1
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Misra J, Mettert EL, Kiley PJ. Functional analysis of the methylerythritol phosphate pathway terminal enzymes IspG and IspH from Zymomonas mobilis. Microbiol Spectr 2024; 12:e0425623. [PMID: 38785428 PMCID: PMC11218510 DOI: 10.1128/spectrum.04256-23] [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: 12/22/2023] [Accepted: 04/05/2024] [Indexed: 05/25/2024] Open
Abstract
Isoprenoids are a diverse family of compounds that are synthesized from two isomeric compounds, isopentenyl diphosphate and dimethylallyl diphosphate. In most bacteria, isoprenoids are produced from the essential methylerythritol phosphate (MEP) pathway. The terminal enzymes of the MEP pathway IspG and IspH are [4Fe-4S] cluster proteins, and in Zymomonas mobilis, the substrates of IspG and IspH accumulate in cells in response to O2, suggesting possible lability of their [4Fe-4S] clusters. Here, we show using complementation assays in Escherichia coli that even under anaerobic conditions, Z. mobilis IspG and IspH are not as functional as their E. coli counterparts, requiring higher levels of expression to rescue viability. A deficit of the sulfur utilization factor (SUF) Fe-S cluster biogenesis pathway did not explain the reduced function of Z. mobilis IspG and IspH since no improvement in viability was observed in E. coli expressing the Z. mobilis SUF pathway or having increased expression of the E. coli SUF pathway. Complementation of single and double mutants with various combinations of Z. mobilis and E. coli IspG and IspH indicated that optimal growth required the pairing of IspG and IspH from the same species. Furthermore, Z. mobilis IspH conferred an O2-sensitive growth defect to E. coli that could be partially rescued by co-expression of Z. mobilis IspG. In vitro analysis showed O2 sensitivity of the [4Fe-4S] cluster of both Z. mobilis IspG and IspH. Altogether, our data indicate an important role of the cognate protein IspG in Z. mobilis IspH function under both aerobic and anaerobic conditions. IMPORTANCE Isoprenoids are one of the largest classes of natural products, exhibiting diversity in structure and function. They also include compounds that are essential for cellular life across the biological world. In bacteria, isoprenoids are derived from two precursors, isopentenyl diphosphate and dimethylallyl diphosphate, synthesized primarily by the methylerythritol phosphate pathway. The aerotolerant Z. mobilis has the potential for methylerythritol phosphate pathway engineering by diverting some of the glucose that is typically efficiently converted into ethanol to produce isoprenoid precursors to make bioproducts and biofuels. Our data revealed the surprising finding that Z. mobilis IspG and IspH need to be co-optimized to improve flux via the methyl erythritol phosphate pathway in part to evade the oxygen sensitivity of IspH.
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Affiliation(s)
- Jyotsna Misra
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Erin L. Mettert
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Patricia J. Kiley
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
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2
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Huang XL. Unveiling the role of inorganic nanoparticles in Earth's biochemical evolution through electron transfer dynamics. iScience 2024; 27:109555. [PMID: 38638571 PMCID: PMC11024932 DOI: 10.1016/j.isci.2024.109555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
This article explores the intricate interplay between inorganic nanoparticles and Earth's biochemical history, with a focus on their electron transfer properties. It reveals how iron oxide and sulfide nanoparticles, as examples of inorganic nanoparticles, exhibit oxidoreductase activity similar to proteins. Termed "life fossil oxidoreductases," these inorganic enzymes influence redox reactions, detoxification processes, and nutrient cycling in early Earth environments. By emphasizing the structural configuration of nanoparticles and their electron conformation, including oxygen defects and metal vacancies, especially electron hopping, the article provides a foundation for understanding inorganic enzyme mechanisms. This approach, rooted in physics, underscores that life's origin and evolution are governed by electron transfer principles within the framework of chemical equilibrium. Today, these nanoparticles serve as vital biocatalysts in natural ecosystems, participating in critical reactions for ecosystem health. The research highlights their enduring impact on Earth's history, shaping ecosystems and interacting with protein metal centers through shared electron transfer dynamics, offering insights into early life processes and adaptations.
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Affiliation(s)
- Xiao-Lan Huang
- Center for Clean Water Technology, School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-6044, USA
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3
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Huang XL, Harmer JR, Schenk G, Southam G. Inorganic Fe-O and Fe-S oxidoreductases: paradigms for prebiotic chemistry and the evolution of enzymatic activity in biology. Front Chem 2024; 12:1349020. [PMID: 38389729 PMCID: PMC10881703 DOI: 10.3389/fchem.2024.1349020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
Oxidoreductases play crucial roles in electron transfer during biological redox reactions. These reactions are not exclusive to protein-based biocatalysts; nano-size (<100 nm), fine-grained inorganic colloids, such as iron oxides and sulfides, also participate. These nanocolloids exhibit intrinsic redox activity and possess direct electron transfer capacities comparable to their biological counterparts. The unique metal ion architecture of these nanocolloids, including electron configurations, coordination environment, electron conductivity, and the ability to promote spontaneous electron hopping, contributes to their transfer capabilities. Nano-size inorganic colloids are believed to be among the earliest 'oxidoreductases' to have 'evolved' on early Earth, playing critical roles in biological systems. Representing a distinct type of biocatalysts alongside metalloproteins, these nanoparticles offer an early alternative to protein-based oxidoreductase activity. While the roles of inorganic nano-sized catalysts in current Earth ecosystems are intuitively significant, they remain poorly understood and underestimated. Their contribution to chemical reactions and biogeochemical cycles likely helped shape and maintain the balance of our planet's ecosystems. However, their potential applications in biomedical, agricultural, and environmental protection sectors have not been fully explored or exploited. This review examines the structure, properties, and mechanisms of such catalysts from a material's evolutionary standpoint, aiming to raise awareness of their potential to provide innovative solutions to some of Earth's sustainability challenges.
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Affiliation(s)
- Xiao-Lan Huang
- NYS Center for Clean Water Technology, School of Marine and Atmospheric Sciences, Stony Brook, NY, United States
| | - Jeffrey R Harmer
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Gerhard Schenk
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Gordon Southam
- Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
- School of the Environment, The University of Queensland, Brisbane, QLD, Australia
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4
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Huang S, Xue Y, Ma Y, Zhou C. Microbial (E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate reductase (IspH) and its biotechnological potential: A mini review. Front Bioeng Biotechnol 2022; 10:1057938. [DOI: 10.3389/fbioe.2022.1057938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/10/2022] [Indexed: 11/30/2022] Open
Abstract
(E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate (HMBPP) reductase (IspH) is a [4Fe-4S] cluster-containing enzyme, involved in isoprenoid biosynthesis as the final enzyme of the methylerythritol phosphate (MEP) pathway found in many bacteria and malaria parasites. In recent years, many studies have revealed that isoprenoid compounds are an alternative to petroleum-derived fuels. Thus, ecofriendly methods harnessing the methylerythritol phosphate pathway in microbes to synthesize isoprenoid compounds and IspH itself have received notable attention from researchers. In addition to its applications in the field of biosynthesis, IspH is considered to be an attractive drug target for infectious diseases such as malaria and tuberculosis due to its survivability in most pathogenic bacterium and its absence in humans. In this mini-review, we summarize previous reports that have systematically illuminated the fundamental and structural properties, substrate binding and catalysis, proposed catalytic mechanism, and novel catalytic activities of IspH. Potential bioengineering and biotechnological applications of IspH are also discussed.
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5
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Jobelius H, Bianchino GI, Borel F, Chaignon P, Seemann M. The Reductive Dehydroxylation Catalyzed by IspH, a Source of Inspiration for the Development of Novel Anti-Infectives. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030708. [PMID: 35163971 PMCID: PMC8837944 DOI: 10.3390/molecules27030708] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/11/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022]
Abstract
The non-mevalonate or also called MEP pathway is an essential route for the biosynthesis of isoprenoid precursors in most bacteria and in microorganisms belonging to the Apicomplexa phylum, such as the parasite responsible for malaria. The absence of this pathway in mammalians makes it an interesting target for the discovery of novel anti-infectives. As last enzyme of this pathway, IspH is an oxygen sensitive [4Fe-4S] metalloenzyme that catalyzes 2H+/2e− reductions and a water elimination by involving non-conventional bioinorganic and bioorganometallic intermediates. After a detailed description of the discovery of the [4Fe-4S] cluster of IspH, this review focuses on the IspH mechanism discussing the results that have been obtained in the last decades using an approach combining chemistry, enzymology, crystallography, spectroscopies, and docking calculations. Considering the interesting druggability of this enzyme, a section about the inhibitors of IspH discovered up to now is reported as well. The presented results constitute a useful and rational help to inaugurate the design and development of new potential chemotherapeutics against pathogenic organisms.
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Affiliation(s)
- Hannah Jobelius
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie de Strasbourg UMR 7177, Université de Strasbourg/CNRS, 4, rue Blaise Pascal, 67070 Strasbourg, France; (H.J.); (G.I.B.); (P.C.)
| | - Gabriella Ines Bianchino
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie de Strasbourg UMR 7177, Université de Strasbourg/CNRS, 4, rue Blaise Pascal, 67070 Strasbourg, France; (H.J.); (G.I.B.); (P.C.)
| | - Franck Borel
- Institut de Biologie Structurale, Université Grenoble Alpes/CEA/CNRS, 38000 Grenoble, France;
| | - Philippe Chaignon
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie de Strasbourg UMR 7177, Université de Strasbourg/CNRS, 4, rue Blaise Pascal, 67070 Strasbourg, France; (H.J.); (G.I.B.); (P.C.)
| | - Myriam Seemann
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie de Strasbourg UMR 7177, Université de Strasbourg/CNRS, 4, rue Blaise Pascal, 67070 Strasbourg, France; (H.J.); (G.I.B.); (P.C.)
- Correspondence:
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6
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Pramastya H, Song Y, Elfahmi EY, Sukrasno S, Quax WJ. Positioning Bacillus subtilis as terpenoid cell factory. J Appl Microbiol 2020; 130:1839-1856. [PMID: 33098223 PMCID: PMC8247319 DOI: 10.1111/jam.14904] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/29/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022]
Abstract
Increasing demands for bioactive compounds have motivated researchers to employ micro‐organisms to produce complex natural products. Currently, Bacillus subtilis has been attracting lots of attention to be developed into terpenoids cell factories due to its generally recognized safe status and high isoprene precursor biosynthesis capacity by endogenous methylerythritol phosphate (MEP) pathway. In this review, we describe the up‐to‐date knowledge of each enzyme in MEP pathway and the subsequent steps of isomerization and condensation of C5 isoprene precursors. In addition, several representative terpene synthases expressed in B. subtilis and the engineering steps to improve corresponding terpenoids production are systematically discussed. Furthermore, the current available genetic tools are mentioned as along with promising strategies to improve terpenoids in B. subtilis, hoping to inspire future directions in metabolic engineering of B. subtilis for further terpenoid cell factory development.
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Affiliation(s)
- H Pramastya
- University of Groningen, Groningen, The Netherlands.,Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - Y Song
- University of Groningen, Groningen, The Netherlands
| | - E Y Elfahmi
- Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - S Sukrasno
- Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - W J Quax
- University of Groningen, Groningen, The Netherlands
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7
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Bhuyan R, Seal A. Exploration and validation of diphosphate-based Plasmodium
LytB inhibitors using computational approaches. J Mol Recognit 2018; 32:e2762. [PMID: 30191613 DOI: 10.1002/jmr.2762] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Rajabrata Bhuyan
- BIF Centre, Department of Biochemistry & Biophysics; University of Kalyani; Kalyani West Bengal India
| | - Alpana Seal
- BIF Centre, Department of Biochemistry & Biophysics; University of Kalyani; Kalyani West Bengal India
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8
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Akob DM, Sutton JM, Fierst JL, Haase KB, Baesman S, Luther GW, Miller LG, Oremland RS. Acetylenotrophy: a hidden but ubiquitous microbial metabolism? FEMS Microbiol Ecol 2018; 94:5026170. [PMID: 29933435 PMCID: PMC7190893 DOI: 10.1093/femsec/fiy103] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/29/2018] [Indexed: 11/12/2022] Open
Abstract
Acetylene (IUPAC name: ethyne) is a colorless, gaseous hydrocarbon, composed of two triple bonded carbon atoms attached to hydrogens (C2H2). When microbiologists and biogeochemists think of acetylene, they immediately think of its use as an inhibitory compound of certain microbial processes and a tracer for nitrogen fixation. However, what is less widely known is that anaerobic and aerobic microorganisms can degrade acetylene, using it as a sole carbon and energy source and providing the basis of a microbial food web. Here, we review what is known about acetylene degrading organisms and introduce the term 'acetylenotrophs' to refer to the microorganisms that carry out this metabolic pathway. In addition, we review the known environmental sources of acetylene and postulate the presence of an hidden acetylene cycle. The abundance of bacteria capable of using acetylene and other alkynes as an energy and carbon source suggests that there are energy cycles present in the environment that are driven by acetylene and alkyne production and consumption that are isolated from atmospheric exchange. Acetylenotrophs may have developed to leverage the relatively high concentrations of acetylene in the pre-Cambrian atmosphere, evolving later to survive in specialized niches where acetylene and other alkynes were produced.
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Affiliation(s)
- Denise M Akob
- U. S. Geological Survey, 12201 Sunrise Valley Dr, MS 430, Reston, VA 20192 USA
| | - John M Sutton
- Department of Biological Sciences, The University of Alabama, SEC 2328, Box 870344, Tuscaloosa, AL 35487 USA
| | - Janna L Fierst
- Department of Biological Sciences, The University of Alabama, SEC 2328, Box 870344, Tuscaloosa, AL 35487 USA
| | - Karl B Haase
- U. S. Geological Survey, 12201 Sunrise Valley Dr, MS 430, Reston, VA 20192 USA
| | - Shaun Baesman
- U. S. Geological Survey, 345 Middlefield Road, MS 480, Menlo Park, CA 94025 USA
| | - George W Luther
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Road, Cannon Laboratory 218, Lewes, DE 19958, USA
| | - Laurence G Miller
- U. S. Geological Survey, 345 Middlefield Road, MS 480, Menlo Park, CA 94025 USA
| | - Ronald S Oremland
- U. S. Geological Survey, 345 Middlefield Road, MS 480, Menlo Park, CA 94025 USA
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9
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Borel F, Barbier E, Krasutsky S, Janthawornpong K, Chaignon P, Poulter CD, Ferrer JL, Seemann M. Further Insight into Crystal Structures of Escherichia coli IspH/LytB in Complex with Two Potent Inhibitors of the MEP Pathway: A Starting Point for Rational Design of New Antimicrobials. Chembiochem 2017; 18:2137-2144. [PMID: 28862365 DOI: 10.1002/cbic.201700363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Indexed: 01/12/2023]
Abstract
IspH, also called LytB, a protein involved in the biosynthesis of isoprenoids through the methylerythritol phosphate pathway, is an attractive target for the development of new antimicrobial drugs. Here, we report crystal structures of Escherichia coli IspH in complex with the two most potent inhibitors: (E)-4-mercapto-3-methylbut-2-en-1-yl diphosphate (TMBPP) and (E)-4-amino-3-methylbut-2-en-1-yl diphosphate (AMBPP) at 1.95 and 1.7 Å resolution, respectively. The structure of the E. coli IspH:TMBPP complex exhibited two conformers of the inhibitor. This unexpected feature was exploited to design and evolve new antimicrobial candidates in silico.
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Affiliation(s)
- Franck Borel
- Institut de Biologie Structurale IBS, Université Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France
| | - Elodie Barbier
- Institut de Biologie Structurale IBS, Université Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France
| | - Sergiy Krasutsky
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT, 84112, USA
| | - Karnjapan Janthawornpong
- Université de Strasbourg, CNRS, Institut de Chimie UMR 7177, Chim Biol&Appl Therap, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - Philippe Chaignon
- Université de Strasbourg, CNRS, Institut de Chimie UMR 7177, Chim Biol&Appl Therap, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - C Dale Poulter
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT, 84112, USA
| | - Jean-Luc Ferrer
- Institut de Biologie Structurale IBS, Université Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France
| | - Myriam Seemann
- Université de Strasbourg, CNRS, Institut de Chimie UMR 7177, Chim Biol&Appl Therap, 4, rue Blaise Pascal, 67070, Strasbourg, France
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10
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O'Dowd B, Williams S, Wang H, No JH, Rao G, Wang W, McCammon JA, Cramer SP, Oldfield E. Spectroscopic and Computational Investigations of Ligand Binding to IspH: Discovery of Non-diphosphate Inhibitors. Chembiochem 2017; 18:914-920. [PMID: 28253432 PMCID: PMC5445010 DOI: 10.1002/cbic.201700052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Indexed: 11/11/2022]
Abstract
Isoprenoid biosynthesis is an important area for anti-infective drug development. One isoprenoid target is (E)-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate (HMBPP) reductase (IspH), which forms isopentenyl diphosphate and dimethylallyl diphosphate from HMBPP in a 2H+ /2e- reduction. IspH contains a 4 Fe-4 S cluster, and in this work, we first investigated how small molecules bound to the cluster by using HYSCORE and NRVS spectroscopies. The results of these, as well as other structural and spectroscopic investigations, led to the conclusion that, in most cases, ligands bound to IspH 4 Fe-4 S clusters by η1 coordination, forming tetrahedral geometries at the unique fourth Fe, ligand side chains preventing further ligand (e.g., H2 O, O2 ) binding. Based on these ideas, we used in silico methods to find drug-like inhibitors that might occupy the HMBPP substrate binding pocket and bind to Fe, leading to the discovery of a barbituric acid analogue with a Ki value of ≈500 nm against Pseudomonas aeruginosa IspH.
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Affiliation(s)
- Bing O'Dowd
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Sarah Williams
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Hongxin Wang
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA, 95616, USA
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Joo Hwan No
- Center for Biophysics and Computational Biology, 607 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Guodong Rao
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Weixue Wang
- Center for Biophysics and Computational Biology, 607 South Mathews Avenue, Urbana, IL, 61801, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093, USA
- Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA, 92093, USA
- National Biomedical Computation Resource, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Stephen P Cramer
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA, 95616, USA
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Eric Oldfield
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA
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11
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Payer SE, Sheng X, Pollak H, Wuensch C, Steinkellner G, Himo F, Glueck SM, Faber K. Exploring the Catalytic Promiscuity of Phenolic Acid Decarboxylases: Asymmetric, 1,6-Conjugate Addition of Nucleophiles Across 4-Hydroxystyrene. Adv Synth Catal 2017; 359:2066-2075. [PMID: 28713228 PMCID: PMC5488193 DOI: 10.1002/adsc.201700247] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/02/2017] [Indexed: 01/29/2023]
Abstract
The catalytic promiscuity of a ferulic acid decarboxylase from Enterobacter sp. (FDC_Es) and phenolic acid decarboxylases (PADs) for the asymmetric conjugate addition of water across the C=C bond of hydroxystyrenes was extended to the N‐, C‐ and S‐nucleophiles methoxyamine, cyanide and propanethiol to furnish the corresponding addition products in up to 91% ee. The products obtained from the biotransformation employing the most suitable enzyme/nucleophile pairs were isolated and characterized after optimizing the reaction conditions. Finally, a mechanistic rationale supported by quantum mechanical calculations for the highly (S)‐selective addition of cyanide is proposed. ![]()
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Affiliation(s)
- Stefan E Payer
- Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
| | - Xiang Sheng
- Arrhenius Laboratory Department of Organic Chemistry Stockholm University SE-106 91 Stockholm Sweden
| | - Hannah Pollak
- Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
| | - Christiane Wuensch
- Austrian Centre of Industrial Biotechnology (ACIB) c/o Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria.,Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
| | - Georg Steinkellner
- Austrian Centre of Industrial Biotechnology (ACIB) c/o Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria.,Center for Molecular Biosciences University of Graz Humboldtstrasse 508010 Graz Austria
| | - Fahmi Himo
- Arrhenius Laboratory Department of Organic Chemistry Stockholm University SE-106 91 Stockholm Sweden
| | - Silvia M Glueck
- Austrian Centre of Industrial Biotechnology (ACIB) c/o Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria.,Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
| | - Kurt Faber
- Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
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12
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The competition between chemistry and biology in assembling iron-sulfur derivatives. Molecular structures and electrochemistry. Part IV. {[Fe3S4](SγCys)3} proteins. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2016.09.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Affiliation(s)
- Annika Frank
- Center for Integrated Protein
Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Michael Groll
- Center for Integrated Protein
Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
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14
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Scheidler C, Sobotta J, Eisenreich W, Wächtershäuser G, Huber C. Unsaturated C3,5,7,9-Monocarboxylic Acids by Aqueous, One-Pot Carbon Fixation: Possible Relevance for the Origin of Life. Sci Rep 2016; 6:27595. [PMID: 27283227 PMCID: PMC4901337 DOI: 10.1038/srep27595] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/20/2016] [Indexed: 11/09/2022] Open
Abstract
All scientific approaches to the origin of life share a common problem: a chemical path to lipids as main constituents of extant cellular enclosures. Here we show by isotope-controlled experiments that unsaturated C3,5,7,9-monocarboxylic acids form by one-pot reaction of acetylene (C2H2) and carbon monoxide (CO) in contact with nickel sulfide (NiS) in hot aqueous medium. The primary products are toto-olefinic monocarboxylic acids with CO-derived COOH groups undergoing subsequent stepwise hydrogenation with CO as reductant. In the resulting unsaturated monocarboxylic acids the double bonds are mainly centrally located with mainly trans-configuration. The reaction conditions are compatible with an origin of life in volcanic-hydrothermal sub-seafloor flow ducts.
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Affiliation(s)
- Christopher Scheidler
- Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstraße 4, D-85747 Garching Germany
| | - Jessica Sobotta
- Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstraße 4, D-85747 Garching Germany
| | - Wolfgang Eisenreich
- Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstraße 4, D-85747 Garching Germany
| | | | - Claudia Huber
- Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstraße 4, D-85747 Garching Germany
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15
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Ge D, Xue Y, Ma Y. Two unexpected promiscuous activities of the iron-sulfur protein IspH in production of isoprene and isoamylene. Microb Cell Fact 2016; 15:79. [PMID: 27169371 PMCID: PMC4864966 DOI: 10.1186/s12934-016-0476-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/27/2016] [Indexed: 12/02/2022] Open
Abstract
Background Bacillus species, possessing the methylerythritol phosphate (MEP) pathway for the synthesis of isoprenoid feedstock, are the highest producers of isoprene among bacteria; however, the enzyme responsible for isoprene synthesis has not been identified. The iron–sulfur protein IspH is the final enzyme of the MEP pathway and catalyses the reductive dehydration of (E)-4-hydroxy-3-methyl-2-butenyl diphosphate (HMBPP) to form isopentenyl diphosphate and dimethylallyl diphosphate (DMAPP). In this study, we demonstrated two unexpected promiscuous activities of IspH from alkaliphilic Bacillus sp. N16-5, which can produce high levels of isoprene. Results Bacillus sp. N16-5 IspH could catalyse the formation of isoprene from HMBPP and the conversion of DMAPP into a mixture of 2-methyl-2-butene and 3-methyl-1-butene. Both reactions require an electron transfer system, such as that used for HMBPP dehydration. Isoprene and isoamylene synthesis in Bacillus sp. N16-5 was investigated and the reaction system was reconstituted in vitro, including IspH, ferredoxin and ferredoxin-NADP+-reductase proteins and NADPH. The roles of specific IspH protein residues were also investigated by site-directed mutagenesis experiments; two variants (H131N and E133Q) were found to have lost the HMBPP reductase activity but could still catalyse the formation of isoprene. Overexpression of IspH H131N in Bacillus sp. N16-5 resulted in a twofold enhancement of isoprene production, and the yield of isoprene from the strain expressing E133Q was increased 300 % compared with the wild-type strain. Conclusions IspH from Bacillus sp. N16-5 is a promiscuous enzyme that can catalyse formation of isoprene and isoamylene. This enzyme, especially the H131N and E133Q variants, could be used for the production of isoprene from HMBPP. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0476-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Deyong Ge
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.,College of Medicine, Anhui University of Science and Technology, Huainan, People's Republic of China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
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16
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Faus I, Reinhard A, Rackwitz S, Wolny JA, Schlage K, Wille HC, Chumakov A, Krasutsky S, Chaignon P, Poulter CD, Seemann M, Schünemann V. Isoprenoidbiosynthese in pathogenen Bakterien: Nukleare inelastische Streuung ermöglicht Einblicke in den ungewöhnlichen [4Fe-4S]-Cluster vom E.- coli-Protein LytB/IspH. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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Abdel-Azeim S, Jedidi A, Eppinger J, Cavallo L. Mechanistic insights into the reductive dehydroxylation pathway for the biosynthesis of isoprenoids promoted by the IspH enzyme. Chem Sci 2015; 6:5643-5651. [PMID: 28757951 PMCID: PMC5511988 DOI: 10.1039/c5sc01693b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/22/2015] [Indexed: 11/21/2022] Open
Abstract
Here, we report an integrated quantum mechanics/molecular mechanics (QM/MM) study of the bio-organometallic reaction pathway of the 2H+/2e- reduction of (E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate (HMBPP) into the so called universal terpenoid precursors isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), promoted by the IspH enzyme. Our results support the viability of the bio-organometallic pathway through rotation of the OH group of HMBPP away from the [Fe4S4] cluster at the core of the catalytic site, to become engaged in a H-bond with Glu126. This rotation is synchronous with π-coordination of the C2[double bond, length as m-dash]C3 double bond of HMBPP to the apical Fe atom of the [Fe4S4] cluster. Dehydroxylation of HMBPP is triggered by a proton transfer from Glu126 to the OH group of HMBPP. The reaction pathway is completed by competitive proton transfer from the terminal phosphate group to the C2 or C4 atom of HMBPP.
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Affiliation(s)
- Safwat Abdel-Azeim
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
| | - Abdesslem Jedidi
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
| | - Jorg Eppinger
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
| | - Luigi Cavallo
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
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18
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Brown AC, Kokoczka R, Parish T. LytB1 and LytB2 of Mycobacterium tuberculosis Are Not Genetically Redundant. PLoS One 2015; 10:e0135638. [PMID: 26309039 PMCID: PMC4550268 DOI: 10.1371/journal.pone.0135638] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 07/23/2015] [Indexed: 11/26/2022] Open
Abstract
Mycobacterium tuberculosis synthesises isoprenoid precursors via the MEP/DOXP pathway and at least five enzymes in the pathway (Dxs1, Dxr/IspC, IspD, IspF, and GcpE/IspG) are required for growth in vitro. We investigated the role of LytB (IspH) in M. tuberculosis; M. tuberculosis is unusual in that it has two homologs–LytB1 and LytB2. We were unable to delete the lytB2 gene unless we provided an additional copy elsewhere, demonstrating that this is the essential homolog. We expressed lytB1 from the lytB2 promoter and confirmed that this could not complement for loss of function of lytB2, despite LytB1 possessing all the previously described conserved critical residues. Interestingly the sole LytB homolog of Mycobacterium smegmatis was able to compensate for loss of LytB2 in M. tuberculosis. We tested translational fusions of LytB1 and LytB2 for functionality in M. tuberculosis, but only a fusion with 90% N-terminal LytB2 and 10% C-terminal LytB1 was functional. In order to identify the key difference between the two proteins, site directed mutagenesis was used to change LytB2 residues into their counterparts in LytB1. None of these amino acid substitutions was essential for function and all lytB2 mutant alleles were functional. In contrast, mutation of the key residues for [Fe4S4] cluster formation, as well as a catalytic residue in LytB1 did not result in functional complementation. Thus, although LytB1 and LytB2 are not genetically redundant, this is not dependent on small amino acid changes, but is likely to be a result of major overall structural differences.
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Affiliation(s)
- Amanda Claire Brown
- Queen Mary University of London, London, E1 2AD, United Kingdom
- Barts & the London School of Medicine and Dentistry, London, E1 2AD, United Kingdom
| | - Rachel Kokoczka
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, 98102, United States of America
| | - Tanya Parish
- Queen Mary University of London, London, E1 2AD, United Kingdom
- Barts & the London School of Medicine and Dentistry, London, E1 2AD, United Kingdom
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, 98102, United States of America
- * E-mail:
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19
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Faus I, Reinhard A, Rackwitz S, Wolny JA, Schlage K, Wille HC, Chumakov A, Krasutsky S, Chaignon P, Poulter CD, Seemann M, Schünemann V. Isoprenoid Biosynthesis in Pathogenic Bacteria: Nuclear Resonance Vibrational Spectroscopy Provides Insight into the Unusual [4Fe-4S] Cluster of the E. coli LytB/IspH Protein. Angew Chem Int Ed Engl 2015; 54:12584-7. [PMID: 26118554 DOI: 10.1002/anie.201502494] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Indexed: 11/10/2022]
Abstract
The LytB/IspH protein catalyzes the last step of the methylerythritol phosphate (MEP) pathway which is used for the biosynthesis of essential terpenoids in most pathogenic bacteria. Therefore, the MEP pathway is a target for the development of new antimicrobial agents as it is essential for microorganisms, yet absent in humans. Substrate-free LytB has a special [4Fe-4S](2+) cluster with a yet unsolved structure. This motivated us to use synchrotron-based nuclear resonance vibrational spectroscopy (NRVS) in combination with quantum chemical-molecular mechanical (QM/MM) calculations to gain more insight into the structure of substrate-free LytB. The apical iron atom of the [4Fe-4S](2+) is clearly linked to three water molecules. We additionally present NRVS data of LytB bound to its natural substrate, (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) and to the inhibitors (E)-4-amino-3-methylbut-2-en-1-yl diphosphate and (E)-4-mercapto-3-methylbut-2-en-1-yl diphosphate.
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Affiliation(s)
- Isabelle Faus
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Annegret Reinhard
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Sergej Rackwitz
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Juliusz A Wolny
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Kai Schlage
- P01, Petra III, DESY, Notkestrasse 85, D-22607 Hamburg (Germany)
| | | | - Aleksandr Chumakov
- ESRF - The European Synchrotron, CS40220, 38043 Grenoble Cedex 9 (France)
| | - Sergiy Krasutsky
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT 84112 (USA)
| | - Philippe Chaignon
- Université de Strasbourg, UMR 7177 CNRS, Institut Le Bel, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg Cedex (France)
| | - C Dale Poulter
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT 84112 (USA)
| | - Myriam Seemann
- Université de Strasbourg, UMR 7177 CNRS, Institut Le Bel, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg Cedex (France).
| | - Volker Schünemann
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany).
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20
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Albertini M, Berto P, Vallese F, Di Valentin M, Costantini P, Carbonera D. Probing the Solvent Accessibility of the [4Fe-4S] Cluster of the Hydrogenase Maturation Protein HydF from Thermotoga neapolitana by HYSCORE and 3p-ESEEM. J Phys Chem B 2015; 119:13680-9. [PMID: 25978307 DOI: 10.1021/acs.jpcb.5b03110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The catalytic site of [FeFe]-hydrogenase, the "H-cluster", composed of a [4Fe-4S] unit connected by a cysteinyl residue to a [2Fe] center coordinated by three CO, two CN(-), and a bridging dithiolate, is assembled in a complex maturation pathway, at present not fully characterized, involving three conserved proteins, HydG, HydE, and HydF. HydF is a complex enzyme, which is thought to act as a scaffold and carrier for the [2Fe] subunit of the H-cluster. This maturase protein contains itself a [4Fe-4S] cluster binding site, with three conserved cysteine residues and a noncysteinyl fourth ligand. In this work, we have exploited 3p-ESEEM and HYSCORE spectroscopies to get insight into the structure and the chemical environment of the [4Fe-4S] cluster of HydF from the hyperthermophilic organism Thermotoga neapolitana. The nature of the fourth ligand and the solvent accessibility of the active site comprising the [4Fe-4S] cluster are discussed on the basis of the spectroscopic results obtained upon H/D exchange. We propose that the noncysteinyl ligated Fe atom of the [4Fe-4S] cluster is the site where the [2Fe] subcluster precursor is anchored and finally processed to be delivered to the hydrogenase (HydA).
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Affiliation(s)
- Marco Albertini
- Department of Chemical Sciences, University of Padova , Via F. Marzolo 1, 35131 Padova, Italy
| | - Paola Berto
- Department of Biomedical Sciences, University of Padova , Viale G. Colombo 3, 35131 Padova, Italy
| | - Francesca Vallese
- Department of Biomedical Sciences, University of Padova , Viale G. Colombo 3, 35131 Padova, Italy
| | - Marilena Di Valentin
- Department of Chemical Sciences, University of Padova , Via F. Marzolo 1, 35131 Padova, Italy
| | - Paola Costantini
- Department of Biology, University of Padova , Viale G. Colombo 3, 35131 Padova, Italy
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova , Via F. Marzolo 1, 35131 Padova, Italy
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21
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Quitterer F, Frank A, Wang K, Rao G, O'Dowd B, Li J, Guerra F, Abdel-Azeim S, Bacher A, Eppinger J, Oldfield E, Groll M. Atomic-Resolution Structures of Discrete Stages on the Reaction Coordinate of the [Fe4S4] Enzyme IspG (GcpE). J Mol Biol 2015; 427:2220-8. [PMID: 25868383 DOI: 10.1016/j.jmb.2015.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/30/2015] [Accepted: 04/02/2015] [Indexed: 11/16/2022]
Abstract
IspG is the penultimate enzyme in non-mevalonate biosynthesis of the universal terpene building blocks isopentenyl diphosphate and dimethylallyl diphosphate. Its mechanism of action has been the subject of numerous studies but remained unresolved due to difficulties in identifying distinct reaction intermediates. Using a moderate reducing agent and an epoxide substrate analogue, we were now able to trap and crystallographically characterize various stages in the IspG-catalyzed conversion of 2-C-methyl-D-erythritol-2,4-cyclo-diphosphate into (E)-1-hydroxy-2-methylbut-2-enyl-4-diphosphate. In addition, the enzyme's structure was determined in complex with several inhibitors. These results, combined with recent electron paramagnetic resonance data, allowed us to deduce a detailed and complete IspG catalytic mechanism, which describes all stages from initial ring opening to formation of (E)-1-hydroxy-2-methylbut-2-enyl-4-diphosphate via discrete radical and carbanion intermediates. The data presented in this article provide a guide for the design of selective drugs against many prokaryotic and eukaryotic pathogens to which the non-mevalonate pathway is essential for survival and virulence.
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Affiliation(s)
- Felix Quitterer
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching D-85747, Germany
| | - Annika Frank
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching D-85747, Germany
| | - Ke Wang
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Guodong Rao
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Bing O'Dowd
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Jikun Li
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Francisco Guerra
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Safwat Abdel-Azeim
- Division of Physical Sciences and Engineering, KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
| | - Adelbert Bacher
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching D-85747, Germany
| | - Jörg Eppinger
- Division of Physical Sciences and Engineering, KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
| | - Eric Oldfield
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Michael Groll
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching D-85747, Germany
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22
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N-Terminal Region of GbIspH1, Ginkgo biloba IspH Type 1, May Be Involved in the pH-Dependent Regulation of Enzyme Activity. Bioinorg Chem Appl 2015; 2015:241479. [PMID: 25892986 PMCID: PMC4393896 DOI: 10.1155/2015/241479] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 02/28/2015] [Indexed: 11/18/2022] Open
Abstract
GbIspH1, IspH type 1 in Ginkgo biloba chloroplast, is the Fe/S enzyme catalyzing the reductive dehydroxylation of HMBPP to isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) at the final step of methylerythritol phosphate pathway in chloroplast. Compared to the bacterial IspH, plant IspH, including GbIspH1, has an additional polypeptide chain at the N-terminus. Here, biochemical function of the N-terminal region of GbIspH1 was investigated with the N-terminal truncated GbIspH1 (GbIspH1-truncated). Both wild type GbIspH1 (GbIspH1-full) and GbIspH1-truncated were catalytically active and produced IPP and DMAPP in a ratio of 15 : 1. Kinetic parameters of KM (17.3 ± 1.9 and 14.9 ± 2.3 µM) and kcat (369 ± 10 and 347 ± 12 min−1) at pH 8.0 were obtained for GbIspH1-full and GbIspH1-truncated, respectively. Interestingly, GbIspH1-full and GbIspH1-truncated showed significantly different pH-dependent activities, and the maximum enzyme activities were obtained at pH 8.0 and 7.5, respectively. However, catalytic activation energies (Ea) of GbIspH1-full and GbIspH1-truncated were almost the same with 36.5 ± 1.6 and 35.0 ± 1.9 kJ/mol, respectively. It was suggested that the N-terminal region of GbIspH1 is involved in the pH-dependent regulation of enzyme activity during photosynthesis.
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23
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Cutsail GE, Telser J, Hoffman BM. Advanced paramagnetic resonance spectroscopies of iron-sulfur proteins: Electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM). BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1370-94. [PMID: 25686535 DOI: 10.1016/j.bbamcr.2015.01.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/29/2015] [Accepted: 01/29/2015] [Indexed: 12/20/2022]
Abstract
The advanced electron paramagnetic resonance (EPR) techniques, electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM) spectroscopies, provide unique insights into the structure, coordination chemistry, and biochemical mechanism of nature's widely distributed iron-sulfur cluster (FeS) proteins. This review describes the ENDOR and ESEEM techniques and then provides a series of case studies on their application to a wide variety of FeS proteins including ferredoxins, nitrogenase, and radical SAM enzymes. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- George E Cutsail
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Joshua Telser
- Department of Biological, Chemical and Physical Sciences, Roosevelt University, Chicago, IL 60605, USA
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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24
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Hassan SS, Tiwari S, Guimarães LC, Jamal SB, Folador E, Sharma NB, de Castro Soares S, Almeida S, Ali A, Islam A, Póvoa FD, de Abreu VAC, Jain N, Bhattacharya A, Juneja L, Miyoshi A, Silva A, Barh D, Turjanski AG, Azevedo V, Ferreira RS. Proteome scale comparative modeling for conserved drug and vaccine targets identification in Corynebacterium pseudotuberculosis. BMC Genomics 2014; 15 Suppl 7:S3. [PMID: 25573232 PMCID: PMC4243142 DOI: 10.1186/1471-2164-15-s7-s3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Corynebacterium pseudotuberculosis (Cp) is a pathogenic bacterium that causes caseous lymphadenitis (CLA), ulcerative lymphangitis, mastitis, and edematous to a broad spectrum of hosts, including ruminants, thereby threatening economic and dairy industries worldwide. Currently there is no effective drug or vaccine available against Cp. To identify new targets, we adopted a novel integrative strategy, which began with the prediction of the modelome (tridimensional protein structures for the proteome of an organism, generated through comparative modeling) for 15 previously sequenced C. pseudotuberculosis strains. This pan-modelomics approach identified a set of 331 conserved proteins having 95-100% intra-species sequence similarity. Next, we combined subtractive proteomics and modelomics to reveal a set of 10 Cp proteins, which may be essential for the bacteria. Of these, 4 proteins (tcsR, mtrA, nrdI, and ispH) were essential and non-host homologs (considering man, horse, cow and sheep as hosts) and satisfied all criteria of being putative targets. Additionally, we subjected these 4 proteins to virtual screening of a drug-like compound library. In all cases, molecules predicted to form favorable interactions and which showed high complementarity to the target were found among the top ranking compounds. The remaining 6 essential proteins (adk, gapA, glyA, fumC, gnd, and aspA) have homologs in the host proteomes. Their active site cavities were compared to the respective cavities in host proteins. We propose that some of these proteins can be selectively targeted using structure-based drug design approaches (SBDD). Our results facilitate the selection of C. pseudotuberculosis putative proteins for developing broad-spectrum novel drugs and vaccines. A few of the targets identified here have been validated in other microorganisms, suggesting that our modelome strategy is effective and can also be applicable to other pathogens.
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25
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Masini T, Hirsch AKH. Development of Inhibitors of the 2C-Methyl-d-erythritol 4-Phosphate (MEP) Pathway Enzymes as Potential Anti-Infective Agents. J Med Chem 2014; 57:9740-63. [DOI: 10.1021/jm5010978] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Tiziana Masini
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh
7, NL-9747
AG Groningen, The Netherlands
| | - Anna K. H. Hirsch
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh
7, NL-9747
AG Groningen, The Netherlands
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26
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Hsieh WY, Sung TY, Wang HT, Hsieh MH. Functional evidence for the critical amino-terminal conserved domain and key amino acids of Arabidopsis 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE. PLANT PHYSIOLOGY 2014; 166:57-69. [PMID: 25037211 PMCID: PMC4149731 DOI: 10.1104/pp.114.243642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The plant 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE (HDR) catalyzes the last step of the methylerythritol phosphate pathway to synthesize isopentenyl diphosphate and its allyl isomer dimethylallyl diphosphate, which are common precursors for the synthesis of plastid isoprenoids. The Arabidopsis (Arabidopsis thaliana) genomic HDR transgene-induced gene-silencing lines are albino, variegated, or pale green, confirming that HDR is essential for plants. We used Escherichia coli isoprenoid synthesis H (Protein Data Bank code 3F7T) as a template for homology modeling to identify key amino acids of Arabidopsis HDR. The predicted model reveals that cysteine (Cys)-122, Cys-213, and Cys-350 are involved in iron-sulfur cluster formation and that histidine (His)-152, His-241, glutamate (Glu)-242, Glu-243, threonine (Thr)-244, Thr-312, serine-379, and asparagine-381 are related to substrate binding or catalysis. Glu-242 and Thr-244 are conserved only in cyanobacteria, green algae, and land plants, whereas the other key amino acids are absolutely conserved from bacteria to plants. We used site-directed mutagenesis and complementation assay to confirm that these amino acids, except His-152 and His-241, were critical for Arabidopsis HDR function. Furthermore, the Arabidopsis HDR contains an extra amino-terminal domain following the transit peptide that is highly conserved from cyanobacteria, and green algae to land plants but not existing in the other bacteria. We demonstrated that the amino-terminal conserved domain was essential for Arabidopsis and cyanobacterial HDR function. Further analysis of conserved amino acids in the amino-terminal conserved domain revealed that the tyrosine-72 residue was critical for Arabidopsis HDR. These results suggest that the structure and reaction mechanism of HDR evolution have become specific for oxygen-evolving photosynthesis organisms and that HDR probably evolved independently in cyanobacteria versus other prokaryotes.
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Affiliation(s)
- Wei-Yu Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Tzu-Ying Sung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hsin-Tzu Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ming-Hsiun Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
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Span I, Wang K, Eisenreich W, Bacher A, Zhang Y, Oldfield E, Groll M. Insights into the binding of pyridines to the iron-sulfur enzyme IspH. J Am Chem Soc 2014; 136:7926-32. [PMID: 24813236 PMCID: PMC4063180 DOI: 10.1021/ja501127j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Indexed: 11/29/2022]
Abstract
(E)-1-Hydroxy-2-methylbut-2-enyl 4-diphosphate reductase (IspH) is a [Fe4S4] cluster-containing enzyme involved in isoprenoid biosynthesis in many bacteria as well as in malaria parasites and is an important drug target. Several inhibitors including amino and thiol substrate analogues, as well as acetylene and pyridine diphosphates, have been reported. Here, we investigate the mode of binding of four pyridine diphosphates to Escherichia coli IspH by using X-ray crystallography. In three cases, one of the iron atoms in the cluster is absent, but in the structure with (pyridin-3-yl)methyl diphosphate, the most potent pyridine-analogue inhibitor reported previously, the fourth iron of the [Fe4S4] cluster is present and interacts with the pyridine ring of the ligand. Based on the results of quantum chemical calculations together with the crystallographic results we propose a side-on η(2) coordination of the nitrogen and the carbon in the 2-position of the pyridine ring to the unique fourth iron in the cluster, which is in the reduced state. The X-ray structure enables excellent predictions using density functional theory of the (14)N hyperfine coupling and quadrupole coupling constants reported previously using HYSCORE spectroscopy, as well as providing a further example of the ability of such [Fe4S4]-containing proteins to form organometallic complexes.
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Affiliation(s)
- Ingrid Span
- Center
for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Ke Wang
- Department
of Chemistry, 600 South
Mathews Avenue, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wolfgang Eisenreich
- Center
for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Adelbert Bacher
- Center
for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Yong Zhang
- Department
of Chemistry, Chemical Biology, and Biomedical Engineering, Stevens Institute of Technology, Castle Point on Hudson, Hoboken, New Jersey 07030, United States
| | - Eric Oldfield
- Department
of Chemistry, 600 South
Mathews Avenue, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Michael Groll
- Center
for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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Wang W, Oldfield E. Biometallorganische Chemie mit IspG und IspH: Struktur, Funktion und Hemmung der an der Isoprenoid-Biosynthese beteiligten [Fe 4S 4]-Proteine. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201306712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Wang W, Oldfield E. Bioorganometallic chemistry with IspG and IspH: structure, function, and inhibition of the [Fe(4)S(4)] proteins involved in isoprenoid biosynthesis. Angew Chem Int Ed Engl 2014; 53:4294-310. [PMID: 24481599 DOI: 10.1002/anie.201306712] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Indexed: 11/12/2022]
Abstract
Enzymes of the methylerythritol phosphate pathway of isoprenoid biosynthesis are attractive anti-infective drug targets. The last two enzymes of this pathway, IspG and IspH, are [Fe4 S4 ] proteins that are not produced by humans and catalyze 2 H(+) / 2 e(-) reductions with novel mechanisms. In this Review, we summarize recent advances in structural, mechanistic, and inhibitory studies of these two enzymes. In particular, mechanistic proposals involving bioorganometallic intermediates are presented, and compared with other mechanistic possibilities. In addition, inhibitors based on substrate analogues as well as developed by rational design and compound-library screening, are discussed. The results presented support bioorganometallic catalytic mechanisms for IspG and IspH, and open up new routes to anti-infective drug design targeting [Fe4 S4 ] clusters in proteins.
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Affiliation(s)
- Weixue Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (USA)
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Affiliation(s)
| | - Salim Al-Babili
- BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Eleanore T. Wurtzel
- The Graduate School and University Center, The City University of New York, New York, New York, USA
- Department of Biological Sciences, Lehman College, The City University of New York, Bronx, New York, USA
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Abstract
Isoprenoids are a large family of compounds synthesized by all free-living organisms. In most bacteria, the common precursors of all isoprenoids are produced by the MEP (methylerythritol 4-phosphate) pathway. The MEP pathway is absent from archaea, fungi and animals (including humans), which synthesize their isoprenoid precursors using the completely unrelated MVA (mevalonate) pathway. Because the MEP pathway is essential in most bacterial pathogens (as well as in the malaria parasites), it has been proposed as a promising new target for the development of novel anti-infective agents. However, bacteria show a remarkable plasticity for isoprenoid biosynthesis that should be taken into account when targeting this metabolic pathway for the development of new antibiotics. For example, a few bacteria use the MVA pathway instead of the MEP pathway, whereas others possess the two full pathways, and some parasitic strains lack both the MVA and the MEP pathways (probably because they obtain their isoprenoids from host cells). Moreover, alternative enzymes and metabolic intermediates to those of the canonical MVA or MEP pathways exist in some organisms. Recent work has also shown that resistance to a block of the first steps of the MEP pathway can easily be developed because several enzymes unrelated to isoprenoid biosynthesis can produce pathway intermediates upon spontaneous mutations. In the present review, we discuss the major advances in our knowledge of the biochemical toolbox exploited by bacteria to synthesize the universal precursors for their essential isoprenoids.
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Span I, Wang K, Wang W, Jauch J, Eisenreich W, Bacher A, Oldfield E, Groll M. Structures of fluoro, amino, and thiol inhibitors bound to the [Fe4S4] protein IspH. Angew Chem Int Ed Engl 2013; 52:2118-21. [PMID: 23307751 PMCID: PMC3734547 DOI: 10.1002/anie.201208469] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Ingrid Span
- Center for Integrated Protein Science Munich, Chemie Department, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany.
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Span I, Wang K, Wang W, Jauch J, Eisenreich W, Bacher A, Oldfield E, Groll M. Fluor-, Amino- und Thiolinhibitoren im Komplex mit dem [Fe4
S4
]-Protein IspH. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208469] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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