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Tort O, Tanco S, Rocha C, Bièche I, Seixas C, Bosc C, Andrieux A, Moutin MJ, Avilés FX, Lorenzo J, Janke C. The cytosolic carboxypeptidases CCP2 and CCP3 catalyze posttranslational removal of acidic amino acids. Mol Biol Cell 2014; 25:3017-27. [PMID: 25103237 PMCID: PMC4230590 DOI: 10.1091/mbc.e14-06-1072] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The posttranslational modification of tubulin plays an important role in regulating microtubule function. Enzymes responsible for deglutamylating tubulin are members of a family of cytosolic carboxypeptidases. By completing the functional characterization of this protein family in mammals, it is demonstrated that CCP2 and CCP3 are deglutamylases. The posttranslational modification of carboxy-terminal tails of tubulin plays an important role in the regulation of the microtubule cytoskeleton. Enzymes responsible for deglutamylating tubulin have been discovered within a novel family of mammalian cytosolic carboxypeptidases. The discovery of these enzymes also revealed the existence of a range of other substrates that are enzymatically deglutamylated. Only four of six mammalian cytosolic carboxypeptidases had been enzymatically characterized. Here we complete the functional characterization of this protein family by demonstrating that CCP2 and CCP3 are deglutamylases, with CCP3 being able to hydrolyze aspartic acids with similar efficiency. Deaspartylation is a novel posttranslational modification that could, in conjunction with deglutamylation, broaden the range of potential substrates that undergo carboxy-terminal processing. In addition, we show that CCP2 and CCP3 are highly regulated proteins confined to ciliated tissues. The characterization of two novel enzymes for carboxy-terminal protein modification provides novel insights into the broadness of this barely studied process.
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Affiliation(s)
- Olivia Tort
- Institut de Biotecnologia i de Biomedicina, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain Institut Curie, 91405 Orsay, France
| | - Sebastián Tanco
- Institut de Biotecnologia i de Biomedicina, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Cecilia Rocha
- Institut Curie, 91405 Orsay, France PSL Research University, 75005 Paris, France Centre National de la Recherche Scientifique, UMR3306, 91405 Orsay, France Institut National de la Santé et de la Recherche Médicale, U1005, 91405 Orsay, France
| | - Ivan Bièche
- PSL Research University, 75005 Paris, France Department of Genetics, Institut Curie, 75248 Paris, France
| | - Cecilia Seixas
- Centro de Estudos de Doenças Crónicas, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1169-056 Lisbon, Portugal
| | - Christophe Bosc
- Institut des Neurosciences de Grenoble, Institut National de la Santé et de la Recherche Médicale, U836, CEA, Université Joseph Fourier, 38042 Grenoble, France Université Grenoble Alpes, 38000 Grenoble, France CEA, Institut de Recherches en Technologies et Sciences pour le Vivant, 38000 Grenoble, France
| | - Annie Andrieux
- Institut des Neurosciences de Grenoble, Institut National de la Santé et de la Recherche Médicale, U836, CEA, Université Joseph Fourier, 38042 Grenoble, France Université Grenoble Alpes, 38000 Grenoble, France CEA, Institut de Recherches en Technologies et Sciences pour le Vivant, 38000 Grenoble, France
| | - Marie-Jo Moutin
- Institut des Neurosciences de Grenoble, Institut National de la Santé et de la Recherche Médicale, U836, CEA, Université Joseph Fourier, 38042 Grenoble, France Université Grenoble Alpes, 38000 Grenoble, France CEA, Institut de Recherches en Technologies et Sciences pour le Vivant, 38000 Grenoble, France
| | - Francesc Xavier Avilés
- Institut de Biotecnologia i de Biomedicina, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Julia Lorenzo
- Institut de Biotecnologia i de Biomedicina, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Carsten Janke
- Institut Curie, 91405 Orsay, France PSL Research University, 75005 Paris, France Centre National de la Recherche Scientifique, UMR3306, 91405 Orsay, France Institut National de la Santé et de la Recherche Médicale, U1005, 91405 Orsay, France
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Alonso-del-Rivero M, Trejo SA, Reytor ML, Rodriguez-de-la-Vega M, Delfin J, Diaz J, González-González Y, Canals F, Chavez MA, Aviles FX. Tri-domain bifunctional inhibitor of metallocarboxypeptidases A and serine proteases isolated from marine annelid Sabellastarte magnifica. J Biol Chem 2012; 287:15427-38. [PMID: 22411994 DOI: 10.1074/jbc.m111.337261] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This study describes a novel bifunctional metallocarboxypeptidase and serine protease inhibitor (SmCI) isolated from the tentacle crown of the annelid Sabellastarte magnifica. SmCI is a 165-residue glycoprotein with a molecular mass of 19.69 kDa (mass spectrometry) and 18 cysteine residues forming nine disulfide bonds. Its cDNA was cloned and sequenced by RT-PCR and nested PCR using degenerated oligonucleotides. Employing this information along with data derived from automatic Edman degradation of peptide fragments, the SmCI sequence was fully characterized, indicating the presence of three bovine pancreatic trypsin inhibitor/Kunitz domains and its high homology with other Kunitz serine protease inhibitors. Enzyme kinetics and structural analyses revealed SmCI to be an inhibitor of human and bovine pancreatic metallocarboxypeptidases of the A-type (but not B-type), with nanomolar K(i) values. SmCI is also capable of inhibiting bovine pancreatic trypsin, chymotrypsin, and porcine pancreatic elastase in varying measures. When the inhibitor and its nonglycosylated form (SmCI N23A mutant) were overproduced recombinantly in a Pichia pastoris system, they displayed the dual inhibitory properties of the natural form. Similarly, two bi-domain forms of the inhibitor (recombinant rSmCI D1-D2 and rSmCI D2-D3) as well as its C-terminal domain (rSmCI-D3) were also overproduced. Of these fragments, only the rSmCI D1-D2 bi-domain retained inhibition of metallocarboxypeptidase A but only partially, indicating that the whole tri-domain structure is required for such capability in full. SmCI is the first proteinaceous inhibitor of metallocarboxypeptidases able to act as well on another mechanistic class of proteases (serine-type) and is the first of this kind identified in nature.
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Affiliation(s)
- Maday Alonso-del-Rivero
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de la Habana, 10400 La Habana, Cuba
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Alonso-del-Rivero M, Trejo SA, Rodríguez de la Vega M, González Y, Bronsoms S, Canals F, Delfín J, Diaz J, Aviles FX, Chávez MA. A novel metallocarboxypeptidase-like enzyme from the marine annelid Sabellastarte magnifica--a step into the invertebrate world of proteases. FEBS J 2009; 276:4875-90. [PMID: 19694804 DOI: 10.1111/j.1742-4658.2009.07187.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
After screening 25 marine invertebrates, a novel metallocarboxypeptidase (SmCP) has been identified by activity and MS analytical approaches, and isolated from the marine annelid Sabellastarte magnifica. The enzyme, which is a minor component of the molecularly complex animal body, as shown by 2D gel electrophoresis, has been purified from crude extracts to homogeneity by affinity chromatography on potato carboxypeptidase inhibitor and by ion exchange chromatography. SmCP is a protease of 33792 Da, displaying N-terminal and internal sequence homologies with M14 metallocarboxypeptidase-like enzymes, as determined by MS and automated Edman degradation. The enzyme contains one atom of Zn per molecule, is activated by Ca2+ and is drastically inhibited by the metal chelator 1,10-phenanthroline, as well as by excess Zn2+ or Cu2+, but moderately so by EDTA. SmCP is also strongly inhibited by specific inhibitors of metallocarboxypeptidases, such as benzylsuccinic acid and the protein inhibitors found in potato and leech (i.e. recombinant forms, both at nanomolar levels). The enzyme displays high peptidase efficiency towards pancreatic carboxypeptidase-A synthetic substrates, such as those with hydrophobic residues at the C-terminus but, remarkably, also towards the acidic ones. This property, previously described as for carboxypeptidase O-like activity, has been shown on long peptide substrates by MS. The results obtained in the present study indicate that SmCP is a novel member of the M14 metallocarboxypeptidases family (assignable to the M14A or pancreatic-like subfamily) with a wider specificity that has not been described previously.
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Mammalian metallopeptidase inhibition at the defense barrier of Ascaris parasite. Proc Natl Acad Sci U S A 2009; 106:1743-7. [PMID: 19179285 DOI: 10.1073/pnas.0812623106] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Roundworms of the genus Ascaris are common parasites of the human gastrointestinal tract. A battery of selective inhibitors protects them from host enzymes and the immune system. Here, a metallocarboxypeptidase (MCP) inhibitor, ACI, was identified in protein extracts from Ascaris by intensity-fading MALDI-TOF mass spectrometry. The 67-residue amino acid sequence of ACI showed no significant homology with any known protein. Heterologous overexpression and purification of ACI rendered a functional molecule with nanomolar equilibrium dissociation constants against MCPs, which denoted a preference for digestive and mast cell A/B-type MCPs. Western blotting and immunohistochemistry located ACI in the body wall, intestine, female reproductive tract, and fertilized eggs of Ascaris, in accordance with its target specificity. The crystal structure of the complex of ACI with human carboxypeptidase A1, one of its potential targets in vivo, revealed a protein with a fold consisting of two tandem homologous domains, each containing a beta-ribbon and two disulfide bonds. These domains are connected by an alpha-helical segment and a fifth disulfide bond. Binding and inhibition are exerted by the C-terminal tail, which enters the funnel-like active-site cavity of the enzyme and approaches the catalytic zinc ion. The findings reported provide a basis for the biological function of ACI, which may be essential for parasitic survival during infection.
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Pantoja-Uceda D, Arolas JL, García P, López-Hernández E, Padró D, Aviles FX, Blanco FJ. The NMR Structure and Dynamics of the Two-Domain Tick Carboxypeptidase Inhibitor Reveal Flexibility in Its Free Form and Stiffness upon Binding to Human Carboxypeptidase B. Biochemistry 2008; 47:7066-78. [DOI: 10.1021/bi800403m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David Pantoja-Uceda
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
| | - Joan L. Arolas
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
| | - Pascal García
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
| | - Eva López-Hernández
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
| | - Daniel Padró
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
| | - Francesc X. Aviles
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
| | - Francisco J. Blanco
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
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Lyons PJ, Callaway MB, Fricker LD. Characterization of carboxypeptidase A6, an extracellular matrix peptidase. J Biol Chem 2008; 283:7054-63. [PMID: 18178555 DOI: 10.1074/jbc.m707680200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carboxypeptidase A6 (CPA6) is a member of the M14 metallocarboxypeptidase family that is highly expressed in the adult mouse olfactory bulb and broadly expressed in embryonic brain and other tissues. A disruption in the human CPA6 gene is linked to Duane syndrome, a defect in the abducens nerve/lateral rectus muscle connection. In this study the cellular distribution, processing, and substrate specificity of human CPA6 were investigated. The 50-kDa pro-CPA6 is routed through the constitutive secretory pathway, processed by furin or a furin-like enzyme into the 37-kDa active form, and secreted into the extracellular matrix. CPA6 cleaves the C-terminal residue from a range of substrates, including small synthetic substrates, larger peptides, and proteins. CPA6 has a preference for large hydrophobic C-terminal amino acids as well as histidine. Peptides with a penultimate glycine or proline are very poorly cleaved. Several neuropeptides were found to be processed by CPA6, including Met- and Leu-enkephalin, angiotensin I, and neurotensin. Whereas CPA6 converts enkephalin and neurotensin into forms known to be inactive toward their receptors, CPA6 converts inactive angiotensin I into the biologically active angiotensin II. Taken together, these data suggest a role for CPA6 in the regulation of neuropeptides in the extracellular environment within the olfactory bulb and other parts of the brain.
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Affiliation(s)
- Peter J Lyons
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Fernández D, Vendrell J, Avilés FX, Fernández-Recio J. Structural and functional characterization of binding sites in metallocarboxypeptidases based on Optimal Docking Area analysis. Proteins 2007; 68:131-44. [PMID: 17407161 DOI: 10.1002/prot.21390] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The metallocarboxypeptidases (MCPs) belonging to the clan MC were studied by the Optimal Docking Area (ODA) method to evaluate protein-protein binding sites and to provide a basis for the identification of binding partners for this class of enzymes. The ODA method identifies surface patches with optimal desolvation energy based on the selection of low-energy docking regions, generated from a set of surface points around the protein. With few exceptions, the ODA method identified surface patches with a significant low-energy docking surface for all the MCPs with known three-dimensional structure. Overall, in 14 out of 24 cases, the detected ODA patches were correctly located (i.e. more than 50% of the predicted residues were in known protein-protein binding sites), yielding a global success rate of 58%. More specifically, the success rate increased up to 80% on the ODA patches detected for the catalytic domains of the M14A subfamily, independently on the partner. Interestingly, the ODA residues on the catalytic domain were correctly located in the interface with the N-terminal pro domain in all MCPs. The spatial distribution of the ODA patches for the different members of the family is in relation to the origin and function of the particular MCP, which allowed distinguishing between them. In good agreement with the experimentally characterized protein interfaces, the total average surface area of the theoretically derived ODA patches for the catalytic domain of MCPs is around 1700 A2 and their content in hydrophobic residues is about 40%. As a particular case, the average surface area of the ODA patches in MCPs of crop insect pests is about twice that of the MCPs of vertebrates, which might be related to their particular function. We recognized two binding regions for the catalytic domain of the MCPs, one of them accounting for nearly all the known intermolecular interactions made up by the enzymes. Protein inhibitors seem to have evolved to dock on this subset of ODA patches, evoking the binding mode of the N-terminal pro domains. The second binding region detected, for which no ligands have been identified so far, seems to be related to the acquisition/maintenance of the native structure of the peptidase. Overall, the ODA method has been successful in identifying low-energy docking areas in a set of structurally and functionally related proteins, suggesting that it can be easily extended to other families in the search for protein-protein binding sites and for their functional significance.
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Affiliation(s)
- Daniel Fernández
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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