1
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Li FR, Wang Q, Pan X, Xu HM, Dong LB. Discovery, Structure, and Engineering of a cis-Geranylfarnesyl Diphosphate Synthase. Angew Chem Int Ed Engl 2024; 63:e202401669. [PMID: 38651244 DOI: 10.1002/anie.202401669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
cis-Prenyltransferases (cis-PTs) catalyze the sequential head-to-tail condensation of isopentenyl diphosphate (IPP) to allylic diphosphates, producing mixed E-Z prenyl diphosphates of varying lengths; however, the specific enzymes synthesizing cis-C25 prenyl diphosphates have not been identified. Herein, we present the discovery and characterization of a cis-geranylfarnesyl diphosphate synthase (ScGFPPS) from Streptomyces clavuligerus. This enzyme demonstrates high catalytic proficiency in generating six distinct cis-polyisoprenoids, including three C25 and three C20 variants. We determined the crystal structure of ScGFPPS. Additionally, we unveil the crystal structure of nerylneryl diphosphate synthase (NNPS), known for synthesizing an all-cis-C20 polyisoprenoid. Comparative structural analysis of ScGFPPS and NNPS has identified key differences that influence product specificity. Through site-directed mutagenesis, we have identified eight single mutations that significantly refine the selectivity of ScGFPPS for cis-polyisoprenoids. Our findings not only expand the functional spectrum of cis-PTs but also provide a structural comparison strategy in cis-PTs engineering.
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Affiliation(s)
- Fang-Ru Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Qingling Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Xingming Pan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Hui-Min Xu
- The Public Laboratory Platform, China Pharmaceutical University, Nanjing, 211198, China
| | - Liao-Bin Dong
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
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2
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Liu J, Liang P. Complexation and evolution of cis-prenyltransferase homologues in Cinnamomum kanehirae deduced from kinetic and functional characterizations. Protein Sci 2023; 32:e4828. [PMID: 37916302 PMCID: PMC10661081 DOI: 10.1002/pro.4828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/20/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023]
Abstract
Eukaryotic dehydrodolichyl diphosphate synthases (DHDDSs), cis-prenyltransferases (cis-PTs) synthesizing precursors of dolichols to mediate glycoprotein biosynthesis require partners, for eample Nus1 in yeast and NgBR in animals, which are cis-PTs homologues without activity but to boost the DHDDSs activity. Unlike animals, plants have multiple cis-PT homologues to pair or stand alone to produce various chain-length products with less known physiological roles. We chose Cinnamomum kanehirae, a tree that contains two DHDDS-like and three NgBR-like proteins from genome analysis, and found that one DHDDS-like protein acted as a homodimeric cis-PT to make a medium-chain C55 product, while the other formed heterodimeric complexes with either one of two NgBR homologues to produce longer-chain products. Both complexes were functional to complement the growth defect of the yeast rer2 deficient strain at a higher temperature. From the roles for the polyprenol and dolichol biosynthesis and sequence motifs, their homologues in various species were compared to reveal their possible evolutionary paths.
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Affiliation(s)
- Jia‐Jin Liu
- Institute of Biochemical SciencesNational Taiwan UniversityTaipeiTaiwan
| | - Po‐Huang Liang
- Institute of Biochemical SciencesNational Taiwan UniversityTaipeiTaiwan
- Institute of Biological ChemistryAcademia SinicaTaipeiTaiwan
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3
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Reconstitution of prenyltransferase activity on nanodiscs by components of the rubber synthesis machinery of the Para rubber tree and guayule. Sci Rep 2022; 12:3734. [PMID: 35260628 PMCID: PMC8904820 DOI: 10.1038/s41598-022-07564-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/22/2022] [Indexed: 11/08/2022] Open
Abstract
Natural rubber of the Para rubber tree (Hevea brasiliensis) is synthesized as a result of prenyltransferase activity. The proteins HRT1, HRT2, and HRBP have been identified as candidate components of the rubber biosynthetic machinery. To clarify the contribution of these proteins to prenyltransferase activity, we established a cell-free translation system for nanodisc-based protein reconstitution and measured the enzyme activity of the protein-nanodisc complexes. Co-expression of HRT1 and HRBP in the presence of nanodiscs yielded marked polyisoprene synthesis activity. By contrast, neither HRT1, HRT2, or HRBP alone nor a complex of HRT2 and HRBP manifested such activity. Similar analysis of guayule (Parthenium argentatum) proteins revealed that three HRT1 homologs (PaCPT1–3) manifested prenyltransferase activity only when co-expressed with PaCBP, the homolog of HRBP. Our results thus indicate that two heterologous subunits form the core prenyltransferase of the rubber biosynthetic machinery. A recently developed structure modeling program predicted the structure of such heterodimer complexes including HRT1/HRBP and PaCPT2/PaCBP. HRT and PaCPT proteins were also found to possess affinity for a lipid membrane in the absence of HRBP or PaCBP, and structure modeling implicated an amphipathic α-helical domain of HRT1 and PaCPT2 in membrane binding of these proteins.
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4
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Tsutsumi H, Moriwaki Y, Terada T, Shimizu K, Shin‐ya K, Katsuyama Y, Ohnishi Y. Structural and Molecular Basis of the Catalytic Mechanism of Geranyl Pyrophosphate C6‐Methyltransferase: Creation of an Unprecedented Farnesyl Pyrophosphate C6‐Methyltransferase. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Hayama Tsutsumi
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Yoshitaka Moriwaki
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Tokyo Japan
| | - Tohru Terada
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Tokyo Japan
| | - Kentaro Shimizu
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Tokyo Japan
| | - Kazuo Shin‐ya
- National Institute of Advanced Industrial Science and Technology (AIST) 2-4-7 Aomi, Koto-ku Tokyo 135-0064 Japan
- Technology Research Association for Next Generation Natural Products Chemistry 2-4-32 Aomi, Koto-ku Tokyo 135-0064 Japan
| | - Yohei Katsuyama
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Tokyo Japan
| | - Yasuo Ohnishi
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Tokyo Japan
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5
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Payros D, Alonso H, Malaga W, Volle A, Mazères S, Déjean S, Valière S, Moreau F, Balor S, Stella A, Combes-Soia L, Burlet-Schiltz O, Bouchez O, Nigou J, Astarie-Dequeker C, Guilhot C. Rv0180c contributes to Mycobacterium tuberculosis cell shape and to infectivity in mice and macrophages. PLoS Pathog 2021; 17:e1010020. [PMID: 34724002 PMCID: PMC8584747 DOI: 10.1371/journal.ppat.1010020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 11/11/2021] [Accepted: 10/08/2021] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium tuberculosis, the main causative agent of human tuberculosis, is transmitted from person to person via small droplets containing very few bacteria. Optimizing the chance to seed in the lungs is therefore a major adaptation to favor survival and dissemination in the human population. Here we used TnSeq to identify genes important for the early events leading to bacterial seeding in the lungs. Beside several genes encoding known virulence factors, we found three new candidates not previously described: rv0180c, rv1779c and rv1592c. We focused on the gene, rv0180c, of unknown function. First, we found that deletion of rv0180c in M. tuberculosis substantially reduced the initiation of infection in the lungs of mice. Next, we established that Rv0180c enhances entry into macrophages through the use of complement-receptor 3 (CR3), a major phagocytic receptor for M. tuberculosis. Silencing CR3 or blocking the CR3 lectin site abolished the difference in entry between the wild-type parental strain and the Δrv0180c::km mutant. However, we detected no difference in the production of both CR3-known carbohydrate ligands (glucan, arabinomannan, mannan), CR3-modulating lipids (phthiocerol dimycocerosate), or proteins in the capsule of the Δrv0180c::km mutant in comparison to the wild-type or complemented strains. By contrast, we established that Rv0180c contributes to the functionality of the bacterial cell envelope regarding resistance to toxic molecule attack and cell shape. This alteration of bacterial shape could impair the engagement of membrane receptors that M. tuberculosis uses to invade host cells, and open a new perspective on the modulation of bacterial infectivity. The epidemic efficiency of tuberculosis bacilli is determined by their capacity to transmit via aerosol. Currently, the bacterial functions that favor Mycobacterium tuberculosis seeding in the lung of naïve host remain mostly unknown. Here we implemented a genome-wide approach to identify M. tuberculosis mutants deficient for seeding and early replication in the lung of mice. In addition to genes known to encode virulence factors, we identified three genes not previously described. We used complementary approaches to characterize the phenotype of a M. tuberculosis mutant with insertion within the rv0180c gene. We found that this mutant is impaired for seeding in the lung of mice and for invasion and replication in human macrophages. In macrophages, the defect relies on a lack of engagement of CR3 receptor. Although we did not detect any difference between the wild type strain and the rv0180c mutant with regard to potential CR3-ligand, we found that the bacterial cell envelope is altered in the rv0180c mutant. Our study provides new insight into bacterial genes required for early interaction of M. tuberculosis with the host and perspective to understand the bacterial functions enhancing infectivity.
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Affiliation(s)
- Delphine Payros
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Henar Alonso
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Wladimir Malaga
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Arnaud Volle
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Serge Mazères
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sébastien Déjean
- Institut de Mathématiques de Toulouse, UMR5219, Université de Toulouse, CNRS, UPS, Toulouse, France
| | | | - Flavie Moreau
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Stéphanie Balor
- Plateforme de Microscopie Électronique Intégrative (METi), Centre de Biologie Intégrative (CBI), CNRS, Toulouse, France
| | - Alexandre Stella
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Lucie Combes-Soia
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | | | - Jérôme Nigou
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Catherine Astarie-Dequeker
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
- * E-mail: (CAD); (CG)
| | - Christophe Guilhot
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
- * E-mail: (CAD); (CG)
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6
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Tsutsumi H, Moriwaki Y, Terada T, Shimizu K, Shin-Ya K, Katsuyama Y, Ohnishi Y. Structural and Molecular Basis of the Catalytic Mechanism of Geranyl Pyrophosphate C6-Methyltransferase: Creation of an Unprecedented Farnesyl Pyrophosphate C6-Methyltransferase. Angew Chem Int Ed Engl 2021; 61:e202111217. [PMID: 34626048 DOI: 10.1002/anie.202111217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Indexed: 11/11/2022]
Abstract
Prenyl pyrophosphate methyltransferases enhance the structural diversity of terpenoids. However, the molecular basis of their catalytic mechanisms is poorly understood. In this study, using multiple strategies, we characterized a geranyl pyrophosphate (GPP) C6-methyltransferase, BezA. Biochemical analysis revealed that BezA requires Mg2+ and solely methylates GPP. The crystal structures of BezA and its complex with S-adenosyl homocysteine were solved at 2.10 and 2.56 Å, respectively. Further analyses using site-directed mutagenesis, molecular docking, molecular dynamics simulations, and quantum mechanics/molecular mechanics calculations revealed the molecular basis of the methylation reaction. Importantly, the function of E170 as a catalytic base to complete the methylation reaction was established. We also succeeded in switching the substrate specificity by introducing a W210A substitution, resulting in an unprecedented farnesyl pyrophosphate C6-methyltransferase.
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Affiliation(s)
- Hayama Tsutsumi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yoshitaka Moriwaki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Kentaro Shimizu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,Technology Research Association for Next Generation Natural Products Chemistry, 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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7
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Kurokawa H, Ambo T, Takahashi S, Koyama T. Crystal structure of Thermobifida fusca cis-prenyltransferase reveals the dynamic nature of its RXG motif-mediated inter-subunit interactions critical for its catalytic activity. Biochem Biophys Res Commun 2020; 532:459-465. [PMID: 32892948 DOI: 10.1016/j.bbrc.2020.08.062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 11/17/2022]
Abstract
cis-Prenyltransferases (cis-PTs) catalyze consecutive condensations of isopentenyl diphosphate to an allylic diphosphate acceptor to produce a linear polyprenyl diphosphate of designated length. Dimer formation is a prerequisite for cis-PTs to catalyze all cis-prenyl condensation reactions. The structure-function relationship of a conserved C-terminal RXG motif in cis-PTs that forms inter-subunit interactions and has a role in catalytic activity has attracted much attention. Here, we solved the crystal structure of a medium-chain cis-PT from Thermobifida fusca that produces dodecaprenyl diphosphate as a polyprenoid glycan carrier for cell wall synthesis. The structure revealed a characteristic dimeric architecture of cis-PTs in which a rigidified RXG motif of one monomer formed inter-subunit hydrogen bonds with the catalytic site of the other monomer, while the RXG motif of the latter remained flexible. Careful analyses suggested the existence of a possible long-range negative cooperativity between the two catalytic sites on the two monomeric subunits that allowed the binding of one subunit to stabilize the formation of the enzyme-substrate ternary complex and facilitated the release of Mg-PPi and subsequent intra-molecular translocation at the counter subunit so that the condensation reaction could occur in consecutive cycles. The current structure reveals the dynamic nature of the RXG motif and provides a rationale for pursuing further investigations to elucidate the inter-subunit cooperativity of cis-PTs.
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Affiliation(s)
- Hirofumi Kurokawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.
| | - Takanori Ambo
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Seiji Takahashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aramaki Aza Aoba 6-6-11, Aoba-ku, Sendai, 980-8579, Japan
| | - Tanetoshi Koyama
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
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8
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Structural basis of heterotetrameric assembly and disease mutations in the human cis-prenyltransferase complex. Nat Commun 2020; 11:5273. [PMID: 33077723 PMCID: PMC7573591 DOI: 10.1038/s41467-020-18970-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/23/2020] [Indexed: 11/17/2022] Open
Abstract
The human cis-prenyltransferase (hcis-PT) is an enzymatic complex essential for protein N-glycosylation. Synthesizing the precursor of the glycosyl carrier dolichol-phosphate, mutations in hcis-PT cause severe human diseases. Here, we reveal that hcis-PT exhibits a heterotetrameric assembly in solution, consisting of two catalytic dehydrodolichyl diphosphate synthase (DHDDS) and inactive Nogo-B receptor (NgBR) heterodimers. Importantly, the 2.3 Å crystal structure reveals that the tetramer assembles via the DHDDS C-termini as a dimer-of-heterodimers. Moreover, the distal C-terminus of NgBR transverses across the interface with DHDDS, directly participating in active-site formation and the functional coupling between the subunits. Finally, we explored the functional consequences of disease mutations clustered around the active-site, and in combination with molecular dynamics simulations, we propose a mechanism for hcis-PT dysfunction in retinitis pigmentosa. Together, our structure of the hcis-PT complex unveils the dolichol synthesis mechanism and its perturbation in disease. The human cis-prenyltransferase (hcis-PT) complex synthesizes the precursor of the glycosyl carrier dolichol-phosphate and as such it is essential for protein N-glycosylation. The crystal structure of the complex reveals unusual tetrameric architecture and provides insights into dolichol synthesis mechanism and functional consequences of disease-associated hcis-PT mutations.
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9
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Edani BH, Grabińska KA, Zhang R, Park EJ, Siciliano B, Surmacz L, Ha Y, Sessa WC. Structural elucidation of the cis-prenyltransferase NgBR/DHDDS complex reveals insights in regulation of protein glycosylation. Proc Natl Acad Sci U S A 2020; 117:20794-20802. [PMID: 32817466 PMCID: PMC7456142 DOI: 10.1073/pnas.2008381117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Cis-prenyltransferase (cis-PTase) catalyzes the rate-limiting step in the synthesis of glycosyl carrier lipids required for protein glycosylation in the lumen of endoplasmic reticulum. Here, we report the crystal structure of the human NgBR/DHDDS complex, which represents an atomic resolution structure for any heterodimeric cis-PTase. The crystal structure sheds light on how NgBR stabilizes DHDDS through dimerization, participates in the enzyme's active site through its C-terminal -RXG- motif, and how phospholipids markedly stimulate cis-PTase activity. Comparison of NgBR/DHDDS with homodimeric cis-PTase structures leads to a model where the elongating isoprene chain extends beyond the enzyme's active site tunnel, and an insert within the α3 helix helps to stabilize this energetically unfavorable state to enable long-chain synthesis to occur. These data provide unique insights into how heterodimeric cis-PTases have evolved from their ancestral, homodimeric forms to fulfill their function in long-chain polyprenol synthesis.
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Affiliation(s)
- Ban H Edani
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Kariona A Grabińska
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Rong Zhang
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Eon Joo Park
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Benjamin Siciliano
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Liliana Surmacz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Ya Ha
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520;
| | - William C Sessa
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520;
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
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10
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Maitra A, Munshi T, Healy J, Martin LT, Vollmer W, Keep NH, Bhakta S. Cell wall peptidoglycan in Mycobacterium tuberculosis: An Achilles' heel for the TB-causing pathogen. FEMS Microbiol Rev 2020; 43:548-575. [PMID: 31183501 PMCID: PMC6736417 DOI: 10.1093/femsre/fuz016] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/07/2019] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB), caused by the intracellular pathogen Mycobacterium tuberculosis, remains one of the leading causes of mortality across the world. There is an urgent requirement to build a robust arsenal of effective antimicrobials, targeting novel molecular mechanisms to overcome the challenges posed by the increase of antibiotic resistance in TB. Mycobacterium tuberculosis has a unique cell envelope structure and composition, containing a peptidoglycan layer that is essential for maintaining cellular integrity and for virulence. The enzymes involved in the biosynthesis, degradation, remodelling and recycling of peptidoglycan have resurfaced as attractive targets for anti-infective drug discovery. Here, we review the importance of peptidoglycan, including the structure, function and regulation of key enzymes involved in its metabolism. We also discuss known inhibitors of ATP-dependent Mur ligases, and discuss the potential for the development of pan-enzyme inhibitors targeting multiple Mur ligases.
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Affiliation(s)
- Arundhati Maitra
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Tulika Munshi
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Jess Healy
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Liam T Martin
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Nicholas H Keep
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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11
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Chen CC, Zhang L, Yu X, Ma L, Ko TP, Guo RT. Versatile cis-isoprenyl Diphosphate Synthase Superfamily Members in Catalyzing Carbon–Carbon Bond Formation. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lilan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xuejing Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
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12
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Ko TP, Xiao X, Guo RT, Huang JW, Liu W, Chen CC. Substrate-analogue complex structure of Mycobacterium tuberculosis decaprenyl diphosphate synthase. Acta Crystallogr F Struct Biol Commun 2019; 75:212-216. [PMID: 30950820 PMCID: PMC6450523 DOI: 10.1107/s2053230x19001213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/22/2019] [Indexed: 12/03/2022] Open
Abstract
Decaprenyl diphosphate synthase from Mycobacterium tuberculosis (MtDPPS, also known as Rv2361c) catalyzes the consecutive elongation of ω,E,Z-farnesyl diphosphate (EZ-FPP) by seven isoprene units by forming new cis double bonds. The protein folds into a butterfly-like homodimer like most other cis-type prenyltransferases. The starting allylic substrate EZ-FPP is bound to the S1 site and the homoallylic substrate to be incorporated, isopentenyl diphosphate, is bound to the S2 site. Here, a 1.55 Å resolution structure of MtDPPS in complex with the substrate analogues geranyl S-thiodiphosphate (GSPP) and isopentenyl S-thiodiphosphate bound to their respective sites in one subunit clearly shows the active-site configuration and the magnesium-coordinated geometry for catalysis. The ligand-binding mode of GSPP in the other subunit indicates a possible pathway of product translocation from the S2 site to the S1 site, as required for the next step of the reaction. The preferred binding of negatively charged effectors to the S1 site also suggests a promising direction for inhibitor design.
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Affiliation(s)
- Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Xiansha Xiao
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic of China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 43420, People’s Republic of China
| | - Jian-Wen Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 43420, People’s Republic of China
| | - Weidong Liu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic of China
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 43420, People’s Republic of China
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13
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Men X, Wang F, Chen GQ, Zhang HB, Xian M. Biosynthesis of Natural Rubber: Current State and Perspectives. Int J Mol Sci 2018; 20:E50. [PMID: 30583567 PMCID: PMC6337083 DOI: 10.3390/ijms20010050] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022] Open
Abstract
Natural rubber is a kind of indispensable biopolymers with great use and strategic importance in human society. However, its production relies almost exclusively on rubber-producing plants Hevea brasiliensis, which have high requirements for growth conditions, and the mechanism of natural rubber biosynthesis remains largely unknown. In the past two decades, details of the rubber chain polymerization and proteins involved in natural rubber biosynthesis have been investigated intensively. Meanwhile, omics and other advanced biotechnologies bring new insight into rubber production and development of new rubber-producing plants. This review summarizes the achievements of the past two decades in understanding the biosynthesis of natural rubber, especially the massive information obtained from the omics analyses. Possibilities of natural rubber biosynthesis in vitro or in genetically engineered microorganisms are also discussed.
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Affiliation(s)
- Xiao Men
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
| | - Fan Wang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guo-Qiang Chen
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
| | - Hai-Bo Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
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14
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Wang Y, Khan A, Chandra Kaushik A, Junaid M, Zhang X, Wei DQ. The systematic modeling studies and free energy calculations of the phenazine compounds as anti-tuberculosis agents. J Biomol Struct Dyn 2018; 37:4051-4069. [PMID: 30332914 DOI: 10.1080/07391102.2018.1537896] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Phenazine compounds have good activity against Mycobacterium tuberculosis (MTB). Based on the reported activities that were obtained in MTB H37Rv, a three-dimensional quantitative structure-activity relationship (3D-QSAR) model was built to design novel compounds against MTB. A fivefold cross-validation method and external validation were used to analyze the accuracy of forecasting. The model has a cross-validation coefficient q2=0.7 and a non-cross-validation coefficient r2 = 0.903, indicating that the model has good predictive possibility. The design of anti-pneumococcus MTB compounds was guided by the obtained 3D-QSAR model, and several compounds with better activity were obtained. To test the activity of these compounds, molecular docking, molecular dynamics simulation, and post-simulation analysis of the already reported drug targets in MTB were carried out. Among the total 15 drug targets, only three targets (Rv2361c, Rv2965c, and Rv3048c) were selected based on the docking results. Initial results reported that these compounds possessed good inhibition activity for Rv2361c. The top nine complexes of Rv2361 ligands were only subjected to MD simulation which resulted in a stable dynamics of the structures and showed a residual fluctuation in inhibitors binding pocket. Free energy reported that overall, the derivatives hold strong energy against the protein target. Energetic contribution results showed that residues, Asp76, Arg80, Asn124, Arg127, Arg244, and Arg250, play a major role in total energy. Systems biology approach validates shortlisted drug effect on the entire system which might be useful to predict potential drug in wet lab as well. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yueqi Wang
- a State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai , P. R. China
| | - Abbas Khan
- a State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai , P. R. China
| | - Aman Chandra Kaushik
- a State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai , P. R. China
| | - Muhammad Junaid
- a State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai , P. R. China
| | - Xuehong Zhang
- a State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai , P. R. China
| | - Dong-Qing Wei
- a State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai , P. R. China
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15
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Malwal SR, Gao J, Hu X, Yang Y, Liu W, Huang JW, Ko TP, Li L, Chen CC, O’Dowd B, Khade RL, Zhang Y, Zhang Y, Oldfield E, Guo RT. Catalytic Role of Conserved Asparagine, Glutamine, Serine, and Tyrosine Residues in Isoprenoid Biosynthesis Enzymes. ACS Catal 2018; 8:4299-4312. [PMID: 30345154 DOI: 10.1021/acscatal.8b00543] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the results of an investigation into the catalytic role of highly conserved amide (asparagine, glutamine) and OH-containing (serine, tyrosine) residues in several prenyltransferases. We first obtained the X-ray structure of cyclolavandulyl diphosphate synthase containing two molecules of the substrate analog dimethylallyl (S)-thiolodiphosphate (DMASPP). The two molecules have similar diphosphate group orientations to those seen in other ζ-fold (cis- head-to-tail and head-to-middle) prenyltransferases with one diphosphate moiety forming a bidentate chelate with Mg2+ in the so-called S1 site (which is typically the allylic binding site in ζ-fold proteins) while the second diphosphate binds to Mg2+ in the so-called S2 site (which is typically the homoallylic binding site in ζ-fold proteins) via a single P1O1 oxygen. The latter interaction can facilitate direct phosphate-mediated proton abstraction via P1O2, or more likely by an indirect mechanism in which P1O2 stabilizes a basic asparagine species that removes H+, which is then eliminated via an Asn-Ser shuttle. The universal occurrence of Asn-Ser pairs in ζ-fold proteins leads to the idea that the highly conserved amide (Asn, Gln) and OH-containing (Tyr) residues seen in many "head-to-head" prenyltransferases such as squalene and dehydrosqualene synthase might play similar roles, in H+ elimination. Structural, bioinformatics and mutagenesis investigations indeed indicate an important role of these residues in catalysis, with the results of density functional theory calculations showing that Asn bound to Mg2+ can act as a general (imine-like) base, while Gln, Tyr and H2O form a proton channel that is adjacent to the conventional (Asp-rich) "active site". Taken together, our results lead to mechanisms of proton-elimination from carbocations in numerous prenyltransferases in which neutral species (Asn, Gln, Ser, Tyr, H2O) act as proton shuttles, complementing the more familiar roles of acidic groups (in Asp and Glu) that bind to Mg2+, and basic groups (primarily Arg) that bind to diphosphates, in isoprenoid biosynthesis.
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Affiliation(s)
- Satish R. Malwal
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Jian Gao
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xiangying Hu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yunyun Yang
- School of Pharmaceutical Sciences and MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Weidong Liu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jian-Wen Huang
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Liping Li
- School of Pharmaceutical Sciences and MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Chun-Chi Chen
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Bing O’Dowd
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Rahul L. Khade
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
| | - Yong Zhang
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
| | - Yonghui Zhang
- School of Pharmaceutical Sciences and MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Eric Oldfield
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Rey-Ting Guo
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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16
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Gao J, Ko T, Chen L, Malwal SR, Zhang J, Hu X, Qu F, Liu W, Huang J, Cheng Y, Chen C, Yang Y, Zhang Y, Oldfield E, Guo R. “Head‐to‐Middle” and “Head‐to‐Tail”
cis
‐Prenyl Transferases: Structure of Isosesquilavandulyl Diphosphate Synthase. Angew Chem Int Ed Engl 2018; 57:683-687. [DOI: 10.1002/anie.201710185] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/17/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Jian Gao
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Tzu‐Ping Ko
- Institute of Biological ChemistryAcademia Sinica Taipei 11529 Taiwan
| | - Lu Chen
- Department of BiochemistryUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Satish R. Malwal
- Department of ChemistryUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Jianan Zhang
- School of Molecular and Cellular BiologyUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Xiangying Hu
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Fiona Qu
- Department of ChemistryUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Weidong Liu
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Jian‐Wen Huang
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Ya‐Shan Cheng
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Chun‐Chi Chen
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Yunyun Yang
- School of Pharmaceutical SciencesTsinghua University Beijing 100084 China
| | - Yonghui Zhang
- School of Pharmaceutical SciencesTsinghua University Beijing 100084 China
| | - Eric Oldfield
- Department of ChemistryUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
- Center for Biophysics and Quantitative BiologyUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Rey‐Ting Guo
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
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17
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Gao J, Ko T, Chen L, Malwal SR, Zhang J, Hu X, Qu F, Liu W, Huang J, Cheng Y, Chen C, Yang Y, Zhang Y, Oldfield E, Guo R. “Head‐to‐Middle” and “Head‐to‐Tail”
cis
‐Prenyl Transferases: Structure of Isosesquilavandulyl Diphosphate Synthase. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201710185] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jian Gao
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Tzu‐Ping Ko
- Institute of Biological ChemistryAcademia Sinica Taipei 11529 Taiwan
| | - Lu Chen
- Department of BiochemistryUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Satish R. Malwal
- Department of ChemistryUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Jianan Zhang
- School of Molecular and Cellular BiologyUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Xiangying Hu
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Fiona Qu
- Department of ChemistryUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Weidong Liu
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Jian‐Wen Huang
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Ya‐Shan Cheng
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Chun‐Chi Chen
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Yunyun Yang
- School of Pharmaceutical SciencesTsinghua University Beijing 100084 China
| | - Yonghui Zhang
- School of Pharmaceutical SciencesTsinghua University Beijing 100084 China
| | - Eric Oldfield
- Department of ChemistryUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
- Center for Biophysics and Quantitative BiologyUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Rey‐Ting Guo
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
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18
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Grabińska KA, Edani BH, Park EJ, Kraehling JR, Sessa WC. A conserved C-terminal R XG motif in the NgBR subunit of cis-prenyltransferase is critical for prenyltransferase activity. J Biol Chem 2017; 292:17351-17361. [PMID: 28842490 DOI: 10.1074/jbc.m117.806034] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/16/2017] [Indexed: 11/06/2022] Open
Abstract
cis-Prenyltransferases (cis-PTs) constitute a large family of enzymes conserved during evolution and present in all domains of life. In eukaryotes and archaea, cis-PT is the first enzyme committed to the synthesis of dolichyl phosphate, an obligate lipid carrier in protein glycosylation reactions. The homodimeric bacterial enzyme, undecaprenyl diphosphate synthase, generates 11 isoprene units and has been structurally and mechanistically characterized in great detail. Recently, we discovered that unlike undecaprenyl diphosphate synthase, mammalian cis-PT is a heteromer consisting of NgBR (Nus1) and hCIT (dehydrodolichol diphosphate synthase) subunits, and this composition has been confirmed in plants and fungal cis-PTs. Here, we establish the first purification system for heteromeric cis-PT and show that both NgBR and hCIT subunits function in catalysis and substrate binding. Finally, we identified a critical RXG sequence in the C-terminal tail of NgBR that is conserved and essential for enzyme activity across phyla. In summary, our findings show that eukaryotic cis-PT is composed of the NgBR and hCIT subunits. The strong conservation of the RXG motif among NgBR orthologs indicates that this subunit is critical for the synthesis of polyprenol diphosphates and cellular function.
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Affiliation(s)
- Kariona A Grabińska
- From the Department of Pharmacology and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Ban H Edani
- From the Department of Pharmacology and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Eon Joo Park
- From the Department of Pharmacology and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Jan R Kraehling
- From the Department of Pharmacology and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut 06520
| | - William C Sessa
- From the Department of Pharmacology and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut 06520
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19
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Grabińska KA, Park EJ, Sessa WC. cis-Prenyltransferase: New Insights into Protein Glycosylation, Rubber Synthesis, and Human Diseases. J Biol Chem 2016; 291:18582-90. [PMID: 27402831 PMCID: PMC5000101 DOI: 10.1074/jbc.r116.739490] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
cis-Prenyltransferases (cis-PTs) constitute a large family of enzymes conserved during evolution and present in all domains of life. cis-PTs catalyze consecutive condensation reactions of allylic diphosphate acceptor with isopentenyl diphosphate (IPP) in the cis (Z) configuration to generate linear polyprenyl diphosphate. The chain lengths of isoprenoid carbon skeletons vary widely from neryl pyrophosphate (C10) to natural rubber (C>10,000). The homo-dimeric bacterial enzyme, undecaprenyl diphosphate synthase (UPPS), has been structurally and mechanistically characterized in great detail and serves as a model for understanding the mode of action of eukaryotic cis-PTs. However, recent experiments have revealed that mammals, fungal, and long-chain plant cis-PTs are heteromeric enzymes composed of two distantly related subunits. In this review, the classification, function, and evolution of cis-PTs will be discussed with a special emphasis on the role of the newly described NgBR/Nus1 subunit and its plants' orthologs as essential, structural components of the cis-PTs activity.
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Affiliation(s)
- Kariona A Grabińska
- From the Department of Pharmacology and Vascular Biology and Therapeutics Program (VBT), Yale University School of Medicine, New Haven, Connecticut 06520
| | - Eon Joo Park
- From the Department of Pharmacology and Vascular Biology and Therapeutics Program (VBT), Yale University School of Medicine, New Haven, Connecticut 06520
| | - William C Sessa
- From the Department of Pharmacology and Vascular Biology and Therapeutics Program (VBT), Yale University School of Medicine, New Haven, Connecticut 06520
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20
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Beran F, Rahfeld P, Luck K, Nagel R, Vogel H, Wielsch N, Irmisch S, Ramasamy S, Gershenzon J, Heckel DG, Köllner TG. Novel family of terpene synthases evolved from trans-isoprenyl diphosphate synthases in a flea beetle. Proc Natl Acad Sci U S A 2016; 113:2922-7. [PMID: 26936952 PMCID: PMC4801258 DOI: 10.1073/pnas.1523468113] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Sesquiterpenes play important roles in insect communication, for example as pheromones. However, no sesquiterpene synthases, the enzymes involved in construction of the basic carbon skeleton, have been identified in insects to date. We investigated the biosynthesis of the sesquiterpene (6R,7S)-himachala-9,11-diene in the crucifer flea beetle Phyllotreta striolata, a compound previously identified as a male-produced aggregation pheromone in several Phyllotreta species. A (6R,7S)-himachala-9,11-diene-producing sesquiterpene synthase activity was detected in crude beetle protein extracts, but only when (Z,E)-farnesyl diphosphate [(Z,E)-FPP] was offered as a substrate. No sequences resembling sesquiterpene synthases from plants, fungi, or bacteria were found in the P. striolata transcriptome, but we identified nine divergent putative trans-isoprenyl diphosphate synthase (trans-IDS) transcripts. Four of these putative trans-IDSs exhibited terpene synthase (TPS) activity when heterologously expressed. Recombinant PsTPS1 converted (Z,E)-FPP to (6R,7S)-himachala-9,11-diene and other sesquiterpenes observed in beetle extracts. RNAi-mediated knockdown of PsTPS1 mRNA in P. striolata males led to reduced emission of aggregation pheromone, confirming a significant role of PsTPS1 in pheromone biosynthesis. Two expressed enzymes showed genuine IDS activity, with PsIDS1 synthesizing (E,E)-FPP, whereas PsIDS3 produced neryl diphosphate, (Z,Z)-FPP, and (Z,E)-FPP. In a phylogenetic analysis, the PsTPS enzymes and PsIDS3 were clearly separated from a clade of known coleopteran trans-IDS enzymes including PsIDS1 and PsIDS2. However, the exon-intron structures of IDS and TPS genes in P. striolata are conserved, suggesting that this TPS gene family evolved from trans-IDS ancestors.
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Affiliation(s)
- Franziska Beran
- Research Group Sequestration and Detoxification in Insects, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany;
| | - Peter Rahfeld
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Katrin Luck
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Raimund Nagel
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Natalie Wielsch
- Department of Mass Spectrometry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Sandra Irmisch
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | | | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Tobias G Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
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21
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Abstract
This article summarizes what is currently known of the structures, physiological roles, involvement in pathogenicity, and biogenesis of a variety of noncovalently bound cell envelope lipids and glycoconjugates of Mycobacterium tuberculosis and other Mycobacterium species. Topics addressed in this article include phospholipids; phosphatidylinositol mannosides; triglycerides; isoprenoids and related compounds (polyprenyl phosphate, menaquinones, carotenoids, noncarotenoid cyclic isoprenoids); acyltrehaloses (lipooligosaccharides, trehalose mono- and di-mycolates, sulfolipids, di- and poly-acyltrehaloses); mannosyl-beta-1-phosphomycoketides; glycopeptidolipids; phthiocerol dimycocerosates, para-hydroxybenzoic acids, and phenolic glycolipids; mycobactins; mycolactones; and capsular polysaccharides.
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22
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Rodriguez JB, Falcone BN, Szajnman SH. Approaches for Designing new Potent Inhibitors of Farnesyl Pyrophosphate Synthase. Expert Opin Drug Discov 2016; 11:307-20. [DOI: 10.1517/17460441.2016.1143814] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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23
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Feng X, Zhu W, Schurig-Briccio LA, Lindert S, Shoen C, Hitchings R, Li J, Wang Y, Baig N, Zhou T, Kim BK, Crick DC, Cynamon M, McCammon JA, Gennis RB, Oldfield E. Antiinfectives targeting enzymes and the proton motive force. Proc Natl Acad Sci U S A 2015; 112:E7073-82. [PMID: 26644565 PMCID: PMC4697371 DOI: 10.1073/pnas.1521988112] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
There is a growing need for new antibiotics. Compounds that target the proton motive force (PMF), uncouplers, represent one possible class of compounds that might be developed because they are already used to treat parasitic infections, and there is interest in their use for the treatment of other diseases, such as diabetes. Here, we tested a series of compounds, most with known antiinfective activity, for uncoupler activity. Many cationic amphiphiles tested positive, and some targeted isoprenoid biosynthesis or affected lipid bilayer structure. As an example, we found that clomiphene, a recently discovered undecaprenyl diphosphate synthase inhibitor active against Staphylococcus aureus, is an uncoupler. Using in silico screening, we then found that the anti-glioblastoma multiforme drug lead vacquinol is an inhibitor of Mycobacterium tuberculosis tuberculosinyl adenosine synthase, as well as being an uncoupler. Because vacquinol is also an inhibitor of M. tuberculosis cell growth, we used similarity searches based on the vacquinol structure, finding analogs with potent (∼0.5-2 μg/mL) activity against M. tuberculosis and S. aureus. Our results give a logical explanation of the observation that most new tuberculosis drug leads discovered by phenotypic screens and genome sequencing are highly lipophilic (logP ∼5.7) bases with membrane targets because such species are expected to partition into hydrophobic membranes, inhibiting membrane proteins, in addition to collapsing the PMF. This multiple targeting is expected to be of importance in overcoming the development of drug resistance because targeting membrane physical properties is expected to be less susceptible to the development of resistance.
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Affiliation(s)
- Xinxin Feng
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Wei Zhu
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | | | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210
| | - Carolyn Shoen
- Central New York Research Corporation, Veterans Affairs Medical Center, Syracuse, NY 13210
| | - Reese Hitchings
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523
| | - Jikun Li
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Yang Wang
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Noman Baig
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Tianhui Zhou
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Boo Kyung Kim
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Dean C Crick
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523
| | - Michael Cynamon
- Central New York Research Corporation, Veterans Affairs Medical Center, Syracuse, NY 13210
| | - J Andrew McCammon
- Department of Pharmacology and Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093; Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093; National Biomedical Computation Resource, University of California San Diego, La Jolla, CA 92093;
| | - Robert B Gennis
- Department of Chemistry, University of Illinois, Urbana, IL 61801; Department of Biochemistry, University of Illinois, Urbana, IL 61801; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Eric Oldfield
- Department of Chemistry, University of Illinois, Urbana, IL 61801; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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24
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Kim MO, Feng X, Feixas F, Zhu W, Lindert S, Bogue S, Sinko W, de Oliveira C, Rao G, Oldfield E, McCammon JA. A Molecular Dynamics Investigation of Mycobacterium tuberculosis Prenyl Synthases: Conformational Flexibility and Implications for Computer-aided Drug Discovery. Chem Biol Drug Des 2014; 85:756-69. [PMID: 25352216 DOI: 10.1111/cbdd.12463] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 09/26/2014] [Accepted: 10/17/2014] [Indexed: 01/09/2023]
Abstract
With the rise in antibiotic resistance, there is interest in discovering new drugs active against new targets. Here, we investigate the dynamic structures of three isoprenoid synthases from Mycobacterium tuberculosis using molecular dynamics (MD) methods with a view to discovering new drug leads. Two of the enzymes, cis-farnesyl diphosphate synthase (cis-FPPS) and cis-decaprenyl diphosphate synthase (cis-DPPS), are involved in bacterial cell wall biosynthesis, while the third, tuberculosinyl adenosine synthase (Rv3378c), is involved in virulence factor formation. The MD results for these three enzymes were then compared with previous results on undecaprenyl diphosphate synthase (UPPS) by means of active site volume fluctuation and principal component analyses. In addition, an analysis of the binding of prenyl diphosphates to cis-FPPS, cis-DPPS, and UPPS utilizing the new MD results is reported. We also screened libraries of inhibitors against cis-DPPS, finding ~1 μm inhibitors, and used the receiver operating characteristic-area under the curve (ROC-AUC) method to test the predictive power of X-ray and MD-derived cis-DPPS receptors. We found that one compound with potent M. tuberculosis cell growth inhibition activity was an IC(50) ~0.5- to 20-μm inhibitor (depending on substrate) of cis-DPPS, a ~660-nm inhibitor of Rv3378c as well as a 4.8-μm inhibitor of cis-FPPS, opening up the possibility of multitarget inhibition involving both cell wall biosynthesis and virulence factor formation.
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Affiliation(s)
- Meekyum Olivia Kim
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Xinxin Feng
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ferran Feixas
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Wei Zhu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Steffen Lindert
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA.,Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Shannon Bogue
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - William Sinko
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
| | - César de Oliveira
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA.,Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Guodong Rao
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - James Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA.,Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA.,Center for Theoretical Biological Physics, University of California San Diego, La Jolla, CA, 92093, USA
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25
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Surmacz L, Plochocka D, Kania M, Danikiewicz W, Swiezewska E. cis-Prenyltransferase atCPT6 produces a family of very short-chain polyisoprenoids in planta. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:240-50. [PMID: 24291644 DOI: 10.1016/j.bbalip.2013.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 11/13/2013] [Accepted: 11/22/2013] [Indexed: 11/28/2022]
Abstract
cis-Prenyltransferases (CPTs) comprise numerous enzymes synthesizing isoprenoid hydrocarbon skeleton with isoprenoid units in the cis (Z) configuration. The chain-length specificity of a particular plant CPT is in most cases unknown despite thecomposition of the accumulated isoprenoids in the tissue of interest being well established. In this report AtCPT6, one of the nine Arabidopsis thaliana CPTs, is shown to catalyze the synthesis of a family of very short-chain polyisoprenoid alcohols of six, seven, and eight isoprenoid units, those of seven units dominating The product specificity of AtCPT6 was established in vivo following its expression in the heterologous system of the yeast Saccharomyces cerevisiae and was confirmed by the absence of specific products in AtCPT6 T-DNA insertion mutants and their overaccumulation in AtCPT6-overexpressing plants. These observations are additionally validated in silico using an AtCPT6 model obtained by homology modeling. AtCPT6 only partially complements the function of the yeast homologue of CPT-Rer2 since it restores the growth but not protein glycosylation in rer2delta yeast.This is the first in planta characterization of specific products of a plant CPT producing polyisoprenoids. Their distribution suggests that a joint activity of several CPTs is required to produce the complex mixture of polyisoprenoid alcohols found in Arabidopsis roots.
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26
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Kolly GS, Boldrin F, Sala C, Dhar N, Hartkoorn RC, Ventura M, Serafini A, McKinney JD, Manganelli R, Cole ST. Assessing the essentiality of the decaprenyl-phospho-d-arabinofuranose pathway in Mycobacterium tuberculosis using conditional mutants. Mol Microbiol 2014; 92:194-211. [PMID: 24517327 DOI: 10.1111/mmi.12546] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2014] [Indexed: 11/29/2022]
Abstract
In Mycobacterium tuberculosis the decaprenyl-phospho-d-arabinofuranose (DPA) pathway is a validated target for the drugs ethambutol and benzothiazinones. To identify other potential drug targets in the pathway, we generated conditional knock-down mutants of each gene involved using the TET-PIP OFF system. dprE1, dprE2, ubiA, prsA, rv2361c, tkt and rpiB were confirmed to be essential under non-permissive conditions, whereas rv3807c was not required for survival. In the most vulnerable group, DprE1-depleted cells died faster in vitro and intracellularly than those lacking UbiA and PrsA. Downregulation of DprE1 and UbiA resulted in similar phenotypes, namely swelling of the bacteria, cell wall damage and lysis as observed at the single cell level, by real time microscopy and electron microscopy. By contrast, depletion of PrsA led to cell elongation and implosion, which was suggestive of a more pleiotropic effect. Drug sensitivity assays with known DPA-inhibitors supported the use of conditional knock-down strains for target-based whole-cell screens. Together, our work provides strong evidence for the vulnerability of all but one of the enzymes in the DPA pathway and generates valuable tools for the identification of lead compounds targeting the different biosynthetic steps. PrsA, phosphoribosyl-pyrophosphate synthetase, appears to be a particularly attractive new target for drug discovery.
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Affiliation(s)
- Gaëlle S Kolly
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, Lausanne, 1015, Switzerland
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27
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Molecular profiling of Mycobacterium tuberculosis identifies tuberculosinyl nucleoside products of the virulence-associated enzyme Rv3378c. Proc Natl Acad Sci U S A 2014; 111:2978-83. [PMID: 24516143 DOI: 10.1073/pnas.1315883111] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To identify lipids with roles in tuberculosis disease, we systematically compared the lipid content of virulent Mycobacterium tuberculosis with the attenuated vaccine strain Mycobacterium bovis bacillus Calmette-Guérin. Comparative lipidomics analysis identified more than 1,000 molecular differences, including a previously unknown, Mycobacterium tuberculosis-specific lipid that is composed of a diterpene unit linked to adenosine. We established the complete structure of the natural product as 1-tuberculosinyladenosine (1-TbAd) using mass spectrometry and NMR spectroscopy. A screen for 1-TbAd mutants, complementation studies, and gene transfer identified Rv3378c as necessary for 1-TbAd biosynthesis. Whereas Rv3378c was previously thought to function as a phosphatase, these studies establish its role as a tuberculosinyl transferase and suggest a revised biosynthetic pathway for the sequential action of Rv3377c-Rv3378c. In agreement with this model, recombinant Rv3378c protein produced 1-TbAd, and its crystal structure revealed a cis-prenyl transferase fold with hydrophobic residues for isoprenoid binding and a second binding pocket suitable for the nucleoside substrate. The dual-substrate pocket distinguishes Rv3378c from classical cis-prenyl transferases, providing a unique model for the prenylation of diverse metabolites. Terpene nucleosides are rare in nature, and 1-TbAd is known only in Mycobacterium tuberculosis. Thus, this intersection of nucleoside and terpene pathways likely arose late in the evolution of the Mycobacterium tuberculosis complex; 1-TbAd serves as an abundant chemical marker of Mycobacterium tuberculosis, and the extracellular export of this amphipathic molecule likely accounts for the known virulence-promoting effects of the Rv3378c enzyme.
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28
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Chan HC, Feng X, Ko TP, Huang CH, Hu Y, Zheng Y, Bogue S, Nakano C, Hoshino T, Zhang L, Lv P, Liu W, Crick DC, Liang PH, Wang AHJ, Oldfield E, Guo RT. Structure and inhibition of tuberculosinol synthase and decaprenyl diphosphate synthase from Mycobacterium tuberculosis. J Am Chem Soc 2014; 136:2892-6. [PMID: 24475925 PMCID: PMC3986019 DOI: 10.1021/ja413127v] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
![]()
We
have obtained the structure of the bacterial diterpene synthase,
tuberculosinol/iso-tuberculosinol synthase (Rv3378c)
from Mycobacterium tuberculosis, a
target for anti-infective therapies that block virulence factor formation.
This phosphatase adopts the same fold as found in the Z- or cis-prenyltransferases. We also obtained structures
containing the tuberculosinyl diphosphate substrate together with
one bisphosphonate inhibitor-bound structure. These structures together
with the results of site-directed mutagenesis suggest an unusual mechanism
of action involving two Tyr residues. Given the similarity in local
and global structure between Rv3378c and the M. tuberculosis cis-decaprenyl diphosphate synthase (DPPS; Rv2361c),
the possibility exists for the development of inhibitors that target
not only virulence but also cell wall biosynthesis, based in part
on the structures reported here.
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Affiliation(s)
- Hsiu-Chien Chan
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology , Tianjin 300308, China
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29
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Engineered heterologous FPP synthases-mediated Z,E-FPP synthesis in E. coli. Metab Eng 2013; 18:53-9. [DOI: 10.1016/j.ymben.2013.04.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 01/21/2013] [Accepted: 04/01/2013] [Indexed: 02/03/2023]
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30
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Gao Y, Honzatko RB, Peters RJ. Terpenoid synthase structures: a so far incomplete view of complex catalysis. Nat Prod Rep 2012; 29:1153-75. [PMID: 22907771 PMCID: PMC3448952 DOI: 10.1039/c2np20059g] [Citation(s) in RCA: 244] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The complexity of terpenoid natural products has drawn significant interest, particularly since their common (poly)isoprenyl origins were discovered. Notably, much of this complexity is derived from the highly variable cyclized and/or rearranged nature of the observed hydrocarbon skeletal structures. Indeed, at least in some cases it is difficult to immediately recognize their derivation from poly-isoprenyl precursors. Nevertheless, these diverse structures are formed by sequential elongation to acyclic precursors, most often with subsequent cyclization and/or rearrangement. Strikingly, the reactions used to assemble and diversify terpenoid backbones share a common carbocationic driven mechanism, although the means by which the initial carbocation is generated does vary. High-resolution crystal structures have been obtained for at least representative examples from each of the various types of enzymes involved in producing terpenoid hydrocarbon backbones. However, while this has certainly led to some insights into the enzymatic structure-function relationships underlying the elongation and simpler cyclization reactions, our understanding of the more complex cyclization and/or rearrangement reactions remains limited. Accordingly, selected examples are discussed here to demonstrate our current understanding, its limits, and potential ways forward.
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Affiliation(s)
- Yang Gao
- Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Richard B. Honzatko
- Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Reuben J. Peters
- Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA 50011, USA
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31
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Sasaki D, Fujihashi M, Okuyama N, Kobayashi Y, Noike M, Koyama T, Miki K. Crystal structure of heterodimeric hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26 reveals that the small subunit is directly involved in the product chain length regulation. J Biol Chem 2010; 286:3729-40. [PMID: 21068379 DOI: 10.1074/jbc.m110.147991] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26 (Ml-HexPPs) is a heterooligomeric type trans-prenyltransferase catalyzing consecutive head-to-tail condensations of three molecules of isopentenyl diphosphates (C(5)) on a farnesyl diphosphate (FPP; C(15)) to form an (all-E) hexaprenyl diphosphate (HexPP; C(30)). Ml-HexPPs is known to function as a heterodimer of two different subunits, small and large subunits called HexA and HexB, respectively. Compared with homooligomeric trans-prenyltransferases, the molecular mechanism of heterooligomeric trans-prenyltransferases is not yet clearly understood, particularly with respect to the role of the small subunits lacking the catalytic motifs conserved in most known trans-prenyltransferases. We have determined the crystal structure of Ml-HexPPs both in the substrate-free form and in complex with 7,11-dimethyl-2,6,10-dodecatrien-1-yl diphosphate ammonium salt (3-DesMe-FPP), an analog of FPP. The structure of HexB is composed of mostly antiparallel α-helices joined by connecting loops. Two aspartate-rich motifs (designated the first and second aspartate-rich motifs) and the other characteristic motifs in HexB are located around the diphosphate part of 3-DesMe-FPP. Despite the very low amino acid sequence identity and the distinct polypeptide chain lengths between HexA and HexB, the structure of HexA is quite similar to that of HexB. The aliphatic tail of 3-DesMe-FPP is accommodated in a large hydrophobic cleft starting from HexB and penetrating to the inside of HexA. These structural features suggest that HexB catalyzes the condensation reactions and that HexA is directly involved in the product chain length control in cooperation with HexB.
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Affiliation(s)
- Daisuke Sasaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Kyoto 606-8502, Japan
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32
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Sato T, Takizawa K, Orito Y, Kudo H, Hoshino T. Insight into C35 terpene Biosyntheses by Nonpathogenic Mycobacterium Species: Functional Analyses of Three Z-Prenyltransferases and Identification of Dehydroheptaprenylcyclines. Chembiochem 2010; 11:1874-81. [DOI: 10.1002/cbic.201000328] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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33
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Umesiri FE, Sanki AK, Boucau J, Ronning DR, Sucheck SJ. Recent advances toward the inhibition of mAG and LAM synthesis in Mycobacterium tuberculosis. Med Res Rev 2010; 30:290-326. [DOI: 10.1002/med.20190] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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34
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Brandt W, Bräuer L, Günnewich N, Kufka J, Rausch F, Schulze D, Schulze E, Weber R, Zakharova S, Wessjohann L. Molecular and structural basis of metabolic diversity mediated by prenyldiphosphate converting enzymes. PHYTOCHEMISTRY 2009; 70:1758-1775. [PMID: 19878958 DOI: 10.1016/j.phytochem.2009.09.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 08/31/2009] [Accepted: 09/01/2009] [Indexed: 05/28/2023]
Abstract
General thermodynamic calculations using the semiempiric PM3 method have led to the conclusion that prenyldiphosphate converting enzymes require at least one divalent metal cation for the activation and cleavage of the diphosphate-prenyl ester bond, or they must provide structural elements for the efficient stabilization of the intermediate prenyl cation. The most important common structural features, which guide the product specificity in both terpene synthases and aromatic prenyl transferases are aromatic amino acid side chains, which stabilize prenyl cations by cation-pi interactions. In the case of aromatic prenyl transferases, a proton abstraction from the phenolic hydroxyl group of the second substrate will enhance the electron density in the phenolic ortho-position at which initial prenylation of the aromatic compound usually occurs. A model of the structure of the integral transmembrane-bound aromatic prenyl transferase UbiA was developed, which currently represents the first structural insight into this group of prenylating enzymes with a fold different from most other aromatic prenyl transferases. Based on this model, the structure-activity relationships and mechanistic aspects of related proteins, for example those of Lithospermum erythrorhizon or the enzyme AuaA from Stigmatella aurantiaca involved in the aurachin biosynthesis, were elucidated. The high similarity of this group of aromatic prenyltransferases to 5-epi-aristolochene synthase is an indication of an evolutionary relationship with terpene synthases (cyclases). This is further supported by the conserved DxxxD motif found in both protein families. In contrast, there is no such relationship to the aromatic prenyl transferases with an ABBA-fold, such as NphB, or to any other known family of prenyl converting enzymes. Therefore, it is possible that these two groups might have different evolutionary ancestors.
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Affiliation(s)
- Wolfgang Brandt
- Leibniz Institute of Plant Biochemistry, Department of Bioorganic Chemistry, Halle (Saale), Germany.
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35
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Liang PH. Reaction kinetics, catalytic mechanisms, conformational changes, and inhibitor design for prenyltransferases. Biochemistry 2009; 48:6562-70. [PMID: 19537817 DOI: 10.1021/bi900371p] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Isoprenoids comprise a family of more than 55000 natural products with great structural variety derived from five-carbon isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP). Allylic diphosphates such as farnesyl diphosphate (FPP) synthesized from DMAPP and IPP serve as outlet points for a great variety of products. A group of prenyltransferases catalyzing chain elongation of FPP to designated lengths by consecutive condensation reactions with specific numbers of IPP are classified as cis and trans types according to the stereochemistry of the double bonds formed by IPP condensation. The complete kinetics of the multistep IPP condensation reactions by both types of enzymes has been determined using steady-state and pre-steady-state approaches. Because their crystal structures were determined in conjunction with biochemical studies, a more thorough understanding of their catalytic mechanisms, protein conformational changes, and product chain-length determination mechanisms has been gained recently. Since these prenyltransferases play important roles, potent inhibitors have been identified and their cocrystal structures have been determined for drug development. In this review, the current knowledge of these prenyltransferases that synthesize prenyl oligomers or polymers is summarized.
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Affiliation(s)
- Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
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36
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Product chain-length determination mechanism of Z,E-farnesyl diphosphate synthase. Biochem Biophys Res Commun 2008; 377:17-22. [PMID: 18790692 DOI: 10.1016/j.bbrc.2008.09.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Accepted: 09/03/2008] [Indexed: 11/22/2022]
Abstract
cis-Prenyltransferases catalyze the consecutive condensation of isopentenyl diphosphate (IPP) with allylic prenyl diphosphates, producing Z,E-mixed prenyl diphosphate. The Mycobacterium tuberculosis Z,E-farnesyl diphosphate synthase Rv1086 catalyzes the condensation of one molecule of IPP with geranyl diphosphate to yield Z,E-farnesyl diphosphate and is classified as a short-chain cis-prenyltransferase. To elucidate the chain-length determination mechanism of the short-chain cis-prenyltransferase, we introduced some substitutive mutations at the characteristic amino acid residues of Rv1086. Among the mutants constructed, L84A showed a dramatic change of catalytic function to synthesize longer prenyl chain products than that of wild type, indicating that Leu84 of Rv1086 plays an important role in product chain-length determination. Mutagenesis at the corresponding residue of a medium-chain cis-prenyltransferase, Micrococcus luteus B-P 26 undecaprenyl diphosphate synthase also resulted in the production of different prenyl chain length from the intrinsic product, suggesting that this position also plays an important role in product chain-length determination for medium-chain cis-prenyltransferases.
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