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Weerasinghe NW, Habibi Y, Uggowitzer KA, Thibodeaux CJ. Exploring the Conformational Landscape of a Lanthipeptide Synthetase Using Native Mass Spectrometry. Biochemistry 2021; 60:1506-1519. [PMID: 33887902 DOI: 10.1021/acs.biochem.1c00085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lanthipeptides are ribosomally synthesized and post-translationally modified peptide (RiPP) natural products. These genetically encoded peptides are biosynthesized by multifunctional enzymes (lanthipeptide synthetases) that possess relaxed substrate specificity and catalyze iterative rounds of post-translational modification. Recent evidence has suggested that some lanthipeptide synthetases are structurally dynamic enzymes that are allosterically activated by precursor peptide binding and that conformational sampling of the enzyme-peptide complex may play an important role in defining the efficiency and sequence of biosynthetic events. These "biophysical" processes, while critical for defining the activity and function of the synthetase, remain very challenging to study with existing methodologies. Herein, we show that native mass spectrometry coupled to ion mobility (native IM-MS) provides a powerful and sensitive means for investigating the conformational landscapes and intermolecular interactions of lanthipeptide synthetases. Namely, we demonstrate that the class II lanthipeptide synthetase (HalM2) and its noncovalent complex with the cognate HalA2 precursor peptide can be delivered into the gas phase in a manner that preserves native structures and intermolecular enzyme-peptide contacts. Moreover, gas phase ion mobility studies of the natively folded ions demonstrate that peptide binding and mutations to dynamic structural elements of HalM2 alter the conformational landscape of the enzyme. Cumulatively, these data support previous claims that lanthipeptide synthetases are structurally dynamic enzymes that undergo functionally relevant conformational changes in response to precursor peptide binding. This work establishes native IM-MS as a versatile approach for characterizing intermolecular interactions and for unraveling the relationships between protein structure and biochemical function in RiPP biosynthetic systems.
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Affiliation(s)
- Nuwani W Weerasinghe
- Department of Chemistry and Centre de Recherche en Biologie Structurale, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Yeganeh Habibi
- Department of Chemistry and Centre de Recherche en Biologie Structurale, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Kevin A Uggowitzer
- Department of Chemistry and Centre de Recherche en Biologie Structurale, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Christopher J Thibodeaux
- Department of Chemistry and Centre de Recherche en Biologie Structurale, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
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2
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Lagedroste M, Smits SHJ, Schmitt L. Importance of the leader peptide sequence on the lanthipeptide secretion level. FEBS J 2021; 288:4348-4363. [PMID: 33482024 DOI: 10.1111/febs.15724] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/27/2020] [Accepted: 01/21/2021] [Indexed: 11/29/2022]
Abstract
Lanthipeptides are ribosomally synthesized and posttranslationally modified peptides. Their precursor peptide comprises of an N-terminal leader peptide and a C-terminal core peptide. Here, the leader peptide is crucial for enzyme recognition especially for the modification enzymes and acts furthermore as a secretion signal for the lanthipeptide exporter. The core peptide is the target site for the posttranslational modifications and contains dehydrated amino acids and lanthionine rings. Nisin produced by the Gram-positive bacterium Lactococcus lactis is one of the best-studied lanthipeptides and used as a model system to study their modification and secretion processes. Nisin is secreted as a precursor peptide. Here, we present an in vivo secretion analysis of NisT in the absence of the modification machinery allowing the secretion of leader peptide mutants and their impact solely on the secretion activity of NisT. Additionally, we created leader peptide hybrids to provide new insights, how the secretion is effected by unnatural leader peptides. The focus on the secretion activity of the transporter alone enabled us to determine the recognition site of NisT within the leader peptide of nisin.
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Affiliation(s)
- Marcel Lagedroste
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Germany
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3
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Virgicin, a novel lanthipeptide from Virgibacillus sp. strain AK90 exhibits inhibitory activity against Gram-positive bacteria. World J Microbiol Biotechnol 2019; 35:133. [PMID: 31432254 DOI: 10.1007/s11274-019-2707-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/02/2019] [Indexed: 12/19/2022]
Abstract
There is a significant increase in the discovery of new antimicrobial compounds in recent past to combat drug resistant pathogens. Members of the genus Bacillus and related genera have been screened extensively due to their ability to produce wide range of antimicrobial compounds. In this study, we have isolated and characterized a new antimicrobial peptide from a marine bacterium identified as Virgibacillus species. The low molecular mass and stability of the antimicrobial substance pointed towards the bacteriocinogenic nature of the compound. The RAST analysis of genome sequence showed presence of a putative bacteriocin biosynthetic cluster containing genes necessary for synthesis of a lanthipeptide. Translated amino acid sequence of mature C-terminal propeptide showed identity with salivaricin A (52.2%) and lacticin A (33.3%). Accordingly, the mass (2417 Da) obtained by MALDI analysis was in agreement with posttranslational modifications of the leader peptide to yield three methyl lanthionine rings and a disulfide bond between two free cysteine residues. The lanthipeptide was named as virgicin, which selectively inhibited the growth of Gram-positive bacteria and biofilm formation by Enterococcus faecalis. Inhibition of biofilm formation by E. faecalis was also observed in in vitro model experiments using hydroxyapatite discs. Thus, virgicin appears to be a promising new bacteriocin to control oral biofilm formation by selective pathogens.
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Repka LM, Chekan JR, Nair SK, van der Donk WA. Mechanistic Understanding of Lanthipeptide Biosynthetic Enzymes. Chem Rev 2017; 117:5457-5520. [PMID: 28135077 PMCID: PMC5408752 DOI: 10.1021/acs.chemrev.6b00591] [Citation(s) in RCA: 313] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
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Lanthipeptides
are ribosomally synthesized and post-translationally
modified peptides (RiPPs) that display a wide variety of biological
activities, from antimicrobial to antiallodynic. Lanthipeptides that
display antimicrobial activity are called lantibiotics. The post-translational
modification reactions of lanthipeptides include dehydration of Ser
and Thr residues to dehydroalanine and dehydrobutyrine, a transformation
that is carried out in three unique ways in different classes of lanthipeptides.
In a cyclization process, Cys residues then attack the dehydrated
residues to generate the lanthionine and methyllanthionine thioether
cross-linked amino acids from which lanthipeptides derive their name.
The resulting polycyclic peptides have constrained conformations that
confer their biological activities. After installation of the characteristic
thioether cross-links, tailoring enzymes introduce additional post-translational
modifications that are unique to each lanthipeptide and that fine-tune
their activities and/or stability. This review focuses on studies
published over the past decade that have provided much insight into
the mechanisms of the enzymes that carry out the post-translational
modifications.
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Affiliation(s)
- Lindsay M Repka
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jonathan R Chekan
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Satish K Nair
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Wilfred A van der Donk
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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Plat A, Kuipers A, Crabb J, Rink R, Moll GN. Mutagenesis of nisin's leader peptide proline strongly modulates export of precursor nisin. Antonie van Leeuwenhoek 2016; 110:321-330. [PMID: 27830473 DOI: 10.1007/s10482-016-0802-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/04/2016] [Indexed: 11/25/2022]
Abstract
The lantibiotic nisin is produced by Lactococcus lactis as a precursor peptide comprising a 23 amino acid leader peptide and a 34 amino acid post-translationally modifiable core peptide. We previously demonstrated that the conserved FNLD part of the leader is essential for intracellular enzyme-catalyzed introduction of lanthionines in the core peptide and also for transporter-mediated export, whereas other positions are subject to large mutational freedom. We here demonstrate that, in the absence of the extracellular leader peptidase, NisP, export of precursor nisin via the modification and transporter enzymes, NisBTC, is strongly affected by multiple substitutions of the leader residue at position -2, but not by substitution of positions in the vicinity of this site. Export levels of precursor nisin increased by more than 70% for position -2 mutants Asp, Thr, Ser, Trp, Lys, Val and decreased more than 70% for Cys, His, Met. In a strain with leader peptidase, the Pro-2Lys and Pro-2Asp precursor nisins were less efficiently cleaved by NisP than wild type precursor nisin. Taken together, the wild type precursor nisin with a proline at position -2 allows balanced export and cleavage efficiencies by precursor nisin's transporter and leader peptidase.
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Affiliation(s)
- Annechien Plat
- Biomade Technology Foundation, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
- Gynecological Oncology, University Medical Center Groningen, 9700 RB, Groningen, The Netherlands
| | - Anneke Kuipers
- Lanthio Pharma, MorphoSys AG, Rozenburglaan 13B, 9727 DL, Groningen, The Netherlands
| | - Joe Crabb
- ImmuCell Corp., 56 Evergreen Drive, Portland, ME, 04130, USA
| | - Rick Rink
- Lanthio Pharma, MorphoSys AG, Rozenburglaan 13B, 9727 DL, Groningen, The Netherlands
| | - Gert N Moll
- Lanthio Pharma, MorphoSys AG, Rozenburglaan 13B, 9727 DL, Groningen, The Netherlands.
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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Baindara P, Chaudhry V, Mittal G, Liao LM, Matos CO, Khatri N, Franco OL, Patil PB, Korpole S. Characterization of the Antimicrobial Peptide Penisin, a Class Ia Novel Lantibiotic from Paenibacillus sp. Strain A3. Antimicrob Agents Chemother 2016; 60:580-91. [PMID: 26574006 PMCID: PMC4704198 DOI: 10.1128/aac.01813-15] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 11/08/2015] [Indexed: 11/20/2022] Open
Abstract
Attempts to isolate novel antimicrobial peptides from microbial sources have been on the rise recently, despite their low efficacy in therapeutic applications. Here, we report identification and characterization of a new efficient antimicrobial peptide from a bacterial strain designated A3 that exhibited highest identity with Paenibacillus ehimensis. Upon purification and subsequent molecular characterization of the antimicrobial peptide, referred to as penisin, we found the peptide to be a bacteriocin-like peptide. Consistent with these results, RAST analysis of the entire genome sequence revealed the presence of a lantibiotic gene cluster containing genes necessary for synthesis and maturation of a lantibiotic. While circular dichroism and one-dimension nuclear magnetic resonance experiments confirmed a random coil structure of the peptide, similar to other known lantibiotics, additional biochemical evidence suggests posttranslational modifications of the core peptide yield six thioether cross-links. The deduced amino acid sequence of the putative biosynthetic gene penA showed approximately 74% similarity with elgicin A and 50% similarity with the lantibiotic paenicidin A. Penisin effectively killed methicillin-resistant Staphylococcus aureus (MRSA) and did not exhibit hemolysis activity. Unlike other lantibiotics, it effectively inhibited the growth of Gram-negative bacteria. Furthermore, 80 mg/kg of body weight of penisin significantly reduced bacterial burden in a mouse thigh infection model and protected BALB/c mice in a bacteremia model entailing infection with Staphylococcus aureus MTCC 96, suggesting that it could be a promising new antimicrobial peptide.
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Affiliation(s)
| | - Vasvi Chaudhry
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Garima Mittal
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Luciano M Liao
- Institute of Chemistry, Federal University of Goiás, Goiânia, Brazil
| | - Carolina O Matos
- Institute of Chemistry, Federal University of Goiás, Goiânia, Brazil
| | - Neeraj Khatri
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Octavio L Franco
- Centro de Analises Proteomicas e Bioquimicas, Pós-graduacão em Ciências Genomicas e Biotecnologia, Brasília, Brazil S-Inova, Programa de Pós-Graduacão em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Prabhu B Patil
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Suresh Korpole
- CSIR Institute of Microbial Technology, Chandigarh, India
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7
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Biosynthesis and transport of the lantibiotic mutacin 1140 produced by Streptococcus mutans. J Bacteriol 2015; 197:1173-84. [PMID: 25605307 DOI: 10.1128/jb.02531-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Lantibiotics are ribosomally synthesized peptide antibiotics composed of an N-terminal leader peptide that is cleaved to yield the active antibacterial peptide. Significant advancements in molecular tools that promote the study of lantibiotic biosynthesis can be used in Streptococcus mutans. Herein, we further our understanding of leader peptide sequence and core peptide structural requirements for the biosynthesis and transport of the lantibiotic mutacin 1140. Our study on mutacin 1140 biosynthesis shows a dedicated secondary cleavage site within the leader peptide and the dependency of transport on core peptide posttranslational modifications (PTMs). The secondary cleavage site on the leader peptide is found at the -9 position, and secondary cleavage occurs before the core peptide is transported out of the cell. The coordinated cleavage at the -9 position was absent in a lanT deletion strain, suggesting that the core peptide interaction with the LanT transporter enables uniform cleavage at the -9 position. Following transport, the LanP protease was found to be tolerant to a wide variety of amino acid substitutions at the primary leader peptide cleavage site, with the exception of arginine at the -1 position. Several leader and core peptide mutations produced core peptide variants that had intermediate stages of PTM enzyme modifications, supporting the concept that PTM enzyme modifications, secondary cleavage, and transport are occurring in a highly coordinated fashion. IMPORTANCE Mutacin 1140 belongs to the class I lantibiotic family of ribosomally synthesized and posttranslationally modified peptides (RiPPs). The biosynthesis of mutacin 1140 is a highly efficient process which does not lead to a discernible level of production of partially modified core peptide variants. The products isolated from an extensive mutagenesis study on the leader and core peptides of mutacin 1140 show that the posttranslational modifications (PTMs) on the core peptide occur under a highly coordinated dynamic process. PTMs are dictated by the distance of the core peptide modifiable residues from PTM enzyme active sites. The formation of lanthionine rings aids in the formation of successive PTMs, as was observed in a peptide variant lacking a C-terminal decarboxylation.
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Houssen WE, Wright SH, Kalverda AP, Thompson GS, Kelly SM, Jaspars M. Solution structure of the leader sequence of the patellamide precursor peptide, PatE1-34. Chembiochem 2011; 11:1867-73. [PMID: 20715266 DOI: 10.1002/cbic.201000305] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The solution structure of the leader sequence of the patellamide precursor peptide was analysed by using CD and determined with NOE-restrained molecular dynamics calculations. This leader sequence is highly conserved in the precursor peptides of some other cyanobactins harbouring heterocycles, and is assumed to play a role in targeting the precursor peptide to the post-translational machinery. The sequence was observed to form an alpha-helix spanning residues 13-28 with a hydrophobic surface on one side of the helix. This hydrophobic surface is proposed to be the site of the initial binding with modifying enzymes.
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Affiliation(s)
- Wael E Houssen
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
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Oman TJ, van der Donk WA. Follow the leader: the use of leader peptides to guide natural product biosynthesis. Nat Chem Biol 2010; 6:9-18. [PMID: 20016494 PMCID: PMC3799897 DOI: 10.1038/nchembio.286] [Citation(s) in RCA: 292] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The avalanche of genomic information in the past decade has revealed that natural product biosynthesis using the ribosomal machinery is much more widespread than originally anticipated. Nearly all of these compounds are crafted through post-translational modifications of a larger precursor peptide that often contains the marching orders for the biosynthetic enzymes. We review here the available information for how the peptide sequences in the precursors govern the post-translational tailoring processes for several classes of natural products. In addition, we highlight the great potential these leader peptide-directed biosynthetic systems offer for engineering conformationally restrained and pharmacophore-rich products with structural diversity that greatly expands the proteinogenic repertoire.
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Affiliation(s)
- Trent J. Oman
- Department of Chemistry, Howard Hughes Medical Institute, and Institute for Genomic Biology. University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Telephone: (217) 244 5360, FAX: (217) 244 8533
| | - Wilfred A. van der Donk
- Department of Chemistry, Howard Hughes Medical Institute, and Institute for Genomic Biology. University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Telephone: (217) 244 5360, FAX: (217) 244 8533
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Nagao JI, Harada Y, Shioya K, Aso Y, Zendo T, Nakayama J, Sonomoto K. Lanthionine introduction into nukacin ISK-1 prepeptide by co-expression with modification enzyme NukM in Escherichia coli. Biochem Biophys Res Commun 2005; 336:507-13. [PMID: 16143300 DOI: 10.1016/j.bbrc.2005.08.125] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2005] [Accepted: 08/17/2005] [Indexed: 11/20/2022]
Abstract
We demonstrated lanthionine introduction into hexa-histidine-tagged (His-tagged) nukacin ISK-1 prepeptide NukA by modification enzyme NukM in Escherichia coli. Co-expression of nukA and nukM, purification of the resulting His-tagged prepeptide by affinity chromatography, and subsequent mass spectrometry analysis showed that the prepeptide was converted into a postulated peptide with decrease in mass of 72Da which resulted from dehydration of four amino acids. Characterization of the resultant prepeptide indicated the presence of unusual amino acids, such as dehydrated amino acid, lanthionine or 3-methyllanthionine, in its C-terminal propeptide moiety. The modified prepeptide encompassing the leader peptide attached to the post-translationally modified propeptide moiety was readily obtained by one-step purification. Our findings will thus be a powerful tool for introducing unusual amino acids aimed at peptide engineering and also helpful to provide new insight for further understanding of lanthionine-forming enzymes for lantibiotics.
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Affiliation(s)
- Jun-Ichi Nagao
- Laboratory of Microbial Technology, Division of Microbial Science and Technology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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Chatterjee C, Paul M, Xie L, van der Donk WA. Biosynthesis and mode of action of lantibiotics. Chem Rev 2005; 105:633-84. [PMID: 15700960 DOI: 10.1021/cr030105v] [Citation(s) in RCA: 556] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Champak Chatterjee
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois, USA
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Roy RS, Kim S, Baleja JD, Walsh CT. Role of the microcin B17 propeptide in substrate recognition: solution structure and mutational analysis of McbA1-26. CHEMISTRY & BIOLOGY 1998; 5:217-28. [PMID: 9545435 DOI: 10.1016/s1074-5521(98)90635-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND The peptide antibiotic microcin B17 (MccB17) contains oxazole and thiazole heterocycles formed by the post-translational modification of four cysteine and four serine residues. An amino-terminal propeptide targets the 69 amino acid precursor of MccB17 (preproMccB17) to the heterocyclization enzyme MccB17 synthetase. The mode of synthetase recognition has been unclear, because there has been limited structural information available on the MccB17 propeptide to date. RESULTS The solution structure of the MccB17 propeptide (McbA1-26), determined using nuclear magnetic resonance, reveals that McbA1-26 is an amphipathic alpha helix. Mutational analysis of 13 propeptide residues showed that Phe8 and Leu12 are essential residues for MccB17 synthetase recognition. A domain of the propeptide was putatively identified as the region that interacts with the synthetase. CONCLUSIONS MccB17 synthetase recognizes key hydrophobic residues within a helical propeptide, allowing the selective heterocyclization of downstream cysteine and serine residues in preproMccB17. The determination of the solution structure of the propeptide should facilitate the investigation of other functions of the propeptide, including a potential role in antibiotic secretion.
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Affiliation(s)
- R S Roy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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