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Lloyd MD, Gregory KS, Acharya KR. Functional implications of unusual NOS and SONOS covalent linkages found in proteins. Chem Commun (Camb) 2024; 60:9463-9471. [PMID: 39109843 DOI: 10.1039/d4cc03191a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2024]
Abstract
The tertiary and quaternary structures of many proteins are stabilized by strong covalent forces, of which disulfide bonds are the most well known. A new type of intramolecular and intermolecular covalent bond has been recently reported, consisting of the Lys and Cys side-chains linked by an oxygen atom (NOS). These post-translational modifications are widely distributed amongst proteins, and are formed under oxidative conditions. Similar linkages are observed during antibiotic biosynthesis, where hydroxylamine intermediates are tethered to the sulfur of enzyme active site Cys residues. These linkages open the way to understanding protein structure and function, give new insights into enzyme catalysis and natural product biosynthesis, and offer new strategies for drug design.
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Affiliation(s)
- Matthew D Lloyd
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK.
| | - Kyle S Gregory
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK.
| | - K Ravi Acharya
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK.
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2
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Vermassen A, Leroy S, Talon R, Provot C, Popowska M, Desvaux M. Cell Wall Hydrolases in Bacteria: Insight on the Diversity of Cell Wall Amidases, Glycosidases and Peptidases Toward Peptidoglycan. Front Microbiol 2019; 10:331. [PMID: 30873139 PMCID: PMC6403190 DOI: 10.3389/fmicb.2019.00331] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 02/08/2019] [Indexed: 11/13/2022] Open
Abstract
The cell wall (CW) of bacteria is an intricate arrangement of macromolecules, at least constituted of peptidoglycan (PG) but also of (lipo)teichoic acids, various polysaccharides, polyglutamate and/or proteins. During bacterial growth and division, there is a constant balance between CW degradation and biosynthesis. The CW is remodeled by bacterial hydrolases, whose activities are carefully regulated to maintain cell integrity or lead to bacterial death. Each cell wall hydrolase (CWH) has a specific role regarding the PG: (i) cell wall amidase (CWA) cleaves the amide bond between N-acetylmuramic acid and L-alanine residue at the N-terminal of the stem peptide, (ii) cell wall glycosidase (CWG) catalyses the hydrolysis of the glycosidic linkages, whereas (iii) cell wall peptidase (CWP) cleaves amide bonds between amino acids within the PG chain. After an exhaustive overview of all known conserved catalytic domains responsible for CWA, CWG, and CWP activities, this review stresses that the CWHs frequently display a modular architecture combining multiple and/or different catalytic domains, including some lytic transglycosylases as well as CW binding domains. From there, direct physiological and collateral roles of CWHs in bacterial cells are further discussed.
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Affiliation(s)
- Aurore Vermassen
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
| | - Sabine Leroy
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
| | - Régine Talon
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
| | | | - Magdalena Popowska
- Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Mickaël Desvaux
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
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3
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Nirasawa S, Nakahara K, Takahashi S. Cloning and characterization of the novel d-aspartyl endopeptidase, paenidase, from Paenibacillus sp. B38. J Biochem 2018; 164:103-112. [DOI: 10.1093/jb/mvy033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 02/26/2018] [Indexed: 02/06/2023] Open
Affiliation(s)
- Satoru Nirasawa
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Kazuhiko Nakahara
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Saori Takahashi
- Akita Research Institute of Food and Brewing, 4-26 Sanuki, Arayamachi, Akita 010-1623, Japan
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Bobba S, Gutheil WG. Multivariate geometrical analysis of catalytic residues in the penicillin-binding proteins. Int J Biochem Cell Biol 2011; 43:1490-9. [PMID: 21740978 DOI: 10.1016/j.biocel.2011.06.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 05/04/2011] [Accepted: 06/22/2011] [Indexed: 12/11/2022]
Abstract
Penicillin-binding proteins (PBPs) are bacterial enzymes involved in the final stages of cell wall biosynthesis, and are targets of the β-lactam antibiotics. They can be subdivided into essential high-molecular-mass (HMM) and non-essential low-molecular-mass (LMM) PBPs, and further divided into subclasses based on sequence homologies. PBPs can catalyze transpeptidase or hydrolase (carboxypeptidase and endopeptidase) reactions. The PBPs are of interest for their role in bacterial cell wall biosynthesis, and as mechanistically interesting enzymes which can catalyze alternative reaction pathways using the same catalytic machinery. A global catalytic residue comparison seemed likely to provide insight into structure-function correlations within the PBPs. More than 90 PBP structures were aligned, and a number (40) of active site geometrical parameters extracted. This dataset was analyzed using both univariate and multivariate statistical methods. Several interesting relationships were observed. (1) Distribution of the dihedral angle for the SXXK-motif Lys side chain (DA_1) was bimodal, and strongly correlated with HMM/transpeptidase vs LMM/hydrolase classification/activity (P<0.001). This structural feature may therefore be associated with the main functional difference between the HMM and LMM PBPs. (2) The distance between the SXXK-motif Lys-NZ atom and the Lys/His-nitrogen atom of the (K/H)T(S)G-motif was highly conserved, suggesting importance for PBP function, and a possibly conserved role in the catalytic mechanism of the PBPs. (3) Principal components-based cluster analysis revealed several distinct clusters, with the HMM Class A and B, LMM Class C, and LMM Class A K15 PBPs forming one "Main" cluster, and demonstrating a globally similar arrangement of catalytic residues within this group.
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Affiliation(s)
- Sudheer Bobba
- Division of Pharmaceutical Sciences, University of Missouri-Kansas City, Kansas City, MO 64108, United States
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5
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Dzhekieva L, Rocaboy M, Kerff F, Charlier P, Sauvage E, Pratt RF. Crystal Structure of a Complex between the Actinomadura R39 dd-Peptidase and a Peptidoglycan-mimetic Boronate Inhibitor: Interpretation of a Transition State Analogue in Terms of Catalytic Mechanism. Biochemistry 2010; 49:6411-9. [DOI: 10.1021/bi100757c] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Liudmila Dzhekieva
- Department of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut 06459
| | - Mathieu Rocaboy
- Centre d’Ingéniere des Proteines, Université de Liège, B-4000 Sart Tilman, Liège, Belgium
| | - Frédéric Kerff
- Centre d’Ingéniere des Proteines, Université de Liège, B-4000 Sart Tilman, Liège, Belgium
| | - Paulette Charlier
- Centre d’Ingéniere des Proteines, Université de Liège, B-4000 Sart Tilman, Liège, Belgium
| | - Eric Sauvage
- Centre d’Ingéniere des Proteines, Université de Liège, B-4000 Sart Tilman, Liège, Belgium
| | - R. F. Pratt
- Department of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut 06459
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Sadeghian H, Sadeghian A, Pordel M, Rahimizadeh M, Jahandari P, Orafaie A, Bakavoli M. Design, synthesis, and structure–activity relationship study of 5-amido-1-(2,4-dinitrophenyl)-1H-4-pyrazolecarbonitrils as DD-carboxypeptidase/penicillin-binding protein inhibitors with Gram-positive antibacterial activity. Med Chem Res 2009. [DOI: 10.1007/s00044-009-9175-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Urbach C, Fastrez J, Soumillion P. A new family of cyanobacterial penicillin-binding proteins. A missing link in the evolution of class A beta-lactamases. J Biol Chem 2008; 283:32516-26. [PMID: 18801739 DOI: 10.1074/jbc.m805375200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
It is largely accepted that serine beta-lactamases evolved from some ancestral DD-peptidases involved in the biosynthesis and maintenance of the bacterial peptidoglycan. DD-peptidases are also called penicillin-binding proteins (PBPs), since they form stable acyl-enzymes with beta-lactam antibiotics, such as penicillins. On the other hand, beta-lactamases react similarly with these antibiotics, but the acyl-enzymes are unstable and rapidly hydrolyzed. Besides, all known PBPs and beta-lactamases share very low sequence similarities, thus rendering it difficult to understand how a PBP could evolve into a beta-lactamase. In this study, we identified a new family of cyanobacterial PBPs featuring the highest sequence similarity with the most widespread class A beta-lactamases. Interestingly, the Omega-loop, which, in the beta-lactamases, carries an essential glutamate involved in the deacylation process, is six amino acids shorter and does not contain any glutamate residue. From this new family of proteins, we characterized PBP-A from Thermosynechococcus elongatus and discovered hydrolytic activity with synthetic thiolesters that are usually good substrates of DD-peptidases. Penicillin degradation pathways as well as acylation and deacylation rates are characteristic of PBPs. In a first attempt to generate beta-lactamase activity, a 90-fold increase in deacylation rate was obtained by introducing a glutamate in the shorter Omega-loop.
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Affiliation(s)
- Carole Urbach
- Laboratoire d'Ingénierie des Protéines et des Peptides, Institut des Sciences de la Vie, Université Catholique de Louvain, Place Croix du Sud 4-5, bte3, 1348 Louvain la-Neuve, Belgium
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Macheboeuf P, Contreras-Martel C, Job V, Dideberg O, Dessen A. Penicillin binding proteins: key players in bacterial cell cycle and drug resistance processes. FEMS Microbiol Rev 2006; 30:673-91. [PMID: 16911039 DOI: 10.1111/j.1574-6976.2006.00024.x] [Citation(s) in RCA: 313] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacterial cell division and daughter cell formation are complex mechanisms whose details are orchestrated by at least a dozen different proteins. Penicillin-binding proteins (PBPs), membrane-associated macromolecules which play key roles in the cell wall synthesis process, have been exploited for over 70 years as the targets of the highly successful beta-lactam antibiotics. The increasing incidence of beta-lactam resistant microorganisms, coupled to progress made in genomics, genetics and immunofluorescence microscopy techniques, have encouraged the intensive study of PBPs from a variety of bacterial species. In addition, the recent publication of high-resolution structures of PBPs from pathogenic organisms have shed light on the complex intertwining of drug resistance and cell division processes. In this review, we discuss structural, functional and biological features of such enzymes which, albeit having initially been identified several decades ago, are now being aggressively pursued as highly attractive targets for the development of novel antibiotherapies.
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Affiliation(s)
- Pauline Macheboeuf
- Institut de Biologie Structurale Jean-Pierre Ebel (CNRS/CEA/UJF), UMR 5075, Laboratoire des Protéines Membranaires, Grenoble, France
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Nicola G, Fedarovich A, Nicholas R, Davies C. A large displacement of the SXN motif of Cys115-modified penicillin-binding protein 5 from Escherichia coli. Biochem J 2006; 392:55-63. [PMID: 16038617 PMCID: PMC1317664 DOI: 10.1042/bj20050449] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Penicillin-binding proteins (PBPs), which are the lethal targets of beta-lactam antibiotics, catalyse the final stages of peptidoglycan biosynthesis of the bacterial cell wall. PBP 5 of Escherichia coli is a D-alanine CPase (carboxypeptidase) that has served as a useful model to elucidate the catalytic mechanism of low-molecular-mass PBPs. Previous studies have shown that modification of Cys115 with a variety of reagents results in a loss of CPase activity and a large decrease in the rate of deacylation of the penicilloyl-PBP 5 complex [Tamura, Imae and Strominger (1976) J. Biol. Chem. 251, 414-423; Curtis and Strominger (1978) J. Biol. Chem. 253, 2584-2588]. The crystal structure of wild-type PBP 5 in which Cys115 fortuitously had formed a covalent adduct with 2-mercaptoethanol was solved at 2.0 A (0.2 nm) resolution, and these results provide a structural rationale for how thiol-directed reagents lower the rate of deacylation. When compared with the structure of the unmodified wild-type enzyme, a major change in the architecture of the active site is observed. The two largest differences are the disordering of a loop comprising residues 74-90 and a shift in residues 106-111, which results in the displacement of Ser110 of the SXN active-site motif. These results support the developing hypothesis that the SXN motif of PBP 5, and especially Ser110, is intimately involved in the catalytic mechanism of deacylation.
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Affiliation(s)
- George Nicola
- *Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, U.S.A
| | - Alena Fedarovich
- *Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, U.S.A
| | - Robert A. Nicholas
- †Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, U.S.A
- Correspondence may be addressed to either of these authors (email or )
| | - Christopher Davies
- *Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, U.S.A
- Correspondence may be addressed to either of these authors (email or )
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Fisher JF, Meroueh SO, Mobashery S. Bacterial resistance to beta-lactam antibiotics: compelling opportunism, compelling opportunity. Chem Rev 2005; 105:395-424. [PMID: 15700950 DOI: 10.1021/cr030102i] [Citation(s) in RCA: 684] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jed F Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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11
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Wilke MS, Hills TL, Zhang HZ, Chambers HF, Strynadka NCJ. Crystal Structures of the Apo and Penicillin-acylated Forms of the BlaR1 β-Lactam Sensor of Staphylococcus aureus. J Biol Chem 2004; 279:47278-87. [PMID: 15322076 DOI: 10.1074/jbc.m407054200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Staphylococcus aureus is among the most prevalent and antibiotic-resistant of pathogenic bacteria. The resistance of S. aureus to prototypal beta-lactam antibiotics is conferred by two mechanisms: (i) secretion of hydrolytic beta-lactamase enzymes and (ii) production of beta-lactam-insensitive penicillin-binding proteins (PBP2a). Despite their distinct modes of resistance, expression of these proteins is controlled by similar regulation systems, including a repressor (BlaI/MecI) and a multidomain transmembrane receptor (BlaR1/MecR1). Resistance is triggered in response to a covalent binding event between a beta-lactam antibiotic and the extracellular sensor domain of BlaR1/MecR1 by transduction of the binding signal to an intracellular protease domain capable of repressor inactivation. This study describes the first crystal structures of the sensor domain of BlaR1 (BlaRS) from S. aureus in both the apo and penicillin-acylated forms. The structures show that the sensor domain resembles the beta-lactam-hydrolyzing class D beta-lactamases, but is rendered a penicillin-binding protein due to the formation of a very stable acyl-enzyme. Surprisingly, conformational changes upon penicillin binding were not observed in our structures, supporting the hypothesis that transduction of the antibiotic-binding signal into the cytosol is mediated by additional intramolecular interactions of the sensor domain with an adjacent extracellular loop in BlaR1.
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Affiliation(s)
- Mark S Wilke
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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Zong Y, Mazmanian SK, Schneewind O, Narayana SVL. The structure of sortase B, a cysteine transpeptidase that tethers surface protein to the Staphylococcus aureus cell wall. Structure 2004; 12:105-12. [PMID: 14725770 DOI: 10.1016/j.str.2003.11.021] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Many surface proteins of Gram-positive bacteria, which play important roles during the pathogenesis of human infections, are anchored to the cell wall envelope by a mechanism requiring sortases. Sortase B, a cysteine transpeptidase from Staphylococcus aureus, cleaves the C-terminal sorting signal of IsdC at the NPQTN motif and tethers the polypeptide to the pentaglycine cell wall cross-bridge. During catalysis, the active site cysteine of sortase and the cleaved substrate form an acyl intermediate, which is then resolved by the amino group of pentaglycine cross-bridges. We report here the crystal structures of SrtBDeltaN30 in complex with two active site inhibitors, MTSET and E64, and with the cell wall substrate analog tripleglycine. These structures reveal, for the first time, the active site disposition and the unique Cys-Arg catalytic machinery of the cysteine transpeptidase, and they also provide useful information for the future design of anti-infective agents against sortases.
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Affiliation(s)
- Yinong Zong
- Center for Biophysical Sciences and Engineering, School of Optometry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Stefanova ME, Tomberg J, Davies C, Nicholas RA, Gutheil WG. Overexpression and enzymatic characterization of Neisseria gonorrhoeae penicillin-binding protein 4. ACTA ACUST UNITED AC 2003; 271:23-32. [PMID: 14686916 DOI: 10.1046/j.1432-1033.2003.03886.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The penicillin-binding proteins (PBPs) are ubiquitous bacterial enzymes involved in cell wall biosynthesis, and are the targets of the beta-lactam antibiotics. The low molecular mass Neisseria gonorrhoeae PBP 4 (NG PBP 4) is the fourth PBP revealed in the gonococcal genome. NG PBP 4 was cloned, overexpressed, purified, and characterized for beta-lactam binding, DD-carboxypeptidase activity, acyl-donor substrate specificity, transpeptidase activity, inhibition by a number of active site directed reagents, and pH profile. NG PBP 4 was efficiently acylated by penicillin (30,000 m-1.s-1). Against a set of five alpha- and epsilon-substituted l-Lys-D-Ala-D-Ala substrates, NG PBP 4 exhibited wide variation in specificity with a preference for N epsilon-acylated substrates, suggesting a possible preference for crosslinked pentapeptide substrates in the cell wall. Substrates with an N epsilon-Cbz group demonstrated pronounced substrate inhibition. NG PBP 4 showed 30-fold higher activity against the depsipeptide Lac-ester substrate than against the analogous peptide substrate, an indication that k2 (acylation) is rate determining for carboxypeptidase activity. No transpeptidase activity was apparent in a model transpeptidase reaction. Among a number of active site-directed agents, N-chlorosuccinimide, elastinal, iodoacetamide, iodoacetic acid, and phenylglyoxal gave substantial inhibition, and methyl boronic acid gave modest inhibition. The pH profile for activity against Ac2-l-Lys-D-Ala-d-Ala (kcat/Km) was bell-shaped, with pKa values at 6.9 and 10.1. Comparison of the enzymatic properties of NG PBP 4 with other DD-carboxypeptidases highlights both similarities and differences within these enzymes, and suggests the possibility of common mechanistic roles for the two highly conserved active site lysines in Class A and C low molecular mass PBPs.
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Affiliation(s)
- Miglena E Stefanova
- Division of Pharmaceutical Sciences, University of Missouri-Kansas City 64110, USA
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