1
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Planas A. Peptidoglycan Deacetylases in Bacterial Cell Wall Remodeling and Pathogenesis. Curr Med Chem 2021; 29:1293-1312. [PMID: 34525907 DOI: 10.2174/0929867328666210915113723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/24/2021] [Accepted: 07/26/2021] [Indexed: 11/22/2022]
Abstract
The bacterial cell wall peptidoglycan (PG) is a dynamic structure that is constantly synthesized, re-modeled and degraded during bacterial division and growth. Post-synthetic modifications modulate the action of endogenous autolysis during PG lysis and remodeling for growth and sporulation, but also they are a mechanism used by pathogenic bacteria to evade the host innate immune system. Modifica-tions of the glycan backbone are limited to the C-2 amine and the C-6 hydroxyl moieties of either Glc-NAc or MurNAc residues. This paper reviews the functional roles and properties of peptidoglycan de-N-acetylases (distinct PG GlcNAc and MurNAc deacetylases) and recent progress through genetic stud-ies and biochemical characterization to elucidate their mechanism of action, 3D structures, substrate specificities and biological functions. Since they are virulence factors in pathogenic bacteria, peptidogly-can deacetylases are potential targets for the design of novel antimicrobial agents.
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Affiliation(s)
- Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià. University Ramon Llull, 08017 Barcelona. Spain
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2
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Catalytic activity regulation through post-translational modification: the expanding universe of protein diversity. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:97-125. [PMID: 32951817 PMCID: PMC7320668 DOI: 10.1016/bs.apcsb.2020.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein composition is restricted by the genetic code to a relatively small number of natural amino acids. Similarly, the known three-dimensional structures adopt a limited number of protein folds. However, proteins exert a large variety of functions and show a remarkable ability for regulation and immediate response to intracellular and extracellular stimuli. To some degree, the wide variability of protein function can be attributed to the post-translational modifications. Post-translational modifications have been observed in all kingdoms of life and give to proteins a significant degree of chemical and consequently functional and structural diversity. Their importance is partly reflected in the large number of genes dedicated to their regulation. So far, hundreds of post-translational modifications have been observed while it is believed that many more are to be discovered along with the technological advances in sequencing, proteomics, mass spectrometry and structural biology. Indeed, the number of studies which report novel post translational modifications is getting larger supporting the notion that their space is still largely unexplored. In this review we explore the impact of post-translational modifications on protein structure and function with emphasis on catalytic activity regulation. We present examples of proteins and protein families whose catalytic activity is substantially affected by the presence of post translational modifications and we describe the molecular basis which underlies the regulation of the protein function through these modifications. When available, we also summarize the current state of knowledge on the mechanisms which introduce these modifications to protein sites.
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3
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Prejanò M, Romeo I, Sgrizzi L, Russo N, Marino T. Why hydroxy-proline improves the catalytic power of the peptidoglycan N-deacetylase enzyme: insight from theory. Phys Chem Chem Phys 2019; 21:23338-23345. [PMID: 31617504 DOI: 10.1039/c9cp03804c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nature exploits different strategies for enhancing the catalytic activity of enzymes, often resorting to producing beneficial mutations. The case of post-translational proline hydroxylation mutation in the active site of polysaccharide deacetylase (PDA) Bc1960 from Bacillus cereus is an interesting example of how small chemical modifications can cause significant improvements in enzymatic activity. In the present study the deacetylation mechanism promoted by both OH-proline (2Hyp) and standard proline (Pro) containing PDA is investigated using density functional theory. Although the mechanism presented for the two examined enzymes is in agreement with protease catalysis in metalloenzymes, the analysis along the potential energy surface (PES) reveals that the intermediate and product benefit energetically from the presence of the hydroxyl group on the proline. Our calculations provide evidence that for PDA-2Hyp, the hydrogen bond network established by the -OH group on the Cα of the proline with its closest neighbors stabilizes the transition states and, consequently, the reaction takes advantage of this. These results further contribute towards explaining the different catalytic activity experimentally observed for the polysaccharide deacetylase enzymes.
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Affiliation(s)
- Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Arcavacata di Rende, CS, Italy.
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4
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Andreou A, Giastas P, Arnaouteli S, Tzanodaskalaki M, Tzartos SJ, Bethanis K, Bouriotis V, Eliopoulos EE. The putative polysaccharide deacetylase Ba0331: cloning, expression, crystallization and structure determination. Acta Crystallogr F Struct Biol Commun 2019; 75:312-320. [PMID: 30950833 PMCID: PMC6450525 DOI: 10.1107/s2053230x19001766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/30/2019] [Indexed: 11/10/2022] Open
Abstract
Ba0331 is a putative polysaccharide deacetylase from Bacillus anthracis, the etiological agent of the disease anthrax, that contributes to adaptation of the bacterium under extreme conditions and to maintenance of the cell shape. In the present study, the crystal structure of Ba0331 was determined at 2.6 Å resolution. The structure consists of two domains: a fibronectin type 3-like (Fn3-like) domain and a NodB catalytic domain. The latter is present in all carbohydrate esterase family 4 enzymes, while a comparative analysis of the Fn3-like domain revealed structural plasticity despite the retention of the conserved Fn3-like domain characteristics.
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Affiliation(s)
- Athena Andreou
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Petros Giastas
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
- Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece
| | - Sofia Arnaouteli
- Department of Biology, Enzyme Biotechnology Group, University of Crete, Vasilika Vouton, 70013 Heraklion, Crete, Greece
| | - Mary Tzanodaskalaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas N. Plastira 100, 70013 Heraklion, Crete, Greece
| | - Socrates J. Tzartos
- Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece
| | - Kostas Bethanis
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Vassilis Bouriotis
- Department of Biology, Enzyme Biotechnology Group, University of Crete, Vasilika Vouton, 70013 Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas N. Plastira 100, 70013 Heraklion, Crete, Greece
| | - Elias E. Eliopoulos
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
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5
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Andreou A, Giastas P, Christoforides E, Eliopoulos EE. Structural and Evolutionary Insights within the Polysaccharide Deacetylase Gene Family of Bacillus anthracis and Bacillus cereus. Genes (Basel) 2018; 9:E386. [PMID: 30065210 PMCID: PMC6115787 DOI: 10.3390/genes9080386] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 02/06/2023] Open
Abstract
Functional and folding constraints impose interdependence between interacting sites along the protein chain that are envisaged through protein sequence evolution. Studying the influence of structure in phylogenetic models requires detailed and reliable structural models. Polysaccharide deacetylases (PDAs), members of the carbohydrate esterase family 4, perform mainly metal-dependent deacetylation of O- or N-acetylated polysaccharides such as peptidoglycan, chitin and acetylxylan through a conserved catalytic core termed the NodB homology domain. Genomes of Bacillus anthracis and its relative Bacillus cereus contain multiple genes of putative or known PDAs. A comparison of the functional domains of the recently determined PDAs from B. anthracis and B. cereus and multiple amino acid and nucleotide sequence alignments and phylogenetic analysis performed on these closely related species showed that there were distinct differences in binding site formation, despite the high conservation on the protein sequence, the folding level and the active site assembly. This may indicate that, subject to biochemical verification, the binding site-forming sequence fragments are under functionally driven evolutionary pressure to accommodate and recognize distinct polysaccharide residues according to cell location, use, or environment. Finally, we discuss the suggestion of the paralogous nature of at least two genes of B. anthracis, ba0330 and ba0331, via specific differences in gene sequence, protein structure, selection pressure and available localization patterns. This study may contribute to understanding the mechanisms under which sequences evolve in their structures and how evolutionary processes enable structural variations.
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Affiliation(s)
- Athena Andreou
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
| | - Petros Giastas
- Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece.
| | - Elias Christoforides
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
| | - Elias E Eliopoulos
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
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6
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Polysaccharide deacetylases serve as new targets for the design of inhibitors against Bacillus anthracis and Bacillus cereus. Bioorg Med Chem 2018; 26:3845-3851. [DOI: 10.1016/j.bmc.2018.06.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/25/2018] [Accepted: 06/30/2018] [Indexed: 02/02/2023]
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7
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Substrate Recognition and Specificity of Chitin Deacetylases and Related Family 4 Carbohydrate Esterases. Int J Mol Sci 2018; 19:ijms19020412. [PMID: 29385775 PMCID: PMC5855634 DOI: 10.3390/ijms19020412] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 01/22/2018] [Accepted: 01/24/2018] [Indexed: 12/27/2022] Open
Abstract
Carbohydrate esterases family 4 (CE4 enzymes) includes chitin and peptidoglycan deacetylases, acetylxylan esterases, and poly-N-acetylglucosamine deacetylases that act on structural polysaccharides, altering their physicochemical properties, and participating in diverse biological functions. Chitin and peptidoglycan deacetylases are not only involved in cell wall morphogenesis and remodeling in fungi and bacteria, but they are also used by pathogenic microorganisms to evade host defense mechanisms. Likewise, biofilm formation in bacteria requires partial deacetylation of extracellular polysaccharides mediated by poly-N-acetylglucosamine deacetylases. Such biological functions make these enzymes attractive targets for drug design against pathogenic fungi and bacteria. On the other side, acetylxylan esterases deacetylate plant cell wall complex xylans to make them accessible to hydrolases, making them attractive biocatalysts for biomass utilization. CE4 family members are metal-dependent hydrolases. They are highly specific for their particular substrates, and show diverse modes of action, exhibiting either processive, multiple attack, or patterned deacetylation mechanisms. However, the determinants of substrate specificity remain poorly understood. Here, we review the current knowledge on the structure, activity, and specificity of CE4 enzymes, focusing on chitin deacetylases and related enzymes active on N-acetylglucosamine-containing oligo and polysaccharides.
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8
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Giastas P, Andreou A, Papakyriakou A, Koutsioulis D, Balomenou S, Tzartos SJ, Bouriotis V, Eliopoulos EE. Structures of the Peptidoglycan N-Acetylglucosamine Deacetylase Bc1974 and Its Complexes with Zinc Metalloenzyme Inhibitors. Biochemistry 2018; 57:753-763. [PMID: 29257674 DOI: 10.1021/acs.biochem.7b00919] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The cell wall peptidoglycan is recognized as a primary target of the innate immune system, and usually its disintegration results in bacterial lysis. Bacillus cereus, a close relative of the highly virulent Bacillus anthracis, contains 10 polysaccharide deacetylases. Among these, the peptidoglycan N-acetylglucosamine deacetylase Bc1974 is the highest homologue to the Bacillus anthracis Ba1977 that is required for full virulence and is involved in resistance to the host's lysozyme. These metalloenzymes belong to the carbohydrate esterase family 4 (CE4) and are attractive targets for the development of new anti-infective agents. Herein we report the first X-ray crystal structures of the NodB domain of Bc1974, the conserved catalytic core of CE4s, in the unliganded form and in complex with four known metalloenzyme inhibitors and two amino acid hydroxamates that target the active site metal. These structures revealed the presence of two conformational states of a catalytic loop known as motif-4 (MT4), which were not observed previously for peptidoglycan deacetylases, but were recently shown in the structure of a Vibrio clolerae chitin deacetylase. By employing molecular docking of a substrate model, we describe a catalytic mechanism that probably involves initial binding of the substrate in a receptive, more open state of MT4 and optimal catalytic activity in the closed state of MT4, consistent with the previous observations. The ligand-bound structures presented here, in addition to the five Bc1974 inhibitors identified, provide a valuable basis for the design of antibacterial agents that target the peptidoglycan deacetylase Ba1977.
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Affiliation(s)
- Petros Giastas
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens , Iera Odos 75, 11855 Athens, Greece.,Department of Neurobiology, Hellenic Pasteur Institute , Vasilissis Sofias 127, 11521 Athens, Greece
| | - Athena Andreou
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens , Iera Odos 75, 11855 Athens, Greece
| | - Athanasios Papakyriakou
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens , Iera Odos 75, 11855 Athens, Greece.,Institute of Biosciences and Applications, NCSR "Demokritos" , 15310 Aghia Paraskevi, Athens, Greece
| | - Dimitris Koutsioulis
- Institute of Molecular Biology and Biotechnology, FORTH , 70013 Heraklion, Crete, Greece
| | - Stavroula Balomenou
- Institute of Molecular Biology and Biotechnology, FORTH , 70013 Heraklion, Crete, Greece.,Department of Biology, Enzyme Biotechnology Group, University of Crete , Vasilika Vouton, 70013 Heraklion, Crete, Greece
| | - Socrates J Tzartos
- Department of Neurobiology, Hellenic Pasteur Institute , Vasilissis Sofias 127, 11521 Athens, Greece
| | - Vassilis Bouriotis
- Institute of Molecular Biology and Biotechnology, FORTH , 70013 Heraklion, Crete, Greece.,Department of Biology, Enzyme Biotechnology Group, University of Crete , Vasilika Vouton, 70013 Heraklion, Crete, Greece
| | - Elias E Eliopoulos
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens , Iera Odos 75, 11855 Athens, Greece
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9
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Fadouloglou VE, Balomenou S, Aivaliotis M, Kotsifaki D, Arnaouteli S, Tomatsidou A, Efstathiou G, Kountourakis N, Miliara S, Griniezaki M, Tsalafouta A, Pergantis SA, Boneca IG, Glykos NM, Bouriotis V, Kokkinidis M. Unusual α-Carbon Hydroxylation of Proline Promotes Active-Site Maturation. J Am Chem Soc 2017; 139:5330-5337. [DOI: 10.1021/jacs.6b12209] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Stavroula Balomenou
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Michalis Aivaliotis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Dina Kotsifaki
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Sofia Arnaouteli
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Anastasia Tomatsidou
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Giorgos Efstathiou
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Nikos Kountourakis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Sofia Miliara
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Marianna Griniezaki
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Aleka Tsalafouta
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Spiros A. Pergantis
- Department
of Chemistry, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Ivo G. Boneca
- Biology
and Genetics of the Bacterial Cell Wall Unit, Institut Pasteur, 75015 Paris, France
- INSERM, Equipe Avenir, Paris, France
| | - Nicholas M. Glykos
- Department
of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, 68100 Alexandroupolis, Greece
| | - Vassilis Bouriotis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
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10
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11
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Lambert C, Lerner TR, Bui NK, Somers H, Aizawa SI, Liddell S, Clark A, Vollmer W, Lovering AL, Sockett RE. Interrupting peptidoglycan deacetylation during Bdellovibrio predator-prey interaction prevents ultimate destruction of prey wall, liberating bacterial-ghosts. Sci Rep 2016; 6:26010. [PMID: 27211869 PMCID: PMC4876506 DOI: 10.1038/srep26010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/22/2016] [Indexed: 11/25/2022] Open
Abstract
The peptidoglycan wall, located in the periplasm between the inner and outer membranes of the cell envelope in Gram-negative bacteria, maintains cell shape and endows osmotic robustness. Predatory Bdellovibrio bacteria invade the periplasm of other bacterial prey cells, usually crossing the peptidoglycan layer, forming transient structures called bdelloplasts within which the predators replicate. Prey peptidoglycan remains intact for several hours, but is modified and then degraded by escaping predators. Here we show predation is altered by deleting two Bdellovibrio N-acetylglucosamine (GlcNAc) deacetylases, one of which we show to have a unique two domain structure with a novel regulatory”plug”. Deleting the deacetylases limits peptidoglycan degradation and rounded prey cell “ghosts” persist after mutant-predator exit. Mutant predators can replicate unusually in the periplasmic region between the peptidoglycan wall and the outer membrane rather than between wall and inner-membrane, yet still obtain nutrients from the prey cytoplasm. Deleting two further genes encoding DacB/PBP4 family proteins, known to decrosslink and round prey peptidoglycan, results in a quadruple mutant Bdellovibrio which leaves prey-shaped ghosts upon predation. The resultant bacterial ghosts contain cytoplasmic membrane within bacteria-shaped peptidoglycan surrounded by outer membrane material which could have promise as “bacterial skeletons” for housing artificial chromosomes.
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Affiliation(s)
- Carey Lambert
- Centre for Genetics and Genomics, School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Thomas R Lerner
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Nhat Khai Bui
- The Centre for Bacterial Cell Biology, Baddiley Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Hannah Somers
- Centre for Genetics and Genomics, School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Shin-Ichi Aizawa
- Department of Life Sciences, Prefectural University of Hiroshima, Shobara, Hiroshima, 727-0023, Japan
| | - Susan Liddell
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - Ana Clark
- Centre for Genetics and Genomics, School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Baddiley Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Andrew L Lovering
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - R Elizabeth Sockett
- Centre for Genetics and Genomics, School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, NG7 2UH, UK
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12
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Hao GF, Xu WF, Yang SG, Yang GF. Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) for Conformational Space Search of Peptide and Miniprotein. Sci Rep 2015; 5:15568. [PMID: 26492886 PMCID: PMC4616061 DOI: 10.1038/srep15568] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/29/2015] [Indexed: 12/03/2022] Open
Abstract
Protein and peptide structure predictions are of paramount importance for understanding their functions, as well as the interactions with other molecules. However, the use of molecular simulation techniques to directly predict the peptide structure from the primary amino acid sequence is always hindered by the rough topology of the conformational space and the limited simulation time scale. We developed here a new strategy, named Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) to identify the native states of a peptide and miniprotein. A cluster of near native structures could be obtained by using the MSA-MD method, which turned out to be significantly more efficient in reaching the native structure compared to continuous MD and conventional SA-MD simulation.
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Affiliation(s)
- Ge-Fei Hao
- Key Laboratory of Pesticide &Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P.R.China
| | - Wei-Fang Xu
- Key Laboratory of Pesticide &Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P.R.China
| | - Sheng-Gang Yang
- Key Laboratory of Pesticide &Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P.R.China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide &Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P.R.China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjing 300072, P.R.China
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13
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Arnaouteli S, Giastas P, Andreou A, Tzanodaskalaki M, Aldridge C, Tzartos SJ, Vollmer W, Eliopoulos E, Bouriotis V. Two Putative Polysaccharide Deacetylases Are Required for Osmotic Stability and Cell Shape Maintenance in Bacillus anthracis. J Biol Chem 2015; 290:13465-78. [PMID: 25825488 PMCID: PMC4505593 DOI: 10.1074/jbc.m115.640029] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Indexed: 11/26/2022] Open
Abstract
Membrane-anchored lipoproteins have a broad range of functions and play key roles in several cellular processes in Gram-positive bacteria. BA0330 and BA0331 are the only lipoproteins among the 11 known or putative polysaccharide deacetylases of Bacillus anthracis. We found that both lipoproteins exhibit unique characteristics. BA0330 and BA0331 interact with peptidoglycan, and BA0330 is important for the adaptation of the bacterium to grow in the presence of a high concentration of salt, whereas BA0331 contributes to the maintenance of a uniform cell shape. They appear not to alter the peptidoglycan structure and do not contribute to lysozyme resistance. The high resolution x-ray structure of BA0330 revealed a C-terminal domain with the typical fold of a carbohydrate esterase 4 and an N-terminal domain unique for this family, composed of a two-layered (4 + 3) β-sandwich with structural similarity to fibronectin type 3 domains. Our data suggest that BA0330 and BA0331 have a structural role in stabilizing the cell wall of B. anthracis.
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Affiliation(s)
- Sofia Arnaouteli
- From the Department of Biology, Enzyme Biotechnology Group, University of Crete, Vasilika Vouton, 70013 Heraklion, Crete, Greece
| | - Petros Giastas
- the Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece
| | - Athina Andreou
- the Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Mary Tzanodaskalaki
- the Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Christine Aldridge
- the Institute for Cell and Molecular Biosciences, Centre for Bacterial Cell Biology, Newcastle University, NE2 4AX Newcastle upon Tyne, United Kingdom, and
| | - Socrates J Tzartos
- the Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece, the Department of Pharmacy, University of Patras, 26504, Patras, Greece
| | - Waldemar Vollmer
- the Institute for Cell and Molecular Biosciences, Centre for Bacterial Cell Biology, Newcastle University, NE2 4AX Newcastle upon Tyne, United Kingdom, and
| | - Elias Eliopoulos
- the Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Vassilis Bouriotis
- From the Department of Biology, Enzyme Biotechnology Group, University of Crete, Vasilika Vouton, 70013 Heraklion, Crete, Greece, the Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece,
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14
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Strunk RJ, Piemonte KM, Petersen NM, Koutsioulis D, Bouriotis V, Perry K, Cole KE. Structure determination of BA0150, a putative polysaccharide deacetylase from Bacillus anthracis. Acta Crystallogr F Struct Biol Commun 2014; 70:156-9. [PMID: 24637747 PMCID: PMC3936449 DOI: 10.1107/s2053230x13034262] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 12/19/2013] [Indexed: 11/10/2022] Open
Abstract
Polysaccharide deacetylases are bacterial enzymes that catalyze the deacetylation of acetylated sugars on the membranes of Gram-positive bacteria, allowing them to be unrecognized by host immune systems. Inhibition of these enzymes would disrupt such pathogenic defensive mechanisms and therefore offers a promising route for the development of novel antibiotic therapeutics. Here, the first X-ray crystal structure of BA0150, a putative polysaccharide deacetylase from Bacillus anthracis, is reported to 2.0 Å resolution. The overall structure maintains the conserved (α/β)8 fold that is characteristic of this family of enzymes. The lack of a catalytic metal ion and a distinctive metal-binding site, however, suggest that this enzyme is not a functional polysaccharide deacetylase.
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Affiliation(s)
- Robert J. Strunk
- Department of Chemistry, Ithaca College, 953 Danby Road, Ithaca, NY 14850, USA
| | - Katrina M. Piemonte
- Department of Chemistry, Ithaca College, 953 Danby Road, Ithaca, NY 14850, USA
| | - Natasha M. Petersen
- Department of Chemistry, Ithaca College, 953 Danby Road, Ithaca, NY 14850, USA
| | - Dimitris Koutsioulis
- Department of Biology, Enzyme Biotechnology Group, University of Crete, PO Box 2209, Vassilika Vouton, 71409 Heraklion, Crete, Greece
| | - Vassilis Bouriotis
- Department of Biology, Enzyme Biotechnology Group, University of Crete, PO Box 2209, Vassilika Vouton, 71409 Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, 70019 Heraklion, Crete, Greece
| | - Kay Perry
- Northeastern Collaborative Access Team (NE-CAT) and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Kathryn E. Cole
- Department of Chemistry, Ithaca College, 953 Danby Road, Ithaca, NY 14850, USA
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Pokrovskaya V, Poloczek J, Little DJ, Griffiths H, Howell PL, Nitz M. Functional characterization of Staphylococcus epidermidis IcaB, a de-N-acetylase important for biofilm formation. Biochemistry 2013; 52:5463-71. [PMID: 23866051 DOI: 10.1021/bi400836g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A polymer of partially de-N-acetylated β-1,6-linked N-acetylglucosamine (dPNAG), also known as the polysaccharide intercellular adhesin (PIA), is an important component of many bacterial biofilm matrices. In Staphyloccocus epidermidis, the poly-N-acetylglucosamine polymer is partially de-N-acetylated by the extracellular protein IcaB. To understand the mechanism of action of IcaB, the enzyme was overexpressed and purified. IcaB demonstrates metal-dependent de-N-acetylase activity on β-1,6-linked N-acetylglucosamine oligomers with a broad preference for divalent metals. Steady-state kinetic analysis reveals the low catalytic efficiency (pentasaccharide kcat/KM 0.03 M(-1) s(-1)) of the enzyme toward the oligomeric substrates. While IcaB displays similar rates of de-N-acetylation with tri- through hexasaccharide PNAG oligomers, position specific de-N-acetylation was only observed with penta- and hexasaccharides. The enzyme preferentially de-N-acetylates the second residue from the reducing terminus in the pentasaccharide and second and third residues from the reducing terminus in the hexasaccharide. The data described here represent an important step toward a detailed understanding of dPNAG biosynthesis in S. epidermidis, an important nosocomial pathogen, as well as in other Gram-positive bacteria. The low catalytic activity of IcaB is consistent with reports of other enzymes which act on biofilm-related polysaccharides, and this emerging trend may indicate a common feature among this group of polysaccharide processing enzymes.
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Affiliation(s)
- Varvara Pokrovskaya
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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