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Brückner S, Müller F, Schadowski L, Kalle T, Weber S, Marino EC, Kutscher B, Möller AM, Adler S, Begerow D, Steinchen W, Bange G, Narberhaus F. (p)ppGpp and moonlighting RNases influence the first step of lipopolysaccharide biosynthesis in Escherichia coli. Microlife 2023; 4:uqad031. [PMID: 37426605 PMCID: PMC10326835 DOI: 10.1093/femsml/uqad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/12/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023]
Abstract
The outer membrane (OM) protects Gram-negative bacteria from harsh environmental conditions and provides intrinsic resistance to many antimicrobial compounds. The asymmetric OM is characterized by phospholipids in the inner leaflet and lipopolysaccharides (LPS) in the outer leaflet. Previous reports suggested an involvement of the signaling nucleotide ppGpp in cell envelope homeostasis in Escherichia coli. Here, we investigated the effect of ppGpp on OM biosynthesis. We found that ppGpp inhibits the activity of LpxA, the first enzyme of LPS biosynthesis, in a fluorometric in vitro assay. Moreover, overproduction of LpxA resulted in elongated cells and shedding of outer membrane vesicles (OMVs) with altered LPS content. These effects were markedly stronger in a ppGpp-deficient background. We further show that RnhB, an RNase H isoenzyme, binds ppGpp, interacts with LpxA, and modulates its activity. Overall, our study uncovered new regulatory players in the early steps of LPS biosynthesis, an essential process with many implications in the physiology and susceptibility to antibiotics of Gram-negative commensals and pathogens.
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Affiliation(s)
- Simon Brückner
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Fabian Müller
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Laura Schadowski
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Tyll Kalle
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Sophia Weber
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Emily C Marino
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Blanka Kutscher
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Anna-Maria Möller
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Sabine Adler
- Evolution of Plants and Fungi, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Dominik Begerow
- Evolution of Plants and Fungi, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
- Organismische Botanik und Mykologie, Institut für Planzenwissenschaften und Mikrobiologie, Fachbereich Biologie, Universität Hamburg,Ohnhorststrasse 18, Hamburg, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Karl-von-Frisch-Strasse 14, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Karl-von-Frisch-Strasse 14, Marburg, Germany
| | - Franz Narberhaus
- Corresponding author. Faculty of Biology and Biotechnology, Microbial Biology, Ruhr University Bochum, Universitätsstrasse 150, NDEF 06/784, 44780 Bochum, Germany. Tel: +492343223100; Fax: +492343214620; E-mail:
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Azhar M, Yousaf M, Maher S, Fatmi MQ. Discovering Potential Bacteriocins Against Pseudomonas fragi: a Subtractive Proteomics and Molecular Dynamic Simulation Study for Food Preservation. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04509-7. [PMID: 37103735 DOI: 10.1007/s12010-023-04509-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 04/28/2023]
Abstract
Food preservation is a schematic and scientific procedure employed for the maintenance and improvement of food's quality, shelf life, and nutritional value. Although, on one hand, ancient conventional methods such as freezing, pasteurization, canning, and chemical methods have the potential to lengthen the shelf life of edible substances, but on the other hand, they can deteriorate its nutritional value as well. Present research focuses on the identification of promising bacteriocins against Pseudomonas fragi via subtractive proteomics pipeline as an alternative approach for food preservation. Bacteriocins are small peptides produced by certain microbes to naturally defend themselves by destroying other closely related bacteria residing in their neighborhood. P. fragi lies among the most notable microbes responsible for the elicitation of food spoilage. Due to increasing emergence and prevalence of multidrug resistance bacteria, there is a need to unravel novel drug targets, crucially involved in food decay process. Based on subtractive scrutinization, UDP-N-acetylglucosamine O-acyltransferase (LpxA) was chosen as promising therapeutic protein target that could play a significant role in progression of food spoilage. Subtilosin A, thuricin-CD, and mutacin B-NY266 were found as the most robust inhibitors of LpxA according to the molecular docking assay results. Molecular dynamic simulations and binding energy calculations via MM/PBSA method of LpxA and three top hit docked complexes, i.e., LpxA-subtilosin A, LpxA-thuricin-CD, and LpxA-mutacin B-NY266, revealed stability throughout simulations and ensured that shortlisted bacteriocins had strong affinity for LpxA.
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Affiliation(s)
- Maria Azhar
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan
| | - Maha Yousaf
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan
| | - Saima Maher
- Department of Chemistry, Sardar Bahadur Khan Women's University, Quetta, Pakistan
| | - M Qaiser Fatmi
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan.
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Khan RJ, Singh E, Jha RK, Kumar A, Bhati SK, Zia MP, Jain M, Singh RP, Muthukumaran J, Singh AK. Identification and prioritization of potential therapeutic molecules against LpxA from Acinetobacter baumannii - A computational study. Curr Res Struct Biol 2023; 5:100096. [PMID: 36895415 PMCID: PMC9988473 DOI: 10.1016/j.crstbi.2023.100096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 01/05/2023] [Accepted: 01/29/2023] [Indexed: 02/17/2023] Open
Abstract
A. baumannii is a ubiquitously found gram-negative, multi-drug resistant bacterial species from the ESKAPE family of pathogens known to be the causative agent for hospital-acquired infections such as pneumonia, meningitis, endocarditis, septicaemia and urinary tract infections. A. baumannii is implicated as a contributor to bloodstream infections in approximately 2% of all worldwide infections. Hence, exploring novel therapeutic agents against the bacterium is essential. LpxA or UDP-N-acetylglucosamine acetyltransferase is an essential enzyme important in Lipid A biosynthesis which catalyses the reversible transfer of an acetyl group on the glucosamine 3-OH of the UDP-GlcNAc which is a crucial step in the biosynthesis of the protective Lipopolysaccharides (LPS) layer of the bacteria which upon disruption can lead to the elimination of the bacterium which delineates LpxA as an appreciable drug target from A. baumannii. The present study performs high throughput virtual screening of LpxA against the enamine-HTSC-large-molecule library and performs toxicity and ADME screening to identify the three promising lead molecules subjected to molecular dynamics simulations. Global and essential dynamics analysis of LpxA and its complexes along with FEL and MM/PBSA based binding free energy delineate Z367461724 and Z219244584 as potential inhibitors against LpxA from A. baumannii.
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Affiliation(s)
- Rameez Jabeer Khan
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P, India
| | - Ekampreet Singh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P, India
| | - Rajat Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P, India
| | - Ankit Kumar
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P, India
| | - Saurabh Kumar Bhati
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P, India
| | - Mahrukh Parveez Zia
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P, India
| | - Monika Jain
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P, India
| | - Rashmi Prabha Singh
- Department of Biotechnology, IILM College of Engineering & Technology, Greater Noida, U.P, India
| | - Jayaraman Muthukumaran
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P, India
| | - Amit Kumar Singh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P, India
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Sacco MD, Defrees K, Zhang X, Lawless W, Nwanochie E, Balsizer A, Darch SE, Renslo AR, Chen Y. Structure-Based Ligand Design Targeting Pseudomonas aeruginosa LpxA in Lipid A Biosynthesis. ACS Infect Dis 2022; 8:1231-1240. [PMID: 35653508 DOI: 10.1021/acsinfecdis.1c00650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzymes involved in lipid A biosynthesis are promising antibacterial drug targets in Gram-negative bacteria. In this study, we use a structure-based design approach to develop a series of novel tetrazole ligands with low μM affinity for LpxA, the first enzyme in the lipid A pathway. Aided by previous structural data, X-ray crystallography, and surface plasmon resonance bioanalysis, we identify 17 hit compounds. Two of these hits were subsequently modified to optimize interactions with three regions of the LpxA active site. This strategy ultimately led to the discovery of ligand L13, which had a KD of 3.0 μM. The results reveal new chemical scaffolds as potential LpxA inhibitors, important binding features for ligand optimization, and protein conformational changes in response to ligand binding. Specifically, they show that a tetrazole ring is well-accommodated in a small cleft formed between Met169, the "hydrophobic-ruler" and His156, both of which demonstrate significant conformational flexibility. Furthermore, we find that the acyl-chain binding pocket is the most tractable region of the active site for realizing affinity gains and, along with a neighboring patch of hydrophobic residues, preferentially binds aliphatic and aromatic groups. The results presented herein provide valuable chemical and structural information for future inhibitor discovery against this important antibacterial drug target.
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Affiliation(s)
- Michael D. Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Kyle Defrees
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, California 94143, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - William Lawless
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Emeka Nwanochie
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Amelia Balsizer
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Sophie E. Darch
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Adam R. Renslo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, California 94143, United States
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
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Li DK, Mu YT, Feng HH. The expression and purification of LpxA of Chlamydia trachomatis and preparation of its polyclonal antibody. Z NATURFORSCH C 2020; 75:313-317. [PMID: 32374296 DOI: 10.1515/znc-2020-0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 04/09/2020] [Indexed: 11/15/2022]
Abstract
The purpose of this study is to purify the LpxA protein of Chlamydia trachomatis (Ct) and prepare the polyclonal antibody against LpxA protein, so as to lay a foundation for studying the function of LpxA protein. The LpxA gene was amplified by PCR. The expression plasmid pET28a-LpxA was constructed by using pET28a as the vector. The fusion protein containing 6 histidine tag was induced by IPTG and purified by Ni2+ chromatography gel. The purified His-LpxA protein was used as an immunogen to immunize New Zealand rabbits subcutaneously through the back to prepare polyclonal antibody. Immunoblotting was used to detect the reaction between the antibody and His-LpxA. The determination of polyclonal antibody titer was detected by ELISA. The relative molecular weight of His-LpxA was 32.8 kDa, and it could be expressed in Escherichia coli. The purity of the purified protein was about 95%. After immunizing New Zealand rabbits, the antiserum was able to recognize the recombinant His-LpxA protein with a titer greater than 1:10240. In this study, LpxA protein was successfully purified and antiserum was prepared, which provided an experimental basis for studying the function of LpxA protein.
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Affiliation(s)
- De-Kun Li
- Department of Ophthalmology, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Ying-Tao Mu
- Department of TCM, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, PR China
| | - Huan-Huan Feng
- Xiangyang No.1 People's Hospital, Hubei University of Medicine, No. 15 Jiefang Road, Xiangyang, Hubei, 441000, PR China
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Arenas J, Pupo E, de Jonge E, Pérez-Ortega J, Schaarschmidt J, van der Ley P, Tommassen J. Substrate specificity of the pyrophosphohydrolase LpxH determines the asymmetry of Bordetella pertussis lipid A. J Biol Chem 2019; 294:7982-7989. [PMID: 30926608 DOI: 10.1074/jbc.ra118.004680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 03/27/2019] [Indexed: 12/17/2022] Open
Abstract
Lipopolysaccharides are anchored to the outer membrane of Gram-negative bacteria by a hydrophobic moiety known as lipid A, which potently activates the host innate immune response. Lipid A of Bordetella pertussis, the causative agent of whooping cough, displays unusual structural asymmetry with respect to the length of the acyl chains at the 3 and 3' positions, which are 3OH-C10 and 3OH-C14 chains, respectively. Both chains are attached by the acyltransferase LpxA, the first enzyme in the lipid A biosynthesis pathway, which, in B. pertussis, has limited chain length specificity. However, this only partially explains the strict asymmetry of lipid A. In attempts to modulate the endotoxicity of B. pertussis lipid A, here we expressed the gene encoding LpxA from Neisseria meningitidis, which specifically attaches 3OH-C12 chains, in B. pertussis This expression was lethal, suggesting that one of the downstream enzymes in the lipid A biosynthesis pathway in B. pertussis cannot handle precursors with a 3OH-C12 chain. We considered that the UDP-diacylglucosamine pyrophosphohydrolase LpxH could be responsible for this defect as well as for the asymmetry of B. pertussis lipid A. Expression of meningococcal LpxH in B. pertussis indeed resulted in new symmetric lipid A species with 3OH-C10 or 3OH-C14 chains at both the 3 and 3' positions, as revealed by MS analysis. Furthermore, co-expression of meningococcal lpxH and lpxA resulted in viable cells that incorporated 3OH-C12 chains in B. pertussis lipid A. We conclude that the asymmetry of B. pertussis lipid A is determined by the acyl chain length specificity of LpxH.
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Affiliation(s)
- Jesús Arenas
- Department of Molecular Microbiology and Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Elder Pupo
- Institute for Translational Vaccinology (Intravacc), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Eline de Jonge
- Department of Molecular Microbiology and Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jesús Pérez-Ortega
- Department of Molecular Microbiology and Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Joerg Schaarschmidt
- Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Peter van der Ley
- Institute for Translational Vaccinology (Intravacc), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Jan Tommassen
- Department of Molecular Microbiology and Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Joo SH, Chung HS. Crystal structure and activity of Francisella novicida UDP-N-acetylglucosamine acyltransferase. Biochem Biophys Res Commun 2016; 478:1223-9. [PMID: 27545601 DOI: 10.1016/j.bbrc.2016.08.098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 08/17/2016] [Indexed: 01/26/2023]
Abstract
The first step of lipid A biosynthesis in Escherichia coli (E. coli) is catalyzed by LpxA (EcLpxA), an acyltransferase selective for UDP-N-acetylglucosamine (UDP-GlcNAc) and R-3-hydroxymyristoyl-acyl carrier protein (3-OH-C14-ACP), and is an essential step in majority of Gram-negative bacteria. Since the majority of lipid A species isolated from F. novicida contains 3-OH-C16 or 3-OH-C18 at its C3 and C3' positions, FnLpxA was thought to be selective for longer acyl chain (3-OH-C16 and 3-OH-C18) over short acyl chain (3-OH-C14, 3-OH-C12, and 3-OH-C10). Here we demonstrate that Francisella novicida (F. novicida) lpxA functionally complements an E. coli lpxA knockout mutant and efficiently transfers 3-OH-C14 as well as 3-OH-C16 in E. coli. Our results implicate that the acyl chain length of lipid A is determined by several factors including acyl chain selectivity of LpxA and downstream enzymes, as well as the composition of the acyl-ACP pool in vivo. We also report the crystal structure of F. novicida LpxA (FnLpxA) at 2.06 Å. The N-terminal parallel beta-helix (LβH) and C-terminal alpha-helical domain are similar to other reported structures of LpxAs. However, our structure indicates that the supposed ruler residues for hydrocarbon length, 171L in one monomer and 168H in the adjacent monomer in a functional trimer of FnLpxA, are located just 3.8 Å apart that renders not enough space for binding of 3-OH-C12 or longer acyl chains. This implicates that FnLpxA may have an alternative hydrophobic pocket, or the acyl chain may bend while binding to FnLpxA. In addition, the FnLpxA structure suggests a potential inhibitor binding site for development of antibiotics.
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Affiliation(s)
- Sang Hoon Joo
- Department of Pharmacy, Catholic University of Daegu, Gyeongbuk 38430, South Korea; Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Hak Suk Chung
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA; Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, South Korea; Department of Biological Chemistry, Korea University of Science and Technology (UST), KIST Campus, Seoul 02792, South Korea.
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Ngo A, Fong KT, Cox DL, Chen X, Fisher AJ. Structures of Bacteroides fragilis uridine 5'-diphosphate-N-acetylglucosamine (UDP-GlcNAc) acyltransferase (Bf LpxA). Acta Crystallogr D Biol Crystallogr 2015; 71:1068-76. [PMID: 25945572 PMCID: PMC4427197 DOI: 10.1107/s1399004715003326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 02/16/2015] [Indexed: 11/11/2022]
Abstract
Uridine 5'-diphosphate-N-acetylglucosamine (UDP-GlcNAc) acyltransferase (LpxA) catalyzes a reversible reaction for adding an O-acyl group to the GlcNAc in UDP-GlcNAc in the first step of lipid A biosynthesis. Lipid A constitutes a major component of lipopolysaccharides, also referred to as endotoxins, which form the outer monolayer of the outer membrane of Gram-negative bacteria. Ligand-free and UDP-GlcNAc-bound crystal structures of LpxA from Bacteroides fragilis NCTC 9343, the most common pathogenic bacteria found in abdominal abscesses, have been determined and are presented here. The enzyme crystallizes in a cubic space group, with the crystallographic threefold axis generating the biological functional homotrimer and with each monomer forming a nine-rung left-handed β-helical (LβH) fold in the N-terminus followed by an α-helical motif in the C-terminus. The structure is highly similar to LpxA from other organisms. Yet, despite sharing a similar LβH structure with LpxAs from Escherichia coli and others, previously unseen calcium ions are observed on the threefold axis in B. fragilis LpxA to help stabilize the trimeric assembly.
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Affiliation(s)
- Alice Ngo
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Kai T. Fong
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Daniel L. Cox
- Department of Physics, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Xi Chen
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Andrew J. Fisher
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
- Department of Molecular and Cellular Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
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Jenkins RJ, Heslip KA, Meagher JL, Stuckey JA, Dotson GD. Structural basis for the recognition of peptide RJPXD33 by acyltransferases in lipid A biosynthesis. J Biol Chem 2014; 289:15527-35. [PMID: 24742680 PMCID: PMC4140908 DOI: 10.1074/jbc.m114.564278] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 04/15/2014] [Indexed: 01/28/2023] Open
Abstract
UDP-N-acetylglucosamine acyltransferase (LpxA) and UDP-3-O-(acyl)-glucosamine acyltransferase (LpxD) constitute the essential, early acyltransferases of lipid A biosynthesis. Recently, an antimicrobial peptide inhibitor, RJPXD33, was identified with dual affinity for LpxA and LpxD. To gain a fundamental understanding of the molecular basis of inhibitor binding, we determined the crystal structure of LpxA from Escherichia coli in complex with RJPXD33 at 1.9 Å resolutions. Our results suggest that the peptide binds in a unique modality that mimics (R)-β-hydroxyacyl pantetheine binding to LpxA and displays how the peptide binds exclusive of the native substrate, acyl-acyl carrier protein. Acyltransferase binding studies with photo-labile RJPXD33 probes and truncations of RJPXD33 validated the structure and provided fundamental insights for future design of small molecule inhibitors. Overlay of the LpxA-RJPXD33 structure with E. coli LpxD identified a complementary peptide binding pocket within LpxD and serves as a model for further biochemical characterization of RJPXD33 binding to LpxD.
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Affiliation(s)
- Ronald J Jenkins
- From the Department of Medicinal Chemistry, College of Pharmacy, and
| | - Kyle A Heslip
- From the Department of Medicinal Chemistry, College of Pharmacy, and
| | - Jennifer L Meagher
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Garry D Dotson
- From the Department of Medicinal Chemistry, College of Pharmacy, and
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