEP has implicated roles in protein and peptide metabolism, as well as the renin-angiotensin system in blood pressure regulation. Despite previous enzyme and substrate characterization, structural details of DNPEP regarding ligand recognition and catalytic mechanism remain to be delineated. Results The crystal structure of human DNPEP complexed with zinc and a substrate analogue aspartate-β-hydroxamate reveals a dodecameric machinery built by domain-swapped dimers, in agreement with electron microscopy data. A structural comparison with bacterial homologues identifies unifying catalytic features among the poorly understood M18 enzymes. The bound ligands in the active site also reveal the coordination mode of the binuclear zinc centre and a substrate specificity pocket for acidic amino acids. Conclusions The DNPEP structure provides a molecular framework to understand its catalysis that is mediated by active site loop swapping, a mechanism likely adopted in other M18 and M42 metallopeptidases that form dodecameric complexes as a self-compartmentalization strategy. Small differences in the substrate binding pocket such as shape and positive charges, the latter conferred by a basic lysine residue, further provide the key to distinguishing substrate preference. Together, the structural knowledge will aid in the development of enzyme-/family-specific aminopeptidase inhibitors.
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Affiliation(s)
- Apirat Chaikuad
- Structural Genomics Consortium, Old Road Research Campus Building, Oxford OX3 7DQ, UK
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19
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Tomkowicz Z, Ostrovsky S, Foro S, Calvo-Perez V, Haase W. Magnetooptical and Structural Investigations of Five Dimeric Cobalt(II) Complexes Mimicking Metalloenzyme Active Sites. Inorg Chem 2012; 51:6046-55. [DOI: 10.1021/ic202529p] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Z. Tomkowicz
- Eduard-Zintl-Institute
of Inorganic and Physical Chemistry, Darmstadt University of Technology, Petersenstrasse 20, 64287
Darmstadt, Germany
- Institute of Physics, Jagiellonian University, Reymonta 4,
30-059 Kraków, Poland
| | - S. Ostrovsky
- Eduard-Zintl-Institute
of Inorganic and Physical Chemistry, Darmstadt University of Technology, Petersenstrasse 20, 64287
Darmstadt, Germany
- Institute of Applied
Physics, Academy of Sciences of Moldova, Academy str. 5, MD-2028 Chisinau, Moldova
| | - S. Foro
- Clemens-Schoepf-Institute
of Organic Chemistry and Biochemistry, Darmstadt University of Technology, Petersenstrasse 23, 64287
Darmstadt, Germany
| | - V. Calvo-Perez
- Facultad Ciencias
Químicas y Farmacéuticas, Universidad de Chile, Casilla 233, Santiago, Chile
| | - W. Haase
- Eduard-Zintl-Institute
of Inorganic and Physical Chemistry, Darmstadt University of Technology, Petersenstrasse 20, 64287
Darmstadt, Germany
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20
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Slutskaya ES, Bezsudnova EY, Mardanov AV, Gumerov VM, Rakitina TV, Popov VO, Lipkin VM. Characterization of a novel M42 aminopeptidase from crenarchaeon Desulfurococcus kamchatkensis. DOKL BIOCHEM BIOPHYS 2012; 442:30-2. [DOI: 10.1134/s1607672912010097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Indexed: 11/23/2022]
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21
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Rosenbaum E, Gabel F, Durá MA, Finet S, Cléry-Barraud C, Masson P, Franzetti B. Effects of hydrostatic pressure on the quaternary structure and enzymatic activity of a large peptidase complex from Pyrococcus horikoshii. Arch Biochem Biophys 2011; 517:104-10. [PMID: 21896270 DOI: 10.1016/j.abb.2011.07.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 07/31/2011] [Indexed: 10/17/2022]
Abstract
While molecular adaptation to high temperature has been extensively studied, the effect of hydrostatic pressure on protein structure and enzymatic activity is still poorly understood. We have studied the influence of pressure on both the quaternary structure and enzymatic activity of the dodecameric TET3 peptidase from Pyrococcus horikoshii. Small angle X-ray scattering (SAXS) revealed a high robustness of the oligomer under high pressure of up to 300 MPa at 25°C as well as at 90°C. The enzymatic activity of TET3 was enhanced by pressure up to 180 MPa. From the pressure behavior of the different rate-constants we have determined the volume changes associated with substrate binding and catalysis. Based on these results we propose that a change in the rate-limiting step occurs around 180 MPa.
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Affiliation(s)
- Eva Rosenbaum
- Group Extremophiles and Large Molecular Assemblies (ELMA), CEA, Institut de Biologie Structurale, Grenoble, France
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22
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Kumaki Y, Ogawa M, Hirano T, Yoshikawa K, Iwasawa N, Yagi T, Hakamata W, Oku T, Nishio T. Family M42 aminopeptidase from the syntrophic bacterium Symbiobacterium thermophilum: Characterization using recombinant protein. J Biosci Bioeng 2011; 111:134-9. [DOI: 10.1016/j.jbiosc.2010.09.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/20/2010] [Accepted: 09/22/2010] [Indexed: 10/18/2022]
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23
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Studies on the parameters controlling the stability of the TET peptidase superstructure from Pyrococcus horikoshii revealed a crucial role of pH and catalytic metals in the oligomerization process. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:1289-94. [PMID: 21130903 DOI: 10.1016/j.bbapap.2010.11.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 11/03/2010] [Accepted: 11/24/2010] [Indexed: 11/21/2022]
Abstract
The TET proteases from Pyrococcus horikoshii are metallopeptidases that form large dodecameric particles with high thermal stability. The influence of various physico-chemical parameters on PhTET3 quaternary structure was investigated. Analytical ultracentrifugation and biochemical analyses showed that the PhTET3 quaternary structure and enzymatic activity are maintained in high salt and that the complex is stable under extreme acidic conditions. Under basic pH conditions the complex disassembled into a low molecular weight species that was identified as folded dimer. Metal analyses showed that the purified enzyme only contains two equivalent of zinc per monomer, corresponding to the metal ions responsible for catalytic activity. When these metals were removed by EDTA treatment, the complex dissociated into the same dimeric species as those observed at high pH. Dodecameric TET particles were obtained from the metal free dimers when 2mM of divalent ions were added to the protein samples. Most of the dimers remained assembled at high temperature. Thus, we have shown that dimers are the building units in the TET oligomerization pathway and that the active site metals are essential in this process.
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24
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Structural basis for the substrate specificity of PepA from Streptococcus pneumoniae, a dodecameric tetrahedral protease. Biochem Biophys Res Commun 2010; 391:431-6. [DOI: 10.1016/j.bbrc.2009.11.075] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Accepted: 11/10/2009] [Indexed: 11/18/2022]
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25
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Structure, Assembly, and Mechanism of a PLP-Dependent Dodecameric l-Aspartate β-Decarboxylase. Structure 2009; 17:517-29. [DOI: 10.1016/j.str.2009.02.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Revised: 02/05/2009] [Accepted: 02/18/2009] [Indexed: 11/17/2022]
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26
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Shaikh TR, Gao H, Baxter WT, Asturias FJ, Boisset N, Leith A, Frank J. SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nat Protoc 2009; 3:1941-74. [PMID: 19180078 DOI: 10.1038/nprot.2008.156] [Citation(s) in RCA: 353] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol describes the reconstruction of biological molecules from the electron micrographs of single particles. Computation here is performed using the image-processing software SPIDER and can be managed using a graphical user interface, termed the SPIDER Reconstruction Engine. Two approaches are described to obtain an initial reconstruction: random-conical tilt and common lines. Once an existing model is available, reference-based alignment can be used, a procedure that can be iterated. Also described is supervised classification, a method to look for homogeneous subsets when multiple known conformations of the molecule may coexist.
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Affiliation(s)
- Tanvir R Shaikh
- Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, USA
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27
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Durá MA, Rosenbaum E, Larabi A, Gabel F, Vellieux FMD, Franzetti B. The structural and biochemical characterizations of a novel TET peptidase complex from Pyrococcus horikoshii reveal an integrated peptide degradation system in hyperthermophilic Archaea. Mol Microbiol 2009; 72:26-40. [DOI: 10.1111/j.1365-2958.2009.06600.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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28
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Delfosse V, Girard E, Birck C, Delmarcelle M, Delarue M, Poch O, Schultz P, Mayer C. Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family. PLoS One 2009; 4:e4712. [PMID: 19266066 PMCID: PMC2651629 DOI: 10.1371/journal.pone.0004712] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2009] [Accepted: 01/28/2009] [Indexed: 11/18/2022] Open
Abstract
Self-compartmentalizing proteases orchestrate protein turnover through an original architecture characterized by a central catalytic chamber. Here we report the first structure of an archaeal member of a new self-compartmentalizing protease family forming a cubic-shaped octamer with D4 symmetry and referred to as CubicO. We solved the structure of the Pyrococcus abyssi Pab87 protein at 2.2 Å resolution using the anomalous signal of the high-phasing-power lanthanide derivative Lu-HPDO3A. A 20 Å wide channel runs through this supramolecular assembly of 0.4 MDa, giving access to a 60 Å wide central chamber holding the eight active sites. Surprisingly, activity assays revealed that Pab87 degrades specifically d-amino acid containing peptides, which have never been observed in archaea. Genomic context of the Pab87 gene showed that it is surrounded by genes involved in the amino acid/peptide transport or metabolism. We propose that CubicO proteases are involved in the processing of d-peptides from environmental origins.
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Affiliation(s)
- Vanessa Delfosse
- Centre de Recherche des Cordeliers, LRMA, INSERM UMR-S 872, Université Pierre et Marie Curie, Paris, France
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29
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Seiradake E, Henaff D, Wodrich H, Billet O, Perreau M, Hippert C, Mennechet F, Schoehn G, Lortat-Jacob H, Dreja H, Ibanes S, Kalatzis V, Wang JP, Finberg RW, Cusack S, Kremer EJ. The cell adhesion molecule "CAR" and sialic acid on human erythrocytes influence adenovirus in vivo biodistribution. PLoS Pathog 2009; 5:e1000277. [PMID: 19119424 PMCID: PMC2607015 DOI: 10.1371/journal.ppat.1000277] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Accepted: 12/17/2008] [Indexed: 01/20/2023] Open
Abstract
Although it has been known for 50 years that adenoviruses (Ads) interact with erythrocytes ex vivo, the molecular and structural basis for this interaction, which has been serendipitously exploited for diagnostic tests, is unknown. In this study, we characterized the interaction between erythrocytes and unrelated Ad serotypes, human 5 (HAd5) and 37 (HAd37), and canine 2 (CAV-2). While these serotypes agglutinate human erythrocytes, they use different receptors, have different tropisms and/or infect different species. Using molecular, biochemical, structural and transgenic animal-based analyses, we found that the primary erythrocyte interaction domain for HAd37 is its sialic acid binding site, while CAV-2 binding depends on at least three factors: electrostatic interactions, sialic acid binding and, unexpectedly, binding to the coxsackievirus and adenovirus receptor (CAR) on human erythrocytes. We show that the presence of CAR on erythrocytes leads to prolonged in vivo blood half-life and significantly reduced liver infection when a CAR-tropic Ad is injected intravenously. This study provides i) a molecular and structural rationale for Ad-erythrocyte interactions, ii) a basis to improve vector-mediated gene transfer and iii) a mechanism that may explain the biodistribution and pathogenic inconsistencies found between human and animal models.
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Affiliation(s)
- Elena Seiradake
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France
| | - Daniel Henaff
- Institut de Génétique Moléculaire de Montpellier, CNRS 5535, Montpellier, France
- Universitiés Montpellier I & II, Montpellier, France
| | - Harald Wodrich
- Institut de Génétique Moléculaire de Montpellier, CNRS 5535, Montpellier, France
- Universitiés Montpellier I & II, Montpellier, France
| | - Olivier Billet
- Institut de Génétique Moléculaire de Montpellier, CNRS 5535, Montpellier, France
- Universitiés Montpellier I & II, Montpellier, France
| | - Matthieu Perreau
- Institut de Génétique Moléculaire de Montpellier, CNRS 5535, Montpellier, France
- Universitiés Montpellier I & II, Montpellier, France
| | - Claire Hippert
- Institut de Génétique Moléculaire de Montpellier, CNRS 5535, Montpellier, France
- Universitiés Montpellier I & II, Montpellier, France
| | - Franck Mennechet
- Institut de Génétique Moléculaire de Montpellier, CNRS 5535, Montpellier, France
- Universitiés Montpellier I & II, Montpellier, France
| | - Guy Schoehn
- Unit of Virus-Host Cell Interactions, UMR 5233, UJF-EMBL-CNRS, Grenoble, France
| | | | - Hanna Dreja
- Institut de Génétique Moléculaire de Montpellier, CNRS 5535, Montpellier, France
- Universitiés Montpellier I & II, Montpellier, France
| | - Sandy Ibanes
- Institut de Génétique Moléculaire de Montpellier, CNRS 5535, Montpellier, France
- Universitiés Montpellier I & II, Montpellier, France
| | - Vasiliki Kalatzis
- Institut de Génétique Moléculaire de Montpellier, CNRS 5535, Montpellier, France
- Universitiés Montpellier I & II, Montpellier, France
| | - Jennifer P. Wang
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Robert W. Finberg
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France
- Unit of Virus-Host Cell Interactions, UMR 5233, UJF-EMBL-CNRS, Grenoble, France
- * E-mail: (SC); (EJK)
| | - Eric J. Kremer
- Institut de Génétique Moléculaire de Montpellier, CNRS 5535, Montpellier, France
- Universitiés Montpellier I & II, Montpellier, France
- * E-mail: (SC); (EJK)
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Frankenstein Z, Sperling J, Sperling R, Eisenstein M. FitEM2EM--tools for low resolution study of macromolecular assembly and dynamics. PLoS One 2008; 3:e3594. [PMID: 18974836 PMCID: PMC2572833 DOI: 10.1371/journal.pone.0003594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 10/09/2008] [Indexed: 11/19/2022] Open
Abstract
Studies of the structure and dynamics of macromolecular assemblies often involve comparison of low resolution models obtained using different techniques such as electron microscopy or atomic force microscopy. We present new computational tools for comparing (matching) and docking of low resolution structures, based on shape complementarity. The matched or docked objects are represented by three dimensional grids where the value of each grid point depends on its position with regard to the interior, surface or exterior of the object. The grids are correlated using fast Fourier transformations producing either matches of related objects or docking models depending on the details of the grid representations. The procedures incorporate thickening and smoothing of the surfaces of the objects which effectively compensates for differences in the resolution of the matched/docked objects, circumventing the need for resolution modification. The presented matching tool FitEM2EMin successfully fitted electron microscopy structures obtained at different resolutions, different conformers of the same structure and partial structures, ranking correct matches at the top in every case. The differences between the grid representations of the matched objects can be used to study conformation differences or to characterize the size and shape of substructures. The presented low-to-low docking tool FitEM2EMout ranked the expected models at the top.
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Affiliation(s)
- Ziv Frankenstein
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Joseph Sperling
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Miriam Eisenstein
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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Abstract
There are more than 100 known adenovirus (AdV) serotypes, including 50 human serotypes. Because AdV-induced disease is relatively species specific, vectors derived from nonhuman serotypes may have wider clinical potential based, in part, on the lack of ubiquitous memory immunity. Whereas a few of the human serotype capsids have been studied at the structural level, none of the nonhuman serotypes has been analyzed. The basis laid by the analysis of human AdV (hAdV) has allowed us to determine and compare the three-dimensional structure of the capsid of canine serotype 2 (CAV-2) to that of hAdV serotype 5 (hAdV-5). We show that CAV-2 capsid has a smoother structure than the human serotypes. Many of the external loops found in the hAdV-5 penton base and the hexon, against which the antibody response is directed, are shorter or absent in CAV-2. On the other hand, the CAV-2 fiber appears to be more complex, with two bends in the shaft. An interesting difference between the human and canine viruses is that the C-terminal part of protein IX is in a different position, making an antenna sticking out of the CAV-2 capsid. The comparison between the two viruses allows the identification of sites that should be easy to modify on the CAV-2 capsid for altering tissue tropism or other biological activities.
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