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Ghebreamlak S, Stoian SA, Lees NS, Cronin B, Smith F, Ross MO, Telser J, Hoffman BM, Duin EC. The Active-Site [4Fe-4S] Cluster in the Isoprenoid Biosynthesis Enzyme IspH Adopts Unexpected Redox States during Ligand Binding and Catalysis. J Am Chem Soc 2024; 146:3926-3942. [PMID: 38291562 DOI: 10.1021/jacs.3c11674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
(E)-4-Hydroxy-3-methylbut-2-enyl diphosphate reductase, or IspH (formerly known as LytB), catalyzes the terminal step of the bacterial methylerythritol phosphate (MEP) pathway for isoprene synthesis. This step converts (E)-4-hydroxy-3-methylbut-2-enyl diphosphate (HMBPP) into one of two possible isomeric products, either isopentenyl diphosphate (IPP) or dimethylallyl diphosphate (DMAPP). This reaction involves the removal of the C4 hydroxyl group of HMBPP and addition of two electrons. IspH contains a [4Fe-4S] cluster in its active site, and multiple cluster-based paramagnetic species of uncertain redox and ligation states can be detected after incubation with reductant, addition of a ligand, or during catalysis. To characterize the clusters in these species, 57Fe-labeled samples of IspH were prepared and studied by electron paramagnetic resonance (EPR), 57Fe electron-nuclear double resonance (ENDOR), and Mössbauer spectroscopies. Notably, this ENDOR study provides a rarely reported, complete determination of the 57Fe hyperfine tensors for all four Fe ions in a [4Fe-4S] cluster. The resting state of the enzyme (Ox) has a diamagnetic [4Fe-4S]2+ cluster. Reduction generates [4Fe-4S]+ (Red) with both S = 1/2 and S = 3/2 spin ground states. When the reduced enzyme is incubated with substrate, a transient paramagnetic reaction intermediate is detected (Int) which is thought to contain a cluster-bound substrate-derived species. The EPR properties of Int are indicative of a 3+ iron-sulfur cluster oxidation state, and the Mössbauer spectra presented here confirm this. Incubation of reduced enzyme with the product IPP induced yet another paramagnetic [4Fe-4S]+ species (Red+P) with S = 1/2. However, the g-tensor of this state is commonly associated with a 3+ oxidation state, while Mössbauer parameters show features typical for 2+ clusters. Implications of these complicated results are discussed.
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Affiliation(s)
- Selamawit Ghebreamlak
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - Sebastian A Stoian
- Department of Chemistry, University of Idaho, 875 Perimeter Drive, MS 2343 Moscow, Idaho 83844, United States
| | - Nicholas S Lees
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Bryan Cronin
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - Forrest Smith
- Department of Drug Discovery & Development, Auburn University, 4306 Walker Building, Auburn, Alabama 36849, United States
| | - Matthew O Ross
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Joshua Telser
- Department of Biological, Chemical and Physical Sciences, Roosevelt University, 430 S. Michigan Avenue, Chicago, Illinois 60605, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Evert C Duin
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
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Brown AC, Suess DLM. Valence Localization in Alkyne and Alkene Adducts of Synthetic [Fe 4S 4] + Clusters. Inorg Chem 2023; 62:1911-1918. [PMID: 35704768 PMCID: PMC9751231 DOI: 10.1021/acs.inorgchem.2c01353] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Reported herein are alkyne and alkene adducts of synthetic [Fe4S4]+ clusters that model intermediates and inhibitor-bound states in enzymes involved in isoprenoid biosynthesis. Treatment of the N-heterocyclic carbene-ligated cluster [(IMes)3Fe4S4(OEt2)][BArF4] (IMes = 1,3-dimesitylimidazol-2-ylidene; [BArF4]- = tetrakis(3,5-bis(trifluoromethyl)phenyl)borate) with phenylacetylene (PhCCH) or cis-cyclooctene (COE) results in displacement of the Et2O ligand to yield the corresponding π complexes, [(IMes)3Fe4S4(PhCCH)][BArF4] and [(IMes)3Fe4S4(COE)][BArF4]. EPR spectroscopic analysis demonstrates that both clusters are doublets with giso > 2 and thus are spectroscopically faithful models of the analogous species characterized in the isoprenoid biosynthetic enzymes IspG and IspH. Structural and Mössbauer spectroscopic analysis reveals that both complexes are best described as [Fe4S4]+ clusters in which the unique Fe site engages in modest back-bonding to the π-acidic ligand. Paramagnetic NMR studies show that, even at room temperature, the alkyne/alkene-bound Fe centers harbor minority spin and therefore adopt an Fe2+ valence. We propose that such valence localization could likewise occur in Fe-S enzymes that interact with π-acidic molecules.
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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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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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Nie QY, Ji ZY, Hu Y, Tang GL. Characterization of Highly Reductive Modification of Tetracycline D-Ring Reveals Enzymatic Conversion of Enone to Alkane. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Qiu-Yue Nie
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Zhen-Yu Ji
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Yu Hu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Gong-Li Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
- School of Chemistry and Materials Science Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, People’s Republic of China
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Hirscher NA, Arnett CH, Oyala PH, Agapie T. Characterization of Cr-Hydrocarbyl Species via Pulse EPR in the Study of Ethylene Tetramerization Catalysis. Organometallics 2020. [DOI: 10.1021/acs.organomet.0c00521] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nathanael A. Hirscher
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Charles H. Arnett
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Paul H. Oyala
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Theodor Agapie
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
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7
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Chaignon P, Petit BE, Vincent B, Allouche L, Seemann M. Methylerythritol Phosphate Pathway: Enzymatic Evidence for a Rotation in the LytB/IspH-Catalyzed Reaction. Chemistry 2020; 26:1032-1036. [PMID: 31756006 DOI: 10.1002/chem.201904676] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Indexed: 11/10/2022]
Abstract
IspH/LytB, an oxygen-sensitive [4Fe-4S] enzyme, catalyzes the last step of the methylerythritol phosphate (MEP) pathway, a target for the development of new antimicrobial agents. This metalloenzyme converts (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) into the two isoprenoid precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Here, the synthesis of (S)-[4-2 H1 ]HMBPP and (R)-[4-2 H1 ]HMBPP is reported together with a detailed NMR analysis of the products formed after their respective incubation with E. coli IspH/LytB in the presence of the biological reduction system used by E. coli to reduce the [4Fe-4S] center. (S)-[4-2 H1 ]HMBPP was converted into [4-2 H1 ]DMAPP and (E)-[4-2 H1 ]IPP, whereas (R)-[4-2 H1 ]HMBPP yielded [4-2 H1 ]DMAPP and (Z)-[4-2 H1 ]IPP, hence providing the direct enzymatic evidence that the mechanism catalyzed by IspH/LytB involves a rotation of the CH2 OH group of the substrate to display it away from the [4Fe-4S].
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Affiliation(s)
- Philippe Chaignon
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie UMR 7177, Université de Strasbourg, CNRS, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - Benoît Eric Petit
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie UMR 7177, Université de Strasbourg, CNRS, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - Bruno Vincent
- Service de R.M.N., Fédération de Chimie Le Bel FR2010, Université de Strasbourg, CNRS, 1, rue Blaise Pascal, 67008, Strasbourg, France
| | - Lionel Allouche
- Service de R.M.N., Fédération de Chimie Le Bel FR2010, Université de Strasbourg, CNRS, 1, rue Blaise Pascal, 67008, Strasbourg, France
| | - Myriam Seemann
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie UMR 7177, Université de Strasbourg, CNRS, 4, rue Blaise Pascal, 67070, Strasbourg, France
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8
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Colaneri MJ, Vitali J. Probing Axial Water Bound to Copper in Tutton Salt Using Single Crystal 17O-ESEEM Spectroscopy. J Phys Chem A 2018; 122:6214-6224. [PMID: 29989412 DOI: 10.1021/acs.jpca.8b04075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Electron spin-echo envelope modulation (ESEEM) signals attributed to axial water bound to Cu2+ have been detected and analyzed in Cu(II)-doped 17O-water-enriched potassium zinc sulfate hexahydrate (Tutton salt) crystals. The magnetic field orientation dependences of low frequency modulations were measured to fit hyperfine and quadrupole coupling tensors of a 17O ( I = 5/2) nucleus. The hyperfine tensor ( A xx, A yy, A zz: 0.13, 0.23, -3.81 MHz) exhibits almost axial symmetry with the largest value directed normal to the metal equatorial plane in the host structure. Comparisons with quantum chemical calculations position this nucleus about 2.3 Å from the copper. The isotropic coupling (-1.15 MHz) is small and reflects the weak axial water interaction with a dx2-y2 unshared orbital of copper. The 17O-water quadrupole interaction parameters ( e2 qQ/ h = 6.4 MHz and η = 0.93) are close to the average of those found in a variety of solid hydrates. In addition, the coupling tensor directions correlate very closely with the O8 water geometry, with the maximum quadrupole direction 3° from the water plane normal, and its minimum coupling about 2° from the H-H direction. In almost all previous magnetic resonance 17O-water studies, the quadrupole tensor orientation was based on theoretical considerations. This work represents one of the few experimental confirmations of its principal axis frame. When Cu2+ dopes into the Tutton salt, a Jahn-Teller distortion interchanges the relative long and intermediate metal O7 and O8 bond lengths of the zinc host. Therefore, only those unit cells containing the impurity conform to the pure copper Tutton structure. This study provides further support for this model. Moreover, coupling interactions from distant H217O such as in the present case have important implications in studies of copper enzymes and proteins where substrates have been proposed to displace weakly bound water in the active site.
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Affiliation(s)
- Michael J Colaneri
- Department of Chemistry and Physics , State University of New York at Old Westbury , Old Westbury , New York 11568 , United States
| | - Jacqueline Vitali
- Department of Physics and Department of Biological, Geological and Environmental Sciences , Cleveland State University , Cleveland , Ohio 44115 , United States
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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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Lin CI, McCarty RM, Liu HW. The Enzymology of Organic Transformations: A Survey of Name Reactions in Biological Systems. Angew Chem Int Ed Engl 2017; 56:3446-3489. [PMID: 27505692 PMCID: PMC5477795 DOI: 10.1002/anie.201603291] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 01/05/2023]
Abstract
Chemical reactions that are named in honor of their true, or at least perceived, discoverers are known as "name reactions". This Review is a collection of biological representatives of named chemical reactions. Emphasis is placed on reaction types and catalytic mechanisms that showcase both the chemical diversity in natural product biosynthesis as well as the parallels with synthetic organic chemistry. An attempt has been made, whenever possible, to describe the enzymatic mechanisms of catalysis within the context of their synthetic counterparts and to discuss the mechanistic hypotheses for those reactions that are currently active areas of investigation. This Review has been categorized by reaction type, for example condensation, nucleophilic addition, reduction and oxidation, substitution, carboxylation, radical-mediated, and rearrangements, which are subdivided by name reactions.
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Affiliation(s)
- Chia-I Lin
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, 78731, USA
| | - Reid M McCarty
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, 78731, USA
| | - Hung-Wen Liu
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, 78731, USA
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Lin C, McCarty RM, Liu H. Die Enzymologie organischer Umwandlungen: Namensreaktionen in biologischen Systemen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201603291] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Chia‐I. Lin
- Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, and Department of Chemistry University of Texas at Austin Austin TX 78731 USA
| | - Reid M. McCarty
- Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, and Department of Chemistry University of Texas at Austin Austin TX 78731 USA
| | - Hung‐wen Liu
- Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, and Department of Chemistry University of Texas at Austin Austin TX 78731 USA
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13
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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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14
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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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15
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Dong M, Horitani M, Dzikovski B, Pandelia ME, Krebs C, Freed JH, Hoffman BM, Lin H. Organometallic Complex Formed by an Unconventional Radical S-Adenosylmethionine Enzyme. J Am Chem Soc 2016; 138:9755-8. [PMID: 27465315 DOI: 10.1021/jacs.6b04155] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Pyrococcus horikoshii Dph2 (PhDph2) is an unusual radical S-adenosylmethionine (SAM) enzyme involved in the first step of diphthamide biosynthesis. It catalyzes the reaction by cleaving SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. To probe the reaction mechanism, we synthesized a SAM analogue (SAMCA), in which the ACP group of SAM is replaced with a 3-carboxyallyl group. SAMCA is cleaved by PhDph2, yielding a paramagnetic (S = 1/2) species, which is assigned to a complex formed between the reaction product, α-sulfinyl-3-butenoic acid, and the [4Fe-4S] cluster. Electron-nuclear double resonance (ENDOR) measurements with (13)C and (2)H isotopically labeled SAMCA support a π-complex between the C═C double bond of α-sulfinyl-3-butenoic acid and the unique iron of the [4Fe-4S] cluster. This is the first example of a radical SAM-related [4Fe-4S](+) cluster forming an organometallic complex with an alkene, shedding additional light on the mechanism of PhDph2 and expanding our current notions for the reactivity of [4Fe-4S] clusters in radical SAM enzymes.
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Affiliation(s)
- Min Dong
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Masaki Horitani
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University , Waltham, Massachusetts 02453, United States
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States.,Howard Hughes Medical Institute, Cornell University , Ithaca, New York 14853, United States
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16
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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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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 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 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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Blachly PG, Sandala GM, Giammona DA, Bashford D, McCammon JA, Noodleman L. Broken-Symmetry DFT Computations for the Reaction Pathway of IspH, an Iron-Sulfur Enzyme in Pathogenic Bacteria. Inorg Chem 2015; 54:6439-61. [PMID: 26098647 PMCID: PMC4568833 DOI: 10.1021/acs.inorgchem.5b00751] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The recently discovered methylerythritol phosphate (MEP) pathway provides new targets for the development of antibacterial and antimalarial drugs. In the final step of the MEP pathway, the [4Fe-4S] IspH protein catalyzes the 2e(-)/2H(+) reductive dehydroxylation of (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP) to afford the isoprenoid precursors isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). Recent experiments have attempted to elucidate the IspH catalytic mechanism to drive inhibitor development. Two competing mechanisms have recently emerged, differentiated by their proposed HMBPP binding modes upon 1e(-) reduction of the [4Fe-4S] cluster: (1) a Birch reduction mechanism, in which HMBPP remains bound to the [4Fe-4S] cluster through its terminal C4-OH group (ROH-bound) until the -OH is cleaved as water; and (2) an organometallic mechanism, in which the C4-OH group rotates away from the [4Fe-4S] cluster, allowing the HMBPP olefin group to form a metallacycle complex with the apical iron (η(2)-bound). We perform broken-symmetry density functional theory computations to assess the energies and reduction potentials associated with the ROH- and η(2)-bound states implicated by these competing mechanisms. Reduction potentials obtained for ROH-bound states are more negative (-1.4 to -1.0 V) than what is typically expected of [4Fe-4S] ferredoxin proteins. Instead, we find that η(2)-bound states are lower in energy than ROH-bound states when the [4Fe-4S] cluster is 1e(-) reduced. Furthermore, η(2)-bound states can already be generated in the oxidized state, yielding reduction potentials of ca. -700 mV when electron addition occurs after rotation of the HMBPP C4-OH group. We demonstrate that such η(2)-bound states are kinetically accessible both when the IspH [4Fe-4S] cluster is oxidized and 1e(-) reduced. The energetically preferred pathway gives 1e(-) reduction of the cluster after substrate conformational change, generating the 1e(-) reduced intermediate proposed in the organometallic mechanism.
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Affiliation(s)
| | - Gregory M Sandala
- ‡Department of Chemistry and Biochemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick E4L 1G8, Canada
| | - Debra Ann Giammona
- §Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Donald Bashford
- §Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | | | - Louis Noodleman
- #Department of Integrative Structural and Computational Biology, CB213, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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19
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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: 26] [Impact Index Per Article: 2.9] [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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20
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Hsieh WY, Hsieh MH. The amino-terminal conserved domain of 4-hydroxy-3-methylbut-2-enyl diphosphate reductase is critical for its function in oxygen-evolving photosynthetic organisms. PLANT SIGNALING & BEHAVIOR 2015; 10:e988072. [PMID: 25723575 PMCID: PMC4622703 DOI: 10.4161/15592324.2014.988072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 09/17/2014] [Accepted: 09/17/2014] [Indexed: 05/22/2023]
Abstract
4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR), also known as isoprenoid synthesis H (IspH) or lysis-tolerant B (LytB), catalyzes the last step of the methylerythritol phosphate pathway to synthesize isopentenyl diphosphate and dimethylallyl diphosphate. The structure and reaction mechanism of IspH have been actively investigated in Escherichia coli but little is known in plants. Compared with the bacterial IspH, cyanobacterial and plant HDRs all contain an extra N-terminal conserved domain (NCD) that is essential for their function. Tyr72 in the NCD and several plant-specific residues around the central active site are critical for Arabidopsis HDR function. These results suggest that the structure and reaction mechanism of HDR/IspH may be different between plants and bacteria. The E. coli IspH is an iron-sulfur protein that is sensitive to oxygen. It is possible that the cyanobacterial HDR may independently evolve from the common ancestor of prokaryotes to obtain the NCD, which may protect the enzyme from high concentration of oxygen during photosynthesis.
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Affiliation(s)
- Wei-Yu Hsieh
- Institute of Plant and Microbial Biology; Academia Sinica; Taipei, Taiwan
| | - Ming-Hsiun Hsieh
- Institute of Plant and Microbial Biology; Academia Sinica; Taipei, Taiwan
- Correspondence to: Ming-Hsiun Hsieh;
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21
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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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22
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Blachly PG, Sandala GM, Giammona D, Liu T, Bashford D, McCammon JA, Noodleman L. Use of Broken-Symmetry Density Functional Theory To Characterize the IspH Oxidized State: Implications for IspH Mechanism and Inhibition. J Chem Theory Comput 2014; 10:3871-3884. [PMID: 25221444 PMCID: PMC4159220 DOI: 10.1021/ct5005214] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Indexed: 12/31/2022]
Abstract
With current therapies becoming less efficacious due to increased drug resistance, new inhibitors of both bacterial and malarial targets are desperately needed. The recently discovered methylerythritol phosphate (MEP) pathway for isoprenoid synthesis provides novel targets for the development of such drugs. Particular attention has focused on the IspH protein, the final enzyme in the MEP pathway, which uses its [4Fe-4S] cluster to catalyze the formation of the isoprenoid precursors IPP and DMAPP from HMBPP. IspH catalysis is achieved via a 2e-/2H+ reductive dehydroxylation of HMBPP; the mechanism by which catalysis is achieved, however, is highly controversial. The work presented herein provides the first step in assessing different routes to catalysis by using computational methods. By performing broken-symmetry density functional theory (BS-DFT) calculations that employ both the conductor-like screening solvation model (DFT/COSMO) and a finite-difference Poisson-Boltzmann self-consistent reaction field methodology (DFT/SCRF), we evaluate geometries, energies, and Mössbauer signatures of the different protonation states that may exist in the oxidized state of the IspH catalytic cycle. From DFT/SCRF computations performed on the oxidized state, we find a state where the substrate, HMBPP, coordinates the apical iron in the [4Fe-4S] cluster as an alcohol group (ROH) to be one of two, isoenergetic, lowest-energy states. In this state, the HMBPP pyrophosphate moiety and an adjacent glutamate residue (E126) are both fully deprotonated, making the active site highly anionic. Our findings that this low-energy state also matches the experimental geometry of the active site and that its computed isomer shifts agree with experiment validate the use of the DFT/SCRF method to assess relative energies along the IspH reaction pathway. Additional studies of IspH catalytic intermediates are currently being pursued.
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Affiliation(s)
- Patrick G. Blachly
- Department
of Chemistry and Biochemistry, University
of California San Diego, 9500 Gilman Drive, Mail Code 0365, La Jolla, California 92093-0365, United States
| | - Gregory M. Sandala
- Department
of Chemistry and Biochemistry, Mount Allison
University, 63C York
Street, Sackville, New Brunswick E4L 1G8, Canada
| | - Debra
Ann Giammona
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, 262
Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Tiqing Liu
- Skaggs School of Pharmacy and Pharmaceutical
Sciences, Howard Hughes Medical
Institute, and Department of Pharmacology, University
of California San Diego, La Jolla, California 92093-0365, United States
| | - Donald Bashford
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, 262
Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - J. Andrew McCammon
- Department
of Chemistry and Biochemistry, University
of California San Diego, 9500 Gilman Drive, Mail Code 0365, La Jolla, California 92093-0365, United States
- Skaggs School of Pharmacy and Pharmaceutical
Sciences, Howard Hughes Medical
Institute, and Department of Pharmacology, University
of California San Diego, La Jolla, California 92093-0365, United States
| | - Louis Noodleman
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, TPC15, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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23
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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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24
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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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25
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Affiliation(s)
- Jiayun He
- Department of Chemistry and
State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Jesse Ling
- Department of Chemistry and
State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Pauline Chiu
- Department of Chemistry and
State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong
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26
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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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27
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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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28
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Guerra F, Wang K, Li J, Wang W, Liu YL, Amin S, Oldfield E. Inhibition of the 4Fe-4S Proteins IspG and IspH: an EPR, ENDOR and HYSCORE Investigation. Chem Sci 2014; 5:1642-1649. [PMID: 24999381 DOI: 10.1039/c3sc53301h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
IspG and IspH are proteins that are involved in isoprenoid biosynthesis in most bacteria as well as in malaria parasites and are important drug targets. They contain cubane-type 4Fe-4S clusters that are involved in unusual 2H+/2e- reductions. Here, we report the results of electron paramagnetic resonance spectroscopic investigations of the binding of amino- and thiolo-HMBPP (HMBPP=E-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate) IspH substrate-analog inhibitors to both proteins, as well as the binding of HMBPP and an acetylene diphosphate inhibitor, to IspG. The results show that amino-HMBPP binds to reduced IspH by Fe-C π-bonding with the olefinic carbons interacting with the unique 4th Fe in the 4Fe-4S cluster, quite different to the direct Fe-N ligation seen with the oxidized protein. No such π-complex is observed when amino-HMBPP binds to reduced IspG. No EPR signal is observed with IspH in the presence of dithionite and thiolo-HMBPP, suggesting that the 4Fe-4S cluster is not reduced, consistent with the presence of a 420 nm feature in the absorption spectrum (characteristic of an oxidized cluster). However, with IspG, the EPR spectrum in the presence of dithionite and thiolo-HMBPP is very similar to that seen with HMBPP. The binding of HMBPP to IspG was studied using hyperfine sublevel correlation spectroscopy with 17O and 13C labeled samples: the results rule out direct Fe-O bonding and indicate π-bonding. Finally, the binding to IspG of a potent acetylene diphosphate inhibitor was studied by using electron-nuclear double resonance spectroscopy with 13C labeled ligands: the large hyperfine couplings indicate strong Fe-C π-bonding with the acetylenic group. These results illustrate a remarkable diversity in binding behavior for HMBPP-analog inhibitors, opening up new routes to inhibitor design of interest in the context of anti-bacterial and anti-malarial drug discovery, as well as "cubane-type" metallo-biochemistry, in general.
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Affiliation(s)
- Francisco Guerra
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801
| | - Ke Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801
| | - Jikun Li
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801
| | - Weixue Wang
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801
| | - Yi-Liang Liu
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801
| | - Shivani Amin
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801
| | - Eric Oldfield
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801 ; Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801
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Zhao L, Chang WC, Xiao Y, Liu HW, Liu P. Methylerythritol phosphate pathway of isoprenoid biosynthesis. Annu Rev Biochem 2013; 82:497-530. [PMID: 23746261 DOI: 10.1146/annurev-biochem-052010-100934] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isoprenoids are a class of natural products with more than 55,000 members. All isoprenoids are constructed from two precursors, isopentenyl diphosphate and its isomer dimethylallyl diphosphate. Two of the most important discoveries in isoprenoid biosynthetic studies in recent years are the elucidation of a second isoprenoid biosynthetic pathway [the methylerythritol phosphate (MEP) pathway] and a modified mevalonic acid (MVA) pathway. In this review, we summarize mechanistic insights on the MEP pathway enzymes. Because many isoprenoids have important biological activities, the need to produce them in sufficient quantities for downstream research efforts or commercial application is apparent. Recent advances in both MVA and MEP pathway-based synthetic biology are also illustrated by reviewing the landmark work of artemisinic acid and taxadien-5α-ol production through microbial fermentations.
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Affiliation(s)
- Lishan Zhao
- Amyris, Inc., Emeryville, California 94608, USA.
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Ceunen S, Geuns JMC. Steviol glycosides: chemical diversity, metabolism, and function. JOURNAL OF NATURAL PRODUCTS 2013; 76:1201-28. [PMID: 23713723 DOI: 10.1021/np400203b] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Steviol glycosides are a group of highly sweet diterpene glycosides discovered in only a few plant species, most notably the Paraguayan shrub Stevia rebaudiana. During the past few decades, the nutritional and pharmacological benefits of these secondary metabolites have become increasingly apparent. While these properties are now widely recognized, many aspects related to their in vivo biochemistry and metabolism and their relationship to the overall plant physiology of S. rebaudiana are not yet understood. Furthermore, the large size of the steviol glycoside pool commonly found within S. rebaudiana leaves implies a significant metabolic investment and poses questions regarding the benefits S. rebaudiana might gain from their accumulation. The current review intends to thoroughly discuss the available knowledge on these issues.
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Affiliation(s)
- Stijn Ceunen
- Laboratory of Functional Biology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 31, BP 2436, B-3001 Heverlee, Belgium
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Li J, Wang K, Smirnova TI, Khade RL, Zhang Y, Oldfield E. Isoprenoid Biosynthesis: Ferraoxetane or Allyl Anion Mechanism for IspH Catalysis? Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302343] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Li J, Wang K, Smirnova TI, Khade RL, Zhang Y, Oldfield E. Isoprenoid biosynthesis: ferraoxetane or allyl anion mechanism for IspH catalysis? Angew Chem Int Ed Engl 2013; 52:6522-5. [PMID: 23649534 PMCID: PMC3821072 DOI: 10.1002/anie.201302343] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Jikun Li
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801 (USA)
| | - Ke Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801 (USA), Fax: (+1)217-244-0997
| | - Tatyana I. Smirnova
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695 (USA)
| | - Rahul L. Khade
- Department of Chemistry, Chemical Biology, and Biomedical Engineering, Stevens Institute of Technology, Castle Point on Hudson, Hoboken NJ 07030 (USA)
| | - Yong Zhang
- Department of Chemistry, Chemical Biology, and Biomedical Engineering, Stevens Institute of Technology, Castle Point on Hudson, Hoboken NJ 07030 (USA)
| | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801 (USA), Fax: (+1)217-244-0997
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33
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Emsley L. Advances in Magnetic Resonance: From Stem Cells to Catalytic Surfaces. J Am Chem Soc 2013; 135:8089-91. [DOI: 10.1021/ja404269a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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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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Janthawornpong K, Krasutsky S, Chaignon P, Rohmer M, Poulter CD, Seemann M. Inhibition of IspH, a [4Fe-4S]2+ enzyme involved in the biosynthesis of isoprenoids via the methylerythritol phosphate pathway. J Am Chem Soc 2013; 135:1816-22. [PMID: 23316732 DOI: 10.1021/ja309557s] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The MEP pathway, which is absent in animals but present in most pathogenic bacteria, in the parasite responsible for malaria and in plant plastids, is a target for the development of antimicrobial drugs. IspH, an oxygen-sensitive [4Fe-4S] enzyme, catalyzes the last step of this pathway and converts (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) into the two isoprenoid precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). A crucial step in the mechanism of this enzyme is the binding of the C4 hydroxyl of HMBPP to the unique fourth iron site in the [4Fe-4S](2+) moiety. Here, we report the synthesis and the kinetic investigations of two new extremely potent inhibitors of E. coli IspH where the OH group of HMBPP is replaced by an amino and a thiol group. (E)-4-Mercapto-3-methylbut-2-en-1-yl diphosphate is a reversible tight-binding inhibitor of IspH with K(i) = 20 ± 2 nM. A detailed kinetic analysis revealed that (E)-4-amino-3-methylbut-2-en-1-yl diphosphate is a reversible slow-binding inhibitor of IspH with K(i) = 54 ± 19 nM. The slow binding behavior of this inhibitor is best described by a one-step mechanism with the slow step consisting of the formation of the enzyme-inhibitor (EI) complex.
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Affiliation(s)
- Karnjapan Janthawornpong
- Université de Strasbourg, CNRS UMR 7177, Institut Le Bel, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg Cedex, France
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36
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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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Kung Y, Runguphan W, Keasling JD. From fields to fuels: recent advances in the microbial production of biofuels. ACS Synth Biol 2012; 1:498-513. [PMID: 23656227 DOI: 10.1021/sb300074k] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Amid grave concerns over global climate change and with increasingly strained access to fossil fuels, the synthetic biology community has stepped up to the challenge of developing microbial platforms for the production of advanced biofuels. The adoption of gasoline, diesel, and jet fuel alternatives derived from microbial sources has the potential to significantly limit net greenhouse gas emissions. In this effort, great strides have been made in recent years toward the engineering of microorganisms to produce transportation fuels derived from alcohol, fatty acid, and isoprenoid biosynthesis. We provide an overview of the biosynthetic pathways devised in the strain development of biofuel-producing microorganisms. We also highlight many of the commonly used and newly devised engineering strategies that have been employed to identify and overcome pathway bottlenecks and problems of toxicity to maximize production titers.
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Affiliation(s)
- Yan Kung
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Weerawat Runguphan
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Departments of Chemical and Biomolecular Engineering and Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
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