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Tossavainen H, Pitkänen I, Antenucci L, Thapa C, Permi P. Chemical shift assignments of the catalytic domain of Staphylococcus aureus LytM. BIOMOLECULAR NMR ASSIGNMENTS 2024; 18:1-5. [PMID: 37914968 PMCID: PMC11082022 DOI: 10.1007/s12104-023-10161-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023]
Abstract
S. aureus resistance to antibiotics has increased rapidly. MRSA strains can simultaneously be resistant to many different classes of antibiotics, including the so-called "last-resort" drugs. Resistance complicates treatment, increases mortality and substantially increases the cost of treatment. The need for new drugs against (multi)resistant S. aureus is high. M23B family peptidoglycan hydrolases, enzymes that can kill S. aureus by cleaving glycine-glycine peptide bonds in S. aureus cell wall are attractive targets for drug development because of their binding specificity and lytic activity. M23B enzymes lysostaphin, LytU and LytM have closely similar catalytic domain structures. They however differ in their lytic activities, which can arise from non-conserved residues in the catalytic groove and surrounding loops or differences in dynamics. We report here the near complete 1H/13C/15N resonance assignment of the catalytic domain of LytM, residues 185-316. The chemical shift data allow comparative structural and functional studies between the enzymes and is essential for understanding how these hydrolases degrade the cell wall.
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Affiliation(s)
- Helena Tossavainen
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
| | - Ilona Pitkänen
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
| | - Lina Antenucci
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
| | - Chandan Thapa
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
| | - Perttu Permi
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland.
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.
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Tossavainen H, Raulinaitis V, Kauppinen L, Pentikäinen U, Maaheimo H, Permi P. Structural and Functional Insights Into Lysostaphin-Substrate Interaction. Front Mol Biosci 2018; 5:60. [PMID: 30018958 PMCID: PMC6038053 DOI: 10.3389/fmolb.2018.00060] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/12/2018] [Indexed: 11/13/2022] Open
Abstract
Lysostaphin from Staphylococcus simulans and its family enzymes rapidly acquire prominence as the next generation agents in treatment of S. aureus infections. The specificity of lysostaphin is promoted by its C-terminal cell wall targeting domain selectivity toward pentaglycine bridges in S. aureus cell wall. Scission of these cross-links is carried out by its N-terminal catalytic domain, a zinc-dependent endopeptidase. Understanding the determinants affecting the efficiency of catalysis and strength and specificity of interactions lies at the heart of all lysostaphin family enzyme applications. To this end, we have used NMR, SAXS and molecular dynamics simulations to characterize lysostaphin structure and dynamics, to address the inter-domain interaction, the enzyme-substrate interaction as well as the catalytic properties of pentaglycine cleavage in solution. Our NMR structure confirms the recent crystal structure, yet, together with the molecular dynamics simulations, emphasizes the dynamic nature of the loops embracing the catalytic site. We found no evidence for inter-domain interaction, but, interestingly, the SAXS data delineate two preferred conformation subpopulations. Catalytic H329 and H360 were observed to bind a second zinc ion, which reduces lysostaphin pentaglycine cleaving activity. Binding of pentaglycine or its lysine derivatives to the targeting domain was found to be of very low affinity. The pentaglycine interaction site was located to the N-terminal groove of the domain. Notably, the targeting domain binds the peptidoglycan stem peptide Ala-d-γ-Glu-Lys-d-Ala-d-Ala with a much higher, micromolar affinity. Binding site mapping reveals two interaction sites of different affinities on the surface of the domain for this peptide.
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Affiliation(s)
- Helena Tossavainen
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Vytas Raulinaitis
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Linda Kauppinen
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
| | - Ulla Pentikäinen
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland.,Turku Centre for Biotechnology, Turku, Finland
| | - Hannu Maaheimo
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Perttu Permi
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.,Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
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Raulinaitis V, Tossavainen H, Aitio O, Juuti JT, Hiramatsu K, Kontinen V, Permi P. Identification and structural characterization of LytU, a unique peptidoglycan endopeptidase from the lysostaphin family. Sci Rep 2017; 7:6020. [PMID: 28729697 PMCID: PMC5519744 DOI: 10.1038/s41598-017-06135-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/08/2017] [Indexed: 02/06/2023] Open
Abstract
We introduce LytU, a short member of the lysostaphin family of zinc-dependent pentaglycine endopeptidases. It is a potential antimicrobial agent for S. aureus infections and its gene transcription is highly upregulated upon antibiotic treatments along with other genes involved in cell wall synthesis. We found this enzyme to be responsible for the opening of the cell wall peptidoglycan layer during cell divisions in S. aureus. LytU is anchored in the plasma membrane with the active part residing in the periplasmic space. It has a unique Ile/Lys insertion at position 151 that resides in the catalytic site-neighbouring loop and is vital for the enzymatic activity but not affecting the overall structure common to the lysostaphin family. Purified LytU lyses S. aureus cells and cleaves pentaglycine, a reaction conveniently monitored by NMR spectroscopy. Substituting the cofactor zinc ion with a copper or cobalt ion remarkably increases the rate of pentaglycine cleavage. NMR and isothermal titration calorimetry further reveal that, uniquely for its family, LytU is able to bind a second zinc ion which is coordinated by catalytic histidines and is therefore inhibitory. The pH-dependence and high affinity of binding carry further physiological implications.
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Affiliation(s)
- Vytas Raulinaitis
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Helena Tossavainen
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Olli Aitio
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Jarmo T Juuti
- Antimicrobial Resistance Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, P.O. Box 30, FI-00271, Helsinki, Finland
| | - Keiichi Hiramatsu
- Research Centre for Infection Control Science, Juntendo University, Bunkyo-ku, Tokyo, Japan
| | - Vesa Kontinen
- Antimicrobial Resistance Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, P.O. Box 30, FI-00271, Helsinki, Finland.,Research Centre for Infection Control Science, Juntendo University, Bunkyo-ku, Tokyo, Japan
| | - Perttu Permi
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland. .,Department of Biological and Environmental Science, and Department of Chemistry, Nanoscience Center, University of Jyvaskyla, P.O. Box 35, FI-40014, Jyvaskyla, Finland.
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