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Rodríguez-Banqueri A, Moliner-Culubret M, Mendes SR, Guevara T, Eckhard U, Gomis-Rüth FX. Structural insights into latency of the metallopeptidase ulilysin (lysargiNase) and its unexpected inhibition by a sulfonyl-fluoride inhibitor of serine peptidases. Dalton Trans 2023; 52:3610-3622. [PMID: 36857690 DOI: 10.1039/d3dt00458a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Peptidases are regulated by latency and inhibitors, as well as compatibilization and cofactors. Ulilysin from Methanosarcina acetivorans, also called lysargiNase, is an archaeal metallopeptidase (MP) that is biosynthesized as a zymogen with a 60-residue N-terminal prosegment (PS). In the presence of calcium, it self-activates to yield the mature enzyme, which specifically cleaves before basic residues and thus complements trypsin in proteomics workflows. Here, we obtained a low-resolution crystal structure of proulilysin, in which 28 protomers arranged as 14 dimers form a continuous double helix of 544 Å pitch that parallels cell axis b of the crystal. The PS includes two α-helices and obstructs the active-site cleft of the catalytic domain (CD) by traversing it in the opposite orientation of a substrate, and a cysteine blocks the catalytic zinc according to a "cysteine-switch mechanism". Moreover, the PS interacts through its first helix with an "S-loop" of the CD, which acts as an "activation segment" that lacks one of two essential calcium cations. Upon PS removal during maturation, the S-loop adopts its competent conformation and binds the second calcium ion. Next, we found that in addition to general MP inhibitors, ulilysin was competitively and reversibly inhibited by 4-(2-aminoethyl)benzenesulfonyl fluoride (AEBSF; Ki = 4 μM). This is a compound that normally forms an irreversible covalent complex with serine peptidases but does not inhibit MPs. A high-resolution crystal structure of the complex revealed that the inhibitor penetrates the specificity pocket of ulilysin. A primary amine of the inhibitor salt-bridges an aspartate at the pocket bottom, thus mimicking the basic side chain of substrates. In contrast, the sulfonyl fluoride warhead is not involved and the catalytic zinc ion is freely accessible. Thus, the usage of inhibitor cocktails of peptidases, which typically contain AEBSF at ∼25-fold higher concentrations than the determined Ki, should be avoided when working with ulilysin. Finally, the structure of the complex, which occurred as a crystallographic dimer recurring in previous mature ulilysin structures, unveiled an N-terminal product fragment that delineated the non-primed side of the cleft. These results complement prior structures of ulilysin with primed-side product fragments and inhibitors.
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Affiliation(s)
- Arturo Rodríguez-Banqueri
- Proteolysis Laboratory; Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona (IBMB), Higher Scientific Research Council (CSIC); Barcelona Science Park; c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain.
| | - Marina Moliner-Culubret
- Proteolysis Laboratory; Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona (IBMB), Higher Scientific Research Council (CSIC); Barcelona Science Park; c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain.
| | - Soraia R Mendes
- Proteolysis Laboratory; Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona (IBMB), Higher Scientific Research Council (CSIC); Barcelona Science Park; c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain.
| | - Tibisay Guevara
- Proteolysis Laboratory; Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona (IBMB), Higher Scientific Research Council (CSIC); Barcelona Science Park; c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain.
| | - Ulrich Eckhard
- Proteolysis Laboratory; Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona (IBMB), Higher Scientific Research Council (CSIC); Barcelona Science Park; c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain.
| | - F Xavier Gomis-Rüth
- Proteolysis Laboratory; Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona (IBMB), Higher Scientific Research Council (CSIC); Barcelona Science Park; c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain.
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Książek M, Goulas T, Mizgalska D, Rodríguez-Banqueri A, Eckhard U, Veillard F, Waligórska I, Benedyk-Machaczka M, Sochaj-Gregorczyk AM, Madej M, Thøgersen IB, Enghild JJ, Cuppari A, Arolas JL, de Diego I, López-Pelegrín M, Garcia-Ferrer I, Guevara T, Dive V, Zani ML, Moreau T, Potempa J, Gomis-Rüth FX. A unique network of attack, defence and competence on the outer membrane of the periodontitis pathogen Tannerella forsythia. Chem Sci 2023; 14:869-888. [PMID: 36755705 PMCID: PMC9890683 DOI: 10.1039/d2sc04166a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Periodontopathogenic Tannerella forsythia uniquely secretes six peptidases of disparate catalytic classes and families that operate as virulence factors during infection of the gums, the KLIKK-peptidases. Their coding genes are immediately downstream of novel ORFs encoding the 98-132 residue potempins (Pot) A, B1, B2, C, D and E. These are outer-membrane-anchored lipoproteins that specifically and potently inhibit the respective downstream peptidase through stable complexes that protect the outer membrane of T. forsythia, as shown in vivo. Remarkably, PotA also contributes to bacterial fitness in vivo and specifically inhibits matrix metallopeptidase (MMP) 12, a major defence component of oral macrophages, thus featuring a novel and highly-specific physiological MMP inhibitor. Information from 11 structures and high-confidence homology models showed that the potempins are distinct β-barrels with either a five-stranded OB-fold (PotA, PotC and PotD) or an eight-stranded up-and-down fold (PotE, PotB1 and PotB2), which are novel for peptidase inhibitors. Particular loops insert like wedges into the active-site cleft of the genetically-linked peptidases to specifically block them either via a new "bilobal" or the classic "standard" mechanism of inhibition. These results discover a unique, tightly-regulated proteolytic armamentarium for virulence and competence, the KLIKK-peptidase/potempin system.
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Affiliation(s)
- Mirosław Książek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland .,Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry Louisville 40202 KY USA
| | - Theodoros Goulas
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain .,Department of Food Science and Nutrition, School of Agricultural Sciences, University of Thessaly Temponera str. Karditsa 43100 Greece
| | - Danuta Mizgalska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland
| | - Arturo Rodríguez-Banqueri
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain
| | - Ulrich Eckhard
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain
| | - Florian Veillard
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland
| | - Irena Waligórska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland
| | - Małgorzata Benedyk-Machaczka
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland
| | - Alicja M. Sochaj-Gregorczyk
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian UniversityGronostajowa 7Kraków 30-387Poland
| | - Mariusz Madej
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland
| | - Ida B. Thøgersen
- Department of Molecular Biology and Genetics, Aarhus UniversityUniversitetsbyen 81Aarhus C 8000Denmark
| | - Jan J. Enghild
- Department of Molecular Biology and Genetics, Aarhus UniversityUniversitetsbyen 81Aarhus C 8000Denmark
| | - Anna Cuppari
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain
| | - Joan L. Arolas
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Parkc/Baldiri Reixac, 15-21Barcelona 08028CataloniaSpain
| | - Iñaki de Diego
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain .,Sample Environment and Characterization Group, European XFEL GmbH Holzkoppel 4 Schenefeld 22869 Germany
| | - Mar López-Pelegrín
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain
| | - Irene Garcia-Ferrer
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain
| | - Tibisay Guevara
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain
| | - Vincent Dive
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), ERL CNRS 9004Gif-sur-Yvette 91191France
| | - Marie-Louise Zani
- Departement de Biochimie, Université de Tours10 Bd. TonelléTours Cedex 37032France
| | | | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland .,Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry Louisville 40202 KY USA
| | - F. Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Parkc/Baldiri Reixac, 15-21Barcelona 08028CataloniaSpain
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Courrol DDS, da Silva CCF, Prado LG, Chura-Chambi RM, Morganti L, de Souza GO, Heinemann MB, Isaac L, Conte FP, Portaro FCV, Rodrigues-da-Silva RN, Barbosa AS. Leptolysin, a Leptospira secreted metalloprotease of the pappalysin family with broad-spectrum activity. Front Cell Infect Microbiol 2022; 12:966370. [PMID: 36081769 PMCID: PMC9445424 DOI: 10.3389/fcimb.2022.966370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/03/2022] [Indexed: 11/22/2022] Open
Abstract
Extracellular proteolytic enzymes are produced by a variety of pathogenic microorganisms, and contribute to host colonization by modulating virulence. Here, we present a first characterization of leptolysin, a Leptospira metalloprotease of the pappalysin family identified in a previous exoproteomic study. Comparative molecular analysis of leptolysin with two other pappalysins from prokaryotes, ulilysin and mirolysin, reveals similarities regarding calcium, zinc, and arginine -binding sites conservation within the catalytic domain, but also discloses peculiarities. Variations observed in the primary and tertiary structures may reflect differences in primary specificities. Purified recombinant leptolysin of L. interrogans was obtained as a ~50 kDa protein. The protease exhibited maximal activity at pH 8.0 and 37°C, and hydrolytic activity was observed in the presence of different salts with maximum efficiency in NaCl. Substrate specificity was assessed using a small number of FRET peptides, and showed a marked preference for arginine residues at the P1 position. L. interrogans leptolysin proteolytic activity on proteinaceous substrates such as proteoglycans and plasma fibronectin was also evaluated. All proteins tested were efficiently degraded over time, confirming the protease´s broad-spectrum activity in vitro. In addition, leptolysin induced morphological alterations on HK-2 cells, which may be partially attributed to extracellular matrix (ECM) degradation. Hemorrhagic foci were observed in the dorsal skin of mice intradermally injected with leptolysin, as a plausible consequence of ECM disarray and vascular endothelium glycocalyx damage. Assuming that leptospiral proteases play an important role in all stages of the infectious process, characterizing their functional properties, substrates and mechanisms of action is of great importance for therapeutic purposes.
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Affiliation(s)
| | | | - Luan Gavião Prado
- Laboratory of Bacteriology, Butantan Institute, São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Rosa Maria Chura-Chambi
- Laboratory of Bacteriology, Butantan Institute, São Paulo, Brazil
- Center of Biotechnology, Energy and Nuclear Research Institute (IPEN)-CNEN/SP), São Paulo, Brazil
| | - Ligia Morganti
- Center of Biotechnology, Energy and Nuclear Research Institute (IPEN)-CNEN/SP), São Paulo, Brazil
| | - Gisele Oliveira de Souza
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Marcos Bryan Heinemann
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Lourdes Isaac
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fernando Paiva Conte
- Pilot Plant Implementation Project, Immunobiological Technology Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | | | - Angela Silva Barbosa
- Laboratory of Bacteriology, Butantan Institute, São Paulo, Brazil
- *Correspondence: Angela Silva Barbosa,
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