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Identification of Mtb GlmU Uridyltransferase Domain Inhibitors by Ligand-Based and Structure-Based Drug Design Approaches. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092805. [PMID: 35566155 PMCID: PMC9105790 DOI: 10.3390/molecules27092805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 01/09/2023]
Abstract
Targeting enzymes that play a role in the biosynthesis of the bacterial cell wall has long been a strategy for antibacterial discovery. In particular, the cell wall of Mycobacterium tuberculosis (Mtb) is a complex of three layers, one of which is Peptidoglycan, an essential component providing rigidity and strength. UDP-GlcNAc, a precursor for the synthesis of peptidoglycan, is formed by GlmU, a bi-functional enzyme. Inhibiting GlmU Uridyltransferase activity has been proven to be an effective anti-bacterial, but its similarity with human enzymes has been a deterrent to drug development. To develop Mtb selective hits, the Mtb GlmU substrate binding pocket was compared with structurally similar human enzymes to identify selectivity determining factors. Substrate binding pockets and conformational changes upon substrate binding were analyzed and MD simulations with substrates were performed to quantify crucial interactions to develop critical pharmacophore features. Thereafter, two strategies were applied to propose potent and selective bacterial GlmU Uridyltransferase domain inhibitors: (i) optimization of existing inhibitors, and (ii) identification by virtual screening. The binding modes of hits identified from virtual screening and ligand growing approaches were evaluated further for their ability to retain stable contacts within the pocket during 20 ns MD simulations. Hits that are predicted to be more potent than existing inhibitors and selective against human homologues could be of great interest for rejuvenating drug discovery efforts towards targeting the Mtb cell wall for antibacterial discovery.
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Kotzé TJ, Duffy S, Avery VM, Jordaan A, Warner DF, Loots L, Smith GS, Chellan P. Synthesis and antimicrobial study of organoiridium amido-sulfadoxine complexes. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2020.120175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Parise D, Teixeira Dornelles Parise M, Pinto Gomide AC, Figueira Aburjaile F, Bentes Kato R, Salgado-Albarrán M, Tauch A, Ariston de Carvalho Azevedo V, Baumbach J. The Transcriptional Regulatory Network of Corynebacterium pseudotuberculosis. Microorganisms 2021; 9:microorganisms9020415. [PMID: 33671149 PMCID: PMC7923171 DOI: 10.3390/microorganisms9020415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/11/2021] [Accepted: 02/14/2021] [Indexed: 12/26/2022] Open
Abstract
Corynebacterium pseudotuberculosis is a Gram-positive, facultative intracellular, pathogenic bacterium that infects several different hosts, yielding serious economic losses in livestock farming. It causes several diseases including oedematous skin disease (OSD) in buffaloes, ulcerative lymphangitis (UL) in horses, and caseous lymphadenitis (CLA) in sheep, goats and humans. Despite its economic and medical-veterinary importance, our understanding concerning this organism’s transcriptional regulatory mechanisms is still limited. Here, we review the state of the art knowledge on transcriptional regulatory mechanisms of this pathogenic species, covering regulatory interactions mediated by two-component systems, transcription factors and sigma factors. Key transcriptional regulatory players involved in virulence and pathogenicity of C. pseudotuberculosis, such as the PhoPR system and DtxR, are in the focus of this review, as these regulators are promising targets for future vaccine design and drug development. We conclude that more experimental studies are needed to further understand the regulatory repertoire of this important zoonotic pathogen, and that regulators are promising targets for future vaccine design and drug development.
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Affiliation(s)
- Doglas Parise
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising-Weihenstephan, Germany; (M.T.D.P.); (M.S.-A.); (J.B.)
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (A.C.P.G.); (R.B.K.); (V.A.d.C.A.)
- Correspondence: or
| | - Mariana Teixeira Dornelles Parise
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising-Weihenstephan, Germany; (M.T.D.P.); (M.S.-A.); (J.B.)
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (A.C.P.G.); (R.B.K.); (V.A.d.C.A.)
| | - Anne Cybelle Pinto Gomide
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (A.C.P.G.); (R.B.K.); (V.A.d.C.A.)
| | | | - Rodrigo Bentes Kato
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (A.C.P.G.); (R.B.K.); (V.A.d.C.A.)
| | - Marisol Salgado-Albarrán
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising-Weihenstephan, Germany; (M.T.D.P.); (M.S.-A.); (J.B.)
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana Cuajimalpa, Mexico City 05348, Mexico
| | - Andreas Tauch
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany;
| | - Vasco Ariston de Carvalho Azevedo
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (A.C.P.G.); (R.B.K.); (V.A.d.C.A.)
| | - Jan Baumbach
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising-Weihenstephan, Germany; (M.T.D.P.); (M.S.-A.); (J.B.)
- Computational BioMedicine lab, Institute of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark
- Chair of Computational Systems Biology, University of Hamburg, 22607 Hamburg, Germany
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Prabha A, Balaji PV. Characterization of left-handed beta helix-domains, and identification and functional annotation of proteins containing such domains. Proteins 2020; 89:6-20. [PMID: 32748987 DOI: 10.1002/prot.25990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 05/12/2020] [Accepted: 07/26/2020] [Indexed: 11/12/2022]
Abstract
Only about 0.3% of the entries in UniProt database have manually curated annotation. Annotation at the molecular level often relies on low-throughput one-protein-at-a-time approach. Computational methods bridge this gap by assigning function based on sequence and/or fold similarity. Left-handed beta helix (LbH) consists of three repeating six-stranded beta-strands forming an 18-mer turn of the helix. Analysis of LbH-domains showed that variations are found in the number of residues in a beta-strand (5-7, 6 being the most common), number of turns (4-10) of the helix, insertions of one or more loops of variable length (0-36 residues), and the location of loop insertion. An 18-mer HMM profile was created which identifies LbH-domain containing proteins using sequence as the only input; the number of false positives is zero when proteins tested were those with known 3D structures. 136 474 entries of TrEMBL database were found to contain LbH-domain. Rules developed by analyzing LbH-domain containing acyltransferases, gamma-class carbonic anhydrases, and nucleotidyltransferases have led to the annotation of 17 389 TrEMBL entries which currently have no functional tag.
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Affiliation(s)
- Anu Prabha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Petety V Balaji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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A preliminary study on quinazolinylaminobenzoyl monopeptide esters as effective Gram-positive bacteriostatic agents. Future Med Chem 2019; 11:407-422. [PMID: 30887814 DOI: 10.4155/fmc-2018-0275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
AIM To investigate a novel series of quinazoline monopeptide esters for the in vitro antibacterial activity. METHODOLOGY/RESULTS The compounds were synthesized via one-pot Dimroth rearrangement of suitable formamidine intermediates with 3-aminobenzoic acid, followed by coupling the resulting acids with amino acid esters and screening for their antibacterial activity by broth dilution method. The compounds 5a, 5b, 5c, 5g, 5i and 5j showed promising activity against the Gram-positive bacteria, 5c and 5g being the most potent against Enterococcus faecalis and Staphylococcus aureus, respectively, with a minimal inhibitory concentration of 0.51 μM. The percentage hemolysis of the compounds ranged from 2.79 to 12.92 at a concentration of 100 μg/ml. The molecular docking studies revealed their GlmU inhibitory action. CONCLUSION The compounds 5a and 5g emerged as antibacterial hits.
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Gomide ACP, Ibraim IC, Alves JTC, de Sá PG, de Oliveira Silva YR, Santana MP, Silva WM, Folador EL, Mariano DCB, de Paula Castro TL, Barbosa S, Dorella FA, Carvalho AF, Pereira FL, Leal CAG, Figueiredo HCP, Azevedo V, Silva A, Folador ARC. Transcriptome analysis of Corynebacterium pseudotuberculosis biovar Equi in two conditions of the environmental stress. Gene 2018; 677:349-360. [PMID: 30098432 DOI: 10.1016/j.gene.2018.08.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/10/2018] [Accepted: 08/06/2018] [Indexed: 11/30/2022]
Abstract
Corynebacterium pseudotuberculosis has been widely studied in an effort to understand its biological evolution. Transcriptomics has revealed possible candidates for virulence and pathogenicity factors of strain 1002 (biovar Ovis). Because C. pseudotuberculosis is classified into two biovars, Ovis and Equi, it was interesting to assess the transcriptional profile of biovar Equi strain 258, the causative agent of ulcerative lymphangitis. The genome of this strain was re-sequenced; the reassembly was completed using optical mapping technology, and the sequence was subsequently re-annotated. Two growth conditions that occur during the host infection process were simulated for the transcriptome: the osmotic and acid medium. Genes that may be associated with the microorganism's resilience under unfavorable conditions were identified through RNAseq, including genes present in pathogenicity islands. The RT-qPCR was performed to confirm the results in biological triplicate for each condition for some genes. The results extend our knowledge of the factors associated with the spread and persistence of C. pseudotuberculosis during the infection process and suggest possible avenues for studies related to the development of vaccines, diagnosis, and therapies that might help minimize damage to agribusinesses.
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Affiliation(s)
- Anne Cybelle Pinto Gomide
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil.
| | - Izabela Coimbra Ibraim
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil
| | - Jorianne T C Alves
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil
| | - Pablo Gomes de Sá
- Federal Rural University of Amazonia, Rodovia PA 140, 2428 Tomé-Açu, PA, Brazil
| | - Yuri Rafael de Oliveira Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil
| | - Mariana Passos Santana
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil
| | - Wanderson Marques Silva
- National Institute of Agricultural Technology, Los Reseros y Nicolás Repetto, Hurlingham 1686, Argentina
| | - Edson Luiz Folador
- Biotechnology Center, Federal University of Paraíba, João Pessoa, Brazil.
| | - Diego C B Mariano
- Department of Computer Sciences, Institute of Exact Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil.
| | - Thiago Luiz de Paula Castro
- Department of Biointeraction, Institute of Health Sciences, Federal University of Bahia, Av. Reitor Miguel Calmon, s/n, Vale do Canela, Bahia, Brazil
| | - Silvanira Barbosa
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil
| | - Fernanda Alves Dorella
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Alex F Carvalho
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Felipe L Pereira
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil.
| | - Carlos A G Leal
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil.
| | - Henrique C P Figueiredo
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Vasco Azevedo
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil.
| | - Artur Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil.
| | - Adriana Ribeiro Carneiro Folador
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil.
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Wang M, Huang M, Gu H, Li S, Ma Y, Wang J. Mutational analysis to identify the residues essential for the acetyltransferase activity of GlmU in Bacillus subtilis. RSC Adv 2017. [DOI: 10.1039/c7ra00086c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Amino acid mutation analysis and molecular modeling to verify the essential residues in acetyltransferase catalytic mechanism of Bs-GlmU.
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Affiliation(s)
- Meng Wang
- School of Bioscience and Bioengineering
- South China University of Technology
- 510006 Guangzhou
- China
| | - Minhua Huang
- School of Bioscience and Bioengineering
- South China University of Technology
- 510006 Guangzhou
- China
| | - Huawei Gu
- School of Bioscience and Bioengineering
- South China University of Technology
- 510006 Guangzhou
- China
| | - Shan Li
- School of Bioscience and Bioengineering
- South China University of Technology
- 510006 Guangzhou
- China
| | - Yi Ma
- School of Bioscience and Bioengineering
- South China University of Technology
- 510006 Guangzhou
- China
| | - Jufang Wang
- School of Bioscience and Bioengineering
- South China University of Technology
- 510006 Guangzhou
- China
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Rapid activity prediction of HIV-1 integrase inhibitors: harnessing docking energetic components for empirical scoring by chemometric and artificial neural network approaches. J Comput Aided Mol Des 2016; 30:471-88. [DOI: 10.1007/s10822-016-9917-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 06/13/2016] [Indexed: 12/22/2022]
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Abstract
The practice of medicine was profoundly transformed by the introduction of the antibiotics (compounds isolated from Nature) and the antibacterials (compounds prepared by synthesis) for the control of bacterial infection. As a result of the extraordinary success of these compounds over decades of time, a timeless biological activity for these compounds has been presumed. This presumption is no longer. The inexorable acquisition of resistance mechanisms by bacteria is retransforming medical practice. Credible answers to this dilemma are far better recognized than they are being implemented. In this perspective we examine (and in key respects, reiterate) the chemical and biological strategies being used to address the challenge of bacterial resistance.
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Affiliation(s)
- Jed F. Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame IN 46556–5670, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame IN 46556–5670, USA
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Soni V, Upadhayay S, Suryadevara P, Samla G, Singh A, Yogeeswari P, Sriram D, Nandicoori VK. Depletion of M. tuberculosis GlmU from Infected Murine Lungs Effects the Clearance of the Pathogen. PLoS Pathog 2015; 11:e1005235. [PMID: 26489015 PMCID: PMC4619583 DOI: 10.1371/journal.ppat.1005235] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/27/2015] [Indexed: 01/06/2023] Open
Abstract
M. tuberculosis N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmUMtb) is a bi-functional enzyme engaged in the synthesis of two metabolic intermediates N-acetylglucosamine-1-phosphate (GlcNAc-1-P) and UDP-GlcNAc, catalyzed by the C- and N-terminal domains respectively. UDP-GlcNAc is a key metabolite essential for the synthesis of peptidoglycan, disaccharide linker, arabinogalactan and mycothiols. While glmUMtb was predicted to be an essential gene, till date the role of GlmUMtb in modulating the in vitro growth of Mtb or its role in survival of pathogen ex vivo / in vivo have not been deciphered. Here we present the results of a comprehensive study dissecting the role of GlmUMtb in arbitrating the survival of the pathogen both in vitro and in vivo. We find that absence of GlmUMtb leads to extensive perturbation of bacterial morphology and substantial reduction in cell wall thickness under normoxic as well as hypoxic conditions. Complementation studies show that the acetyl- and uridyl- transferase activities of GlmUMtb are independently essential for bacterial survival in vitro, and GlmUMtb is also found to be essential for mycobacterial survival in THP-1 cells as well as in guinea pigs. Depletion of GlmUMtb from infected murine lungs, four weeks post infection, led to significant reduction in the bacillary load. The administration of Oxa33, a novel oxazolidine derivative that specifically inhibits GlmUMtb, to infected mice resulted in significant decrease in the bacillary load. Thus our study establishes GlmUMtb as a strong candidate for intervention measures against established tuberculosis infections. The synthesis of the Mtb cell wall involves a cascade of reactions catalyzed by cytosolic and cell membrane-bound enzymes. The reaction catalyzed by GlmUMtb (an enzyme with acetyltransferase and uridyltransferase activities) generates UDP-GlcNAc, a central nucleotide-sugar building block of the cell wall. Apart from cell wall synthesis UDP-GlcNAc is an essential metabolite participating in other cellular processes including disaccharide linker and mycothiol biosynthesis. GlmUMtb shares very little sequence similarity with eukaryotic acetyltransferase and uridyltransferase enzymes. Many pathogens have alternative pathway(s) for foraging GlcNAc from the host. The present study was undertaken to see the effects of depleting GlmUMtb on pathogen survival in the host animal. We have generated a conditional gene replacement mutant of glmUMtb and find that depletion of GlmUMtb at any stage of bacterial growth or in mice infected with Mtb including a well-established infection, results in irreversible bacterial death due to perturbation of cell wall synthesis. We have developed a novel anti-GlmUMtb inhibitor (Oxa33), identified its binding site on GlmUMtb, and shown its specificity for GlmUMtb. The study demonstrates that GlmUMtb is a promising target for therapeutic intervention and Oxa33 can be pursued as a lead molecule.
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Affiliation(s)
- Vijay Soni
- National Institute of Immunology, New Delhi, India
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Hyderabad, India
| | | | - Priyanka Suryadevara
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - Ganesh Samla
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - Archana Singh
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Perumal Yogeeswari
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Hyderabad, India
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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 (BfLpxA). ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 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] [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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