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Lioe TS, Xie Z, Wu J, Li W, Sun L, Feng Q, Sekar R, Tefsen B, Ruiz-Carrillo D. The Mycobacterium tuberculosis prolyl dipeptidyl peptidase cleaves the N-terminal peptide of the immunoprotein CXCL-10. Biol Chem 2023; 404:633-643. [PMID: 36632703 DOI: 10.1515/hsz-2022-0265] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023]
Abstract
Dipeptidyl peptidases constitute a class of non-classical serine proteases that regulate an array of biological functions, making them pharmacologically attractive enzymes. With this work, we identified and characterized a dipeptidyl peptidase from Mycobacterium tuberculosis (MtDPP) displaying a strong preference for proline residues at the P1 substrate position and an unexpectedly high thermal stability. MtDPP was also characterized with alanine replacements of residues of its active site that yielded, for the most part, loss of catalysis. We show that MtDPP catalytic activity is inhibited by well-known human DPP4 inhibitors. Using MALDI-TOF mass spectrometry we also describe that in vitro, MtDPP mediates the truncation of the C-X-C motif chemokine ligand 10, indicating a plausible role in immune modulation for this mycobacterial enzyme.
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Affiliation(s)
- Trillion Surya Lioe
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, Jiangsu 215123, P. R. China
| | - Ziwen Xie
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, Jiangsu 215123, P. R. China
| | - Jianfang Wu
- Department of Chemistry, School of Science, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, Jiangsu 215123, P. R. China
| | - Wenlong Li
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, Jiangsu 215123, P. R. China
| | - Li Sun
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, Jiangsu 215123, P. R. China
| | - Qiaoli Feng
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, Jiangsu 215123, P. R. China
| | - Raju Sekar
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, Jiangsu 215123, P. R. China
| | - Boris Tefsen
- Ronin Institute, Montclair, NJ 07043, USA.,Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - David Ruiz-Carrillo
- European Molecular Biology Laboratory, Notkestraße 85, D-22607 Hamburg, Germany
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Lamers S, Feng Q, Cheng Y, Yu S, Sun B, Lukman M, Jiang J, Ruiz-Carrillo D. Structural and kinetic characterization of Porphyromonas gingivalis glutaminyl cyclase. Biol Chem 2021; 402:759-768. [PMID: 33823093 DOI: 10.1515/hsz-2020-0298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/16/2021] [Indexed: 11/15/2022]
Abstract
Porphyromonas gingivalis is a bacterial species known to be involved in the pathogenesis of chronic periodontitis, that more recently has been as well associated with Alzheimer's disease. P. gingivalis expresses a glutaminyl cyclase (PgQC) whose human ortholog is known to participate in the beta amyloid peptide metabolism. We have elucidated the crystal structure of PgQC at 1.95 Å resolution in unbound and in inhibitor-complexed forms. The structural characterization of PgQC confirmed that PgQC displays a mammalian fold rather than a bacterial fold. Our biochemical characterization indicates that PgQC uses a mammalian-like catalytic mechanism enabled by the residues Asp149, Glu182, Asp183, Asp218, Asp267 and His299. In addition, we could observe that a non-conserved Trp193 may drive differences in the binding affinity of ligands which might be useful for drug development. With a screening of a small molecule library, we have identified a benzimidazole derivative rendering PgQC inhibition in the low micromolar range that might be amenable for further medicinal chemistry development.
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Affiliation(s)
- Sebastiaan Lamers
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
| | - Qiaoli Feng
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
| | - Yili Cheng
- Department of Health and Environmental Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
| | - Sihong Yu
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
| | - Bo Sun
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai201204, China
| | - Maxwell Lukman
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
| | - Jie Jiang
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
| | - David Ruiz-Carrillo
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
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3
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Zhao Y, Feng Q, Zhou X, Zhang Y, Lukman M, Jiang J, Ruiz-Carrillo D. Mycobacterium tuberculosis puromycin hydrolase displays a prolyl oligopeptidase fold and an acyl aminopeptidase activity. Proteins 2021; 89:614-622. [PMID: 33426726 DOI: 10.1002/prot.26044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/11/2020] [Accepted: 12/31/2020] [Indexed: 12/20/2022]
Abstract
Puromycin-hydrolizing peptidases have been described as members of the prolyl oligopeptidase peptidase family. These enzymes are present across all domains of life but still little is known of the homologs found in the pathogenic bacterium Mycobacterium tuberculosis. The crystal structure of a M. tuberculosis puromycin hydrolase peptidase has been determined at 3 Angstrom resolution, revealing a conserved prolyl oligopeptidase fold, defined by α/β-hydrolase and β-propeller domains with two distinctive loops that occlude access of large substrates to the active site. The enzyme displayed amino peptidase activity with a substrate specificity preference for hydrophobic residues in the decreasing order of phenylalanine, leucine, alanine and proline. The enzyme's active site is lined by residues Glu564 for the coordination of the substrates amino terminal moiety and His561, Val608, Tyr78, Trp306, Phe563 and Ty567 for the accommodation of hydrophobic substrates. The availability of a crystal structure for puromycin hydrolase of M. tuberculosis shall facilitate the development of inhibitors with therapeutic applications.
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Affiliation(s)
- YuanHao Zhao
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Qiaoli Feng
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Xiao Zhou
- Department of Health and Environmental Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Yan Zhang
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Maxwell Lukman
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Jie Jiang
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - David Ruiz-Carrillo
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
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4
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Dai L, Lin J, Said AB, Yau YH, Shochat SG, Ruiz-Carrillo D, Sun K, Chandrasekaran R, Sze SK, Lescar J, Cheung PC. Pellino1 specifically binds to phospho-Thr18 of p53 and is recruited to sites of DNA damage. Biochem Biophys Res Commun 2019; 513:714-720. [PMID: 30987826 DOI: 10.1016/j.bbrc.2019.03.095] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/16/2019] [Indexed: 12/23/2022]
Abstract
Pellino1 is an E3 ubiquitin ligase that plays a key role in positive regulation of innate immunity signaling, specifically required for the production of interferon when induced by viral double-stranded RNA. We report the identification of the tumor suppressor protein, p53, as a binding partner of Pellino1. Their interaction has a Kd of 42 ± 2 μM and requires phosphorylation of Thr18 within p53 and association with the forkhead-associated (FHA) domain of Pellino1. We employed laser micro-irradiation and live cell microscopy to show that Pellino1 is recruited to newly occurring DNA damage sites, via its FHA domain. Mutation of a hitherto unidentified nuclear localization signal within the N-terminus of Pellino1 led to its exclusion from the nucleus. This study provides evidence that Pellino1 translocates to damaged DNA in the nucleus and has a functional role in p53 signaling and the DNA damage response.
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Affiliation(s)
- Liang Dai
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jianqing Lin
- School of Biological Sciences, Nanyang Technological University, Singapore; Nanyang Institute of Structural Biology, Nanyang Technological University, Singapore
| | | | - Yin Hoe Yau
- School of Biological Sciences, Nanyang Technological University, Singapore
| | | | | | - Kang Sun
- School of Biological Sciences, Nanyang Technological University, Singapore
| | | | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore; Nanyang Institute of Structural Biology, Nanyang Technological University, Singapore.
| | - Peter Cf Cheung
- School of Biological Sciences, Nanyang Technological University, Singapore.
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Ruiz-Carrillo D, Koch B, Parthier C, Wermann M, Dambe T, Buchholz M, Ludwig HH, Heiser U, Rahfeld JU, Stubbs MT, Schilling S, Demuth HU. Structures of Glycosylated Mammalian Glutaminyl Cyclases Reveal Conformational Variability near the Active Center. Biochemistry 2011; 50:6280-8. [DOI: 10.1021/bi200249h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David Ruiz-Carrillo
- Probiodrug AG, Weinbergweg 22, D-06120 Halle (Saale), Germany
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Birgit Koch
- Probiodrug AG, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | - Christoph Parthier
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Michael Wermann
- Probiodrug AG, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | - Tresfore Dambe
- PSF AG, Robert-Roessle-Strasse 10, D-13092 Berlin, Germany
| | - Mirko Buchholz
- Probiodrug AG, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | | | - Ulrich Heiser
- Probiodrug AG, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | | | - Milton T. Stubbs
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
- Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle (Saale), Germany
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Schulz I, Zeitschel U, Rudolph T, Ruiz-Carrillo D, Rahfeld JU, Gerhartz B, Bigl V, Demuth HU, Rossner S. Subcellular localization suggests novel functions for prolyl endopeptidase in protein secretion. J Neurochem 2005; 94:970-9. [PMID: 16092940 DOI: 10.1111/j.1471-4159.2005.03237.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [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: 01/12/2023]
Abstract
For a long time, prolyl endopeptidase (PEP) was believed to inactivate neuropeptides in the extracellular space. However, reports on the intracellular activity of PEP suggest additional, as yet unidentified, physiological functions for this enzyme. Here, we demonstrate using biochemical methods of subcellular fractionation, immunocytochemical double-labelling procedures and localization of PEP-enhanced green fluorescent protein fusion proteins that PEP is mainly localized to the perinuclear space, and is associated with the microtubulin cytoskeleton in human neuroblastoma and glioma cell lines. Disassembly of the microtubules by nocodazole treatment disrupts both the fibrillar tubulin and PEP labelling. Furthermore, in a two-hybrid screen, PEP was identified as binding partner of tubulin. These findings indicate novel functions for PEP in axonal transport and/or protein secretion. Indeed, a metabolic labelling approach revealed that both PEP inhibition and PEP antisense mRNA expression result in enhanced peptide/protein secretion from human U-343 glioma cells. Because disturbances in intracellular transport and protein secretion mechanisms are associated with a number of ageing-associated neurodegenerative diseases, cell-permeable PEP inhibitors may be useful for the application in a variety of related clinical conditions.
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