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Huang X, Sun Y, Osawa Y, Chen YE, Zhang H. Computational redesign of cytochrome P450 CYP102A1 for highly stereoselective omeprazole hydroxylation by UniDesign. J Biol Chem 2023; 299:105050. [PMID: 37451479 PMCID: PMC10413352 DOI: 10.1016/j.jbc.2023.105050] [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: 05/24/2023] [Revised: 07/03/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023] Open
Abstract
Cytochrome P450 CYP102A1 is a prototypic biocatalyst that has great potential in chemical synthesis, drug discovery, and biotechnology. CYP102A1 variants engineered by directed evolution and/or rational design are capable of catalyzing the oxidation of a wide range of organic compounds. However, it is difficult to foresee the outcome of engineering CYP102A1 for a compound of interest. Here, we introduce UniDesign as a computational framework for enzyme design and engineering. We tested UniDesign by redesigning CYP102A1 for stereoselective metabolism of omeprazole (OMP), a proton pump inhibitor, starting from an active but nonstereoselective triple mutant (TM: A82F/F87V/L188Q). To shift stereoselectivity toward (R)-OMP, we computationally scanned three active site positions (75, 264, and 328) for mutations that would stabilize the binding of the transition state of (R)-OMP while destabilizing that of (S)-OMP and picked three variants, namely UD1 (TM/L75I), UD2 (TM/A264G), and UD3 (TM/A328V), for experimentation, based on computed energy scores and models. UD1, UD2, and UD3 exhibit high turnover rates of 55 ± 4.7, 84 ± 4.8, and 79 ± 5.7 min-1, respectively, for (R)-OMP hydroxylation, whereas the corresponding rates for (S)-OMP are only 2.2 ± 0.19, 6.0 ± 0.68, and 14 ± 2.8 min-1, yielding an enantiomeric excess value of 92, 87, and 70%, respectively. These results suggest the critical roles of L75I, A264G, and A328V in steering OMP in the optimal orientation for stereoselective oxidation and demonstrate the utility of UniDesign for engineering CYP102A1 to produce drug metabolites of interest. The results are discussed in the context of protein structures.
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Affiliation(s)
- Xiaoqiang Huang
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.
| | - Yudong Sun
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yoichi Osawa
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA
| | - Y Eugene Chen
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Haoming Zhang
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA.
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2
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Li B, Guan X, Yang S, Zou Y, Liu W, Houk KN. Mechanism of the Stereoselective Catalysis of Diels-Alderase PyrE3 Involved in Pyrroindomycin Biosynthesis. J Am Chem Soc 2022; 144:5099-5107. [PMID: 35258962 DOI: 10.1021/jacs.2c00015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The biosynthesis of pyrroindomycins A and B features a complexity-building [4 + 2] cycloaddition cascade, which generates the spirotetramate core under the catalytic effects of monofunctional Diels-Alderases PyrE3 and PyrI4. We recently showed that the main functions of PyrI4 include acid catalysis and induced-fit/conformational selection. We now present quantum mechanical and molecular dynamics studies implicating a different mode of action by PyrE3, which prearranges an anionic polyene substrate into a high-energy reactive conformation at which an inverse-electron-demand Diels-Alder reaction can occur with a low barrier. Stereoselection is realized by strong binding interactions at the endo stereochemical relationship and a local steric constraint on the endo-1,3-diene unit. These findings, illustrating distinct mechanisms for PyrE3 and PyrI4, highlight how nature has evolved multiple ways to catalyze Diels-Alder reactions.
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Affiliation(s)
- Bo Li
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Xingyi Guan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Song Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Yike Zou
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
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3
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Jiang Y, Qu G, Sheng X, Tong F, Sun Z. Unraveling the mechanism of enantio-controlling switches of an alcohol dehydrogenase toward sterically small ketone. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00031h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Efficient synthesis of chiral compounds under mild conditions is highly desirable in the chemical and pharmaceutical communities, but it often faces difficulties. Although various enzymes have been harnessed as biocatalysts...
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4
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Yang Z, Kulik HJ. Protein Dynamics and Substrate Protonation States Mediate the Catalytic Action of trans-4-Hydroxy-l-Proline Dehydratase. J Phys Chem B 2021; 125:7774-7784. [PMID: 34236200 DOI: 10.1021/acs.jpcb.1c05320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzyme trans-4-hydroxy-l-proline (Hyp) dehydratase (HypD) is among the most abundant glycyl radical enzymes (GREs) in the healthy human gut microbiome and is considered a promising antibiotic target for the prominent antibiotic-resistant pathogen Clostridium difficile. Although an enzymatic mechanism has been proposed, the role of the greater HypD protein environment in mediating radical reactivity is not well understood. To fill this gap in understanding, we investigate HypD across multiple time- and length-scales using electronic structure modeling and classical molecular dynamics. We observe that the Hyp substrate protonation state significantly alters both its enzyme-free reactivity and its dynamics within the enzyme active site. Accurate coupled-cluster modeling suggests the deprotonated form of Hyp to be the most reactive protonation state for C5-Hpro-S activation. In the protein environment, hydrophobic interactions modulate the positioning of the Cys434 radical to enhance the reactivity of C5-Hpro-S abstraction. Long-time dynamics reveal that changing Hyp protonation states triggers the switching of a Leu643-gated water tunnel, a functional feature that has not yet been observed for members of the GRE superfamily.
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Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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5
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Computational investigations of allostery in aromatic amino acid biosynthetic enzymes. Biochem Soc Trans 2021; 49:415-429. [PMID: 33544132 DOI: 10.1042/bst20200741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/22/2022]
Abstract
Allostery, in which binding of ligands to remote sites causes a functional change in the active sites, is a fascinating phenomenon observed in enzymes. Allostery can occur either with or without significant conformational changes in the enzymes, and the molecular basis of its mechanism can be difficult to decipher using only experimental techniques. Computational tools for analyzing enzyme sequences, structures, and dynamics can provide insights into the allosteric mechanism at the atomic level. Combining computational and experimental methods offers a powerful strategy for the study of enzyme allostery. The aromatic amino acid biosynthesis pathway is essential in microorganisms and plants. Multiple enzymes involved in this pathway are sensitive to feedback regulation by pathway end products and are known to use allostery to control their activities. To date, four enzymes in the aromatic amino acid biosynthesis pathway have been computationally investigated for their allosteric mechanisms, including 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase, anthranilate synthase, chorismate mutase, and tryptophan synthase. Here we review the computational studies and findings on the allosteric mechanisms of these four enzymes. Results from these studies demonstrate the capability of computational tools and encourage future computational investigations of allostery in other enzymes of this pathway.
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6
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Fine-Tuning of Sequence Specificity by Near Attack Conformations in Enzyme-Catalyzed Peptide Hydrolysis. Catalysts 2020. [DOI: 10.3390/catal10060684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The catalytic role of near attack conformations (NACs), molecular states that lie on the pathway between the ground state (GS) and transition state (TS) of a chemical reaction, is not understood completely. Using a computational approach that combines Bürgi–Dunitz theory with all-atom molecular dynamics simulations, the role of NACs in catalyzing the first stages of HIV-1 protease peptide hydrolysis was previously investigated using a substrate that represents the recognized SP1-NC cleavage site of the HIV-1 Gag polyprotein. NACs were found to confer no catalytic effect over the uncatalyzed reaction there ( Δ Δ G N ‡ ∼ 0 kcal/mol). Here, using the same approach, the role of NACs across multiple substrates that each represent a further recognized cleavage site is investigated. Overall rate enhancement varies by | Δ Δ G ‡ | ∼ 12–15 kcal/mol across this set, and although NACs contribute a small and approximately constant barrier to the uncatalyzed reaction (< Δ G N ‡ u > = 4.3 ± 0.3 kcal/mol), they are found to contribute little significant catalytic effect ( | Δ Δ G N ‡ | ∼ 0–2 kcal/mol). Furthermore, no correlation is exhibited between NAC contributions and the overall energy barrier ( R 2 = 0.01). However, these small differences in catalyzed NAC contributions enable rates to match those required for the kinetic order of processing. Therefore, NACs may offer an alternative and subtle mode compared to non-NAC contributions for fine-tuning reaction rates during complex evolutionary sequence selection processes—in this case across cleavable polyproteins whose constituents exhibit multiple functions during the virus life-cycle.
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Unke OT, Koner D, Patra S, Käser S, Meuwly M. High-dimensional potential energy surfaces for molecular simulations: from empiricism to machine learning. MACHINE LEARNING-SCIENCE AND TECHNOLOGY 2020. [DOI: 10.1088/2632-2153/ab5922] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Chang M, Zhou Y, Wang H, Liu Z, Zhang Y, Feng Y. Crystal structure of the multifunctional SAM-dependent enzyme LepI provides insights into its catalytic mechanism. Biochem Biophys Res Commun 2019; 515:255-260. [PMID: 31101338 DOI: 10.1016/j.bbrc.2019.05.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 05/03/2019] [Indexed: 01/13/2023]
Abstract
Pericyclic reactions are among the most powerful synthetic transformations widely applied in the synthesis of multiple regioselective and stereoselective carbon-carbon bonds. LepI is a recently identified S-adenosyl-l-methionine (SAM)-dependent enzyme, which could catalyze dehydration, Diels-Alder reaction, and the retro-Claisen rearrangement reactions. However, the mechanism underlying these reactions by LepI remains elusive. Here we report the structure of LepI in complex with SAM as its co-factor, which adopts a typical class I methyltransferase fold. Docking studies are performed to investigate the binding modes of various substrates/products and provide insights into the catalytic mechanism of the multiple reactions catalyzed by LepI. Our study suggests that the dehydration reaction may start from the deprotonation of the hydroxyl group on the pyridone ring of the substrate by LepIH133, during which R295 and D296 play important roles in substrate binding and stabilizing the reaction intermediate. The stereoselective dehydration is accomplished through the trans-conformer of the leaving alcohol group which is trapped by nearby residues. The pericyclic reactions following dehydration are facilitated by the hydrophobic and hydrophilic interactions in the binding pocket. H133 and R295, two residues not conserved in other methyltransferases, might account for the unique activity of LepI among the SAM-dependent methyltransferase family. Together, this study provides important structural insights into the unique reactions catalyzed by LepI and will shed light on the knowledge of mechanisms of pericyclic reactions.
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Affiliation(s)
- Min Chang
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Yu Zhou
- National Institute of Biological Sciences, Beijing, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, PR China
| | - Hao Wang
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Zihe Liu
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Yi Zhang
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Yue Feng
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China.
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9
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Chang Z, Ansbacher T, Zhang L, Yang Y, Ko TP, Zhang G, Liu W, Huang JW, Dai L, Guo RT, Major DT, Chen CC. Crystal structure of LepI, a multifunctional SAM-dependent enzyme which catalyzes pericyclic reactions in leporin biosynthesis. Org Biomol Chem 2019; 17:2070-2076. [PMID: 30628619 DOI: 10.1039/c8ob02758g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
LepI is a novel multifunctional enzyme that catalyzes stereoselective dehydration, Diels-Alder reaction, and retro-Claisen rearrangement. Here we report the crystal structure of LepI in complex with its co-factor S-adenosyl methionine (SAM). LepI forms a tetramer via the N-terminal helical domain and binds to a SAM molecule in the C-terminal catalytic domain. The binding modes of various LepI substrates are investigated by docking simulations, which suggest that the substrates are bound via both hydrophobic and hydrophilic forces, as well as cation-π interactions with the positively charged SAM. The reaction starts with a dehydration step in which H133 possibly deprotonates the pyridone hydroxyl group of the substrate, while D296 might protonate an alkyl-chain hydroxyl group. Subsequent pericyclization may be facilitated by the correct fold of the substrate's alkyl chain and a thermodynamic driving force towards σ-bonds at the expense of π-bonds. These results provide structural insights into LepI catalysis and are important in understanding the mechanism of enzymatic pericyclization.
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Affiliation(s)
- Zhenying Chang
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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10
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Brickel S, Meuwly M. Molecular Determinants for Rate Acceleration in the Claisen Rearrangement Reaction. J Phys Chem B 2018; 123:448-456. [DOI: 10.1021/acs.jpcb.8b11059] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Sebastian Brickel
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel CH-4056, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel CH-4056, Switzerland
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11
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Freindorf M, Tao Y, Sethio D, Cremer D, Kraka E. New mechanistic insights into the Claisen rearrangement of chorismate – a Unified Reaction Valley Approach study. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1530464] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Yunwen Tao
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Daniel Sethio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
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12
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Qu G, Lonsdale R, Yao P, Li G, Liu B, Reetz MT, Sun Z. Methodology Development in Directed Evolution: Exploring Options when Applying Triple-Code Saturation Mutagenesis. Chembiochem 2018; 19:239-246. [PMID: 29314451 DOI: 10.1002/cbic.201700562] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 35032 Marburg Germany
| | - Peiyuan Yao
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
| | - Guangyue Li
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 35032 Marburg Germany
| | - Beibei Liu
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 35032 Marburg Germany
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
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13
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Burschowsky D, Krengel U, Uggerud E, Balcells D. Quantum chemical modeling of the reaction path of chorismate mutase based on the experimental substrate/product complex. FEBS Open Bio 2017; 7:789-797. [PMID: 28593134 PMCID: PMC5458464 DOI: 10.1002/2211-5463.12224] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 02/26/2017] [Accepted: 03/22/2017] [Indexed: 11/10/2022] Open
Abstract
Chorismate mutase is a well-known model enzyme, catalyzing the Claisen rearrangement of chorismate to prephenate. Recent high-resolution crystal structures along the reaction coordinate of this enzyme enabled computational analyses at unprecedented detail. Using quantum chemical simulations, we investigated how the catalytic reaction mechanism is affected by electrostatic and hydrogen-bond interactions. Our calculations showed that the transition state (TS) was mainly stabilized electrostatically, with Arg90 playing the leading role. The effect was augmented by selective hydrogen-bond formation to the TS in the wild-type enzyme, facilitated by a small-scale local induced fit. We further identified a previously underappreciated water molecule, which separates the negative charges during the reaction. The analysis includes the wild-type enzyme and a non-natural enzyme variant, where the catalytic arginine was replaced with an isosteric citrulline residue.
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Affiliation(s)
- Daniel Burschowsky
- Department of Chemistry University of Oslo Norway.,Present address: Leicester Institute of Structural and Chemical Biology University of Leicester Leicester UK
| | - Ute Krengel
- Department of Chemistry University of Oslo Norway
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14
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Mycobacterium tuberculosis chorismate mutase: A potential target for TB. Bioorg Med Chem 2017; 25:1725-1736. [PMID: 28202315 DOI: 10.1016/j.bmc.2017.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/01/2017] [Indexed: 12/27/2022]
Abstract
Mycobacterium tuberculosis chorismate mutase (MtbCM) catalyzes the rearrangement of chorismate to prephenate in the shikimate biosynthetic pathway to form the essential amino acids, phenylalanine and tyrosine. Two genes encoding chorismate mutase have been identified in Mtb. The secretory form,∗MtbCM (encoded by Rv1885c) is assumed to play a key role in pathogenesis of tuberculosis. Also, the inhibition of MtbCM may hinder the supply of nutrients to the organism. Indeed, the existence of chorismate mutase (CM) in bacteria, fungi and higher plants but not in human and low sequence homology among known CM makes it an interesting target for the discovery of anti-tubercular agents. The present article mainly focuses on the recent developments in the structure, function and inhibition of MtbCM. The understanding of various aspects of MtbCM as presented in the current article may facilitate the design and subsequent chemical synthesis of new inhibitors against ∗MtbCM, that could lead to the discovery and development of novel and potent anti-tubercular agents in future.
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15
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Nazmi AR, Lang EJM, Bai Y, Allison TM, Othman MH, Panjikar S, Arcus VL, Parker EJ. Interdomain Conformational Changes Provide Allosteric Regulation en Route to Chorismate. J Biol Chem 2016; 291:21836-21847. [PMID: 27502275 DOI: 10.1074/jbc.m116.741637] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/30/2016] [Indexed: 11/06/2022] Open
Abstract
Multifunctional proteins play a variety of roles in metabolism. Here, we examine the catalytic function of the combined 3-deoxy-d-arabino heptulosonate-7-phosphate synthase (DAH7PS) and chorismate mutase (CM) from Geobacillus sp. DAH7PS operates at the start of the biosynthetic pathway for aromatic metabolites, whereas CM operates in a dedicated branch of the pathway for the biosynthesis of amino acids tyrosine and phenylalanine. In line with sequence predictions, the two catalytic functions are located in distinct domains, and these two activities can be separated and retain functionality. For the full-length protein, prephenate, the product of the CM reaction, acts as an allosteric inhibitor for the DAH7PS. The crystal structure of the full-length protein with prephenate bound and the accompanying small angle x-ray scattering data reveal the molecular mechanism of the allostery. Prephenate binding results in the tighter association between the dimeric CM domains and the tetrameric DAH7PS, occluding the active site and therefore disrupting DAH7PS function. Acquisition of a physical gating mechanism to control catalytic function through gene fusion appears to be a general mechanism for providing allostery for this enzyme.
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Affiliation(s)
- Ali Reza Nazmi
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Eric J M Lang
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Yu Bai
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Timothy M Allison
- the Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 5QY, United Kingdom
| | - Mohamad H Othman
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Santosh Panjikar
- the Australian Synchrotron, Clayton, Melbourne, Victoria 3168, Australia.,the Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia
| | - Vickery L Arcus
- the School of Science, University of Waikato, Hamilton 3240, New Zealand, and
| | - Emily J Parker
- the Maurice Wilkins Centre, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
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16
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de Lima WEA, Francisco A, da Cunha EFF, Radic Z, Taylor P, França TCC, Ramalho TC. Mechanistic studies of new oximes reactivators of human butyryl cholinesterase inhibited by cyclosarin and sarin. J Biomol Struct Dyn 2016; 35:1272-1282. [PMID: 27125569 DOI: 10.1080/07391102.2016.1178173] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Butyryl cholinesterase (BChE) has been seen as a key enzyme in the search for new strategies in the treatment of poisoning by organophosphates (OPs), since human BChE (HssBChE), complexed with the appropriate oxime, can be a suitable scavenger and deactivator for OPs in the blood stream. However, the efficacy of HssBChE is limited by its strict stoichiometric scavenging, slow reactivation, and propensity for aging. The improvement of the reactivation rate by new and more efficient oximes could contribute to mitigate this problem and increase the HssBChE efficiency as scavenger. Several oximes have been synthesized and tested with this goal, some with promising results, but the mechanistic aspects of the reactivation reaction are not fully understood yet. In order to better investigate this mechanism, docking and mixed quantum and molecular mechanics combined with principal components analysis were performed here to evaluate the capacity of reactivation and determine the preferred route for the reactivation reaction of two new oximes on HssBChE inhibited by the neurotoxic agents cyclosarin and sarin. Plots of potential energies were calculated and all the transition states of the reactional mechanism were determined. Our results showed a good correlation with experimental data and pointed to the most efficient oxime with both OPs. The protocol used could be a suitable tool for a preliminary evaluation of the HssBChE reactivation rates by new oximes.
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Affiliation(s)
- Willian E Amaral de Lima
- a Laboratory of Molecular Modeling, Chemistry Department , Federal University of Lavras , Lavras , MG 37200-000 , Brazil
| | - Ander Francisco
- a Laboratory of Molecular Modeling, Chemistry Department , Federal University of Lavras , Lavras , MG 37200-000 , Brazil
| | - Elaine F F da Cunha
- a Laboratory of Molecular Modeling, Chemistry Department , Federal University of Lavras , Lavras , MG 37200-000 , Brazil
| | - Zoran Radic
- b Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California at San Diego , San Diego , CA , USA
| | - Palmer Taylor
- b Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California at San Diego , San Diego , CA , USA
| | - Tanos C C França
- c Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD) , Military Institute of Engineering , Rio de Janeiro , RJ 22290-270 , Brazil.,d Department of Chemistry & Biochemistry , Concordia University , Montreal , QC , Canada.,e Faculty of Informatics and Management, Center for Basic and Applied Research , University of Hradec Kralove , Hradec Kralove , Czech Republic
| | - Teodorico C Ramalho
- a Laboratory of Molecular Modeling, Chemistry Department , Federal University of Lavras , Lavras , MG 37200-000 , Brazil.,e Faculty of Informatics and Management, Center for Basic and Applied Research , University of Hradec Kralove , Hradec Kralove , Czech Republic
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17
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Culbertson JE, Chung DH, Ziebart KT, Espiritu E, Toney MD. Conversion of aminodeoxychorismate synthase into anthranilate synthase with Janus mutations: mechanism of pyruvate elimination catalyzed by chorismate enzymes. Biochemistry 2015; 54:2372-84. [PMID: 25710100 DOI: 10.1021/acs.biochem.5b00013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The central importance of chorismate enzymes in bacteria, fungi, parasites, and plants combined with their absence in mammals makes them attractive targets for antimicrobials and herbicides. Two of these enzymes, anthranilate synthase (AS) and aminodeoxychorismate synthase (ADCS), are structurally and mechanistically similar. The first catalytic step, amination at C2, is common between them, but AS additionally catalyzes pyruvate elimination, aromatizing the aminated intermediate to anthranilate. Despite prior attempts, the conversion of a pyruvate elimination-deficient enzyme into an elimination-proficient one has not been reported. Janus, a bioinformatics method for predicting mutations required to functionally interconvert homologous enzymes, was employed to predict mutations to convert ADCS into AS. A genetic selection on a library of Janus-predicted mutations was performed. Complementation of an AS-deficient strain of Escherichia coli grown on minimal medium led to several ADCS mutants that allow growth in 6 days compared to 2 days for wild-type AS. The purified mutant enzymes catalyze the conversion of chorismate to anthranilate at rates that are ∼50% of the rate of wild-type ADCS-catalyzed conversion of chorismate to aminodeoxychorismate. The residues mutated do not contact the substrate. Molecular dynamics studies suggest that pyruvate elimination is controlled by the conformation of the C2-aminated intermediate. Enzymes that catalyze elimination favor the equatorial conformation, which presents the C2-H to a conserved active site lysine (Lys424) for deprotonation and maximizes stereoelectronic activation. Acid/base catalysis of pyruvate elimination was confirmed in AS and salicylate synthase by showing incorporation of a solvent-derived proton into the pyruvate methyl group and by solvent kinetic isotope effects on pyruvate elimination catalyzed by AS.
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Affiliation(s)
- Justin E Culbertson
- †Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Dong hee Chung
- †Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Kristin T Ziebart
- ‡Department of Chemistry, Oregon State University, Corvallis, Oregon 97331-4003, United States
| | - Eduardo Espiritu
- §Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Michael D Toney
- †Department of Chemistry, University of California, Davis, Davis, California 95616, United States
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18
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Lameira J, Ram Prasad B, Chu ZT, Warshel A. Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization. Proteins 2015; 83:318-30. [PMID: 25388538 PMCID: PMC4300294 DOI: 10.1002/prot.24717] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 10/30/2014] [Accepted: 11/03/2014] [Indexed: 11/05/2022]
Abstract
The enzyme catechol O-methyltransferase (COMT) catalyzes the transfer of a methyl group from S-adenosylmethionine to dopamine and related catechols. The search for the origin of COMT catalysis has led to different proposals and hypothesis, including the entropic, the NAC, and the compression proposals as well as the more reasonable electrostatic idea. Thus, it is important to understand the catalytic power of this enzyme and to examine the validity of different proposals and in particular the repeated recent implication of the compression idea. The corresponding analysis should be done by well-defined physically-based considerations that involve computations rather than circular interpretations of experimental results. Thus, we explore here the origin of the catalytic efficiency of COMT by using the empirical valence bond and the linear response approximation approaches. The results demonstrate that the catalytic effect of COMT is mainly due to electrostatic preorganization effects. It is also shown that the compression, NAC and entropic proposals do not account for the catalytic effect.
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Affiliation(s)
- Jeronimo Lameira
- University of Southern California, Department of Chemistry, SGM 418, 3620 McClintosk Avenue, Los Angeles, California 90089, United States
- Faculdade de Biotecnologia e Laboratório de Planejamento e Desenvolvimento de Fármacos; Universidade Federal do Pará, 66075-110, Belém, PA, Brazil
| | - B Ram Prasad
- University of Southern California, Department of Chemistry, SGM 418, 3620 McClintosk Avenue, Los Angeles, California 90089, United States
| | - Zhen T. Chu
- University of Southern California, Department of Chemistry, SGM 418, 3620 McClintosk Avenue, Los Angeles, California 90089, United States
| | - Arieh Warshel
- University of Southern California, Department of Chemistry, SGM 418, 3620 McClintosk Avenue, Los Angeles, California 90089, United States
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19
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Sadiq SK, Coveney PV. Computing the Role of Near Attack Conformations in an Enzyme-Catalyzed Nucleophilic Bimolecular Reaction. J Chem Theory Comput 2014; 11:316-24. [DOI: 10.1021/ct5008845] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- S. Kashif Sadiq
- Infection
Biology Unit, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C/Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Peter V. Coveney
- Centre
for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, United Kingdom
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20
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Electrostatic transition state stabilization rather than reactant destabilization provides the chemical basis for efficient chorismate mutase catalysis. Proc Natl Acad Sci U S A 2014; 111:17516-21. [PMID: 25422475 DOI: 10.1073/pnas.1408512111] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
For more than half a century, transition state theory has provided a useful framework for understanding the origins of enzyme catalysis. As proposed by Pauling, enzymes accelerate chemical reactions by binding transition states tighter than substrates, thereby lowering the activation energy compared with that of the corresponding uncatalyzed process. This paradigm has been challenged for chorismate mutase (CM), a well-characterized metabolic enzyme that catalyzes the rearrangement of chorismate to prephenate. Calculations have predicted the decisive factor in CM catalysis to be ground state destabilization rather than transition state stabilization. Using X-ray crystallography, we show, in contrast, that a sluggish variant of Bacillus subtilis CM, in which a cationic active-site arginine was replaced by a neutral citrulline, is a poor catalyst even though it effectively preorganizes chorismate for the reaction. A series of high-resolution molecular snapshots of the reaction coordinate, including the apo enzyme, and complexes with substrate, transition state analog and product, demonstrate that an active site, which is only complementary in shape to a reactive substrate conformer, is insufficient for effective catalysis. Instead, as with other enzymes, electrostatic stabilization of the CM transition state appears to be crucial for achieving high reaction rates.
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21
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Cao H, Hall J, Hille R. Substrate orientation and specificity in xanthine oxidase: crystal structures of the enzyme in complex with indole-3-acetaldehyde and guanine. Biochemistry 2014; 53:533-41. [PMID: 24397336 DOI: 10.1021/bi401465u] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Xanthine oxidase is a molybdenum-containing hydroxylase that catalyzes the hydroxylation of sp(2)-hybridized carbon centers in a variety of aromatic heterocycles as well as aldehydes. Crystal structures of the oxidase form of the bovine enzyme in complex with a poor substrate indole-3-acetaldehyde and the nonsubstrate guanine have been determined, both at a resolution of 1.6 Å. In each structure, a specific and unambiguous orientation of the substrate in the active site is observed in which the hydroxylatable site is oriented away from the active site molybdenum center. The orientation seen with indole-3-acetaldehyde has the substrate positioned with the indole ring rather than the exocyclic aldehyde nearest the molybdenum center, indicating that the substrate must rotate some 30° in the enzyme active site to permit hydroxylation of the aldehyde group (as observed experimentally), accounting for the reduced reactivity of the enzyme toward this substrate. The principal product of hydroxylation of indole-3-acetaldehyde by the bovine enzyme is confirmed to be indole-3-carboxylic acid based on its characteristic UV-vis spectrum, and the kinetics of enzyme reduction are reported. With guanine, the dominant orientation seen crystallographically has the C-8 position that might be hydroxylated pointed away from the active site molybdenum center, in a configuration resembling that seen previously with hypoxanthine (a substrate that is effectively hydroxylated at position 2). The ∼180° reorientation required to permit reaction is sterically prohibited, indicating that substrate (mis)orientation in the active site is a major factor precluding formation of the highly mutagenic 8-hydroxyguanine.
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Affiliation(s)
- Hongnan Cao
- Department of Biochemistry, University of California , Riverside, California 92521, United States
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22
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Vanzin D, Fiori S, França Biondo PB, Feltrim G, Gracetto AC, Tessaro AL, Politi MJ, Caetano W, Hioka N. Microenvironment Effects on the Kinetics of the Alkaline Hydrolysis of Bispyridinium Conformers. INT J CHEM KINET 2013. [DOI: 10.1002/kin.20803] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Douglas Vanzin
- Departamento de Química; Universidade Estadual de Maringá; 87020-900 Maringá PR Brazil
| | - Simone Fiori
- Departamento de Química; Universidade Estadual de Maringá; 87020-900 Maringá PR Brazil
| | | | - Gisele Feltrim
- Departamento de Química; Universidade Estadual de Maringá; 87020-900 Maringá PR Brazil
| | - Augusto C. Gracetto
- Universidade Tecnológica Federal do Paraná-Campus Apucarana; 86812-460 Apucarana PR Brazil
| | - André L. Tessaro
- Universidade Tecnológica Federal do Paraná-Campus Apucarana; 86812-460 Apucarana PR Brazil
| | - Mario José Politi
- Instituto de Química; Universidade de São Paulo; 05508-000 São Paulo SP Brazil
| | - Wilker Caetano
- Departamento de Química; Universidade Estadual de Maringá; 87020-900 Maringá PR Brazil
| | - Noboru Hioka
- Departamento de Química; Universidade Estadual de Maringá; 87020-900 Maringá PR Brazil
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23
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Pu M, Privalov T. Ab initio dynamics trajectory study of the heterolytic cleavage of H2 by a Lewis acid [B(C6F5)3] and a Lewis base [P(tBu)3]. J Chem Phys 2013; 138:154305. [DOI: 10.1063/1.4799932] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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24
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Olucha J, Meneely KM, Lamb AL. Modification of residue 42 of the active site loop with a lysine-mimetic side chain rescues isochorismate-pyruvate lyase activity in Pseudomonas aeruginosa PchB. Biochemistry 2012; 51:7525-32. [PMID: 22970849 DOI: 10.1021/bi300472n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PchB is an isochorismate-pyruvate lyase from Pseudomonas aeruginosa. A positively charged lysine residue is located in a flexible loop that behaves as a lid to the active site, and the lysine residue is required for efficient production of salicylate. A variant of PchB that lacks the lysine at residue 42 has a reduced catalytic free energy of activation of up to 4.4 kcal/mol. Construction of a lysine isosteric residue bearing a positive charge at the appropriate position leads to the recovery of 2.5-2.7 kcal/mol (about 60%) of the 4.4 kcal/mol by chemical rescue. Exogenous addition of ethylamine to the K42A variant leads to a neglible recovery of activity (0.180 kcal/mol, roughly 7% rescue), whereas addition of propylamine caused an additional modest loss in catalytic power (0.056 kcal/mol, or 2% loss). This is consistent with the view that (a) the lysine-42 residue is required in a specific conformation to stabilize the transition state and (b) the correct conformation is achieved for a lysine-mimetic side chain at site 42 in the course of loop closure, as expected for transition-state stabilization by the side chain ammonio function. That the positive charge is the main effector of transition state stabilization is shown by the construction of a lysine-isosteric residue capable of exerting steric effects and hydrogen bonding but not electrostatic effects, leading to a modest increase of catalytic power (0.267-0.505 kcal/mol of catalytic free energy, or roughly 6-11% rescue).
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Affiliation(s)
- José Olucha
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
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25
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Ramadhar TR, Batey RA. Accurate prediction of experimental free energy of activation barriers for the aliphatic-Claisen rearrangement through DFT calculations. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.08.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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26
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Abstract
One of the fundamental questions of enzymology is how catalytic power is derived. This review focuses on recent developments in the structure--function relationships of chorismate-utilizing enzymes involved in siderophore biosynthesis to provide insight into the biocatalysis of pericyclic reactions. Specifically, salicylate synthesis by the two-enzyme pathway in Pseudomonas aeruginosa is examined. The isochorismate-pyruvate lyase is discussed in the context of its homologues, the chorismate mutases, and the isochorismate synthase is compared to its homologues in the MST family (menaquinone, siderophore, or tryptophan biosynthesis) of enzymes. The tentative conclusion is that the activities observed cannot be reconciled by inspection of the active site participants alone. Instead, individual activities must arise from unique dynamic properties of each enzyme that are tuned to promote specific chemistries.
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Affiliation(s)
- Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States.
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27
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Olucha J, Ouellette AN, Luo Q, Lamb AL. pH Dependence of catalysis by Pseudomonas aeruginosa isochorismate-pyruvate lyase: implications for transition state stabilization and the role of lysine 42. Biochemistry 2011; 50:7198-207. [PMID: 21751784 DOI: 10.1021/bi200599j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An isochorismate-pyruvate lyase with adventitious chorismate mutase activity from Pseudomonas aerugionsa (PchB) achieves catalysis of both pericyclic reactions in part by the stabilization of reactive conformations and in part by electrostatic transition-state stabilization. When the active site loop Lys42 is mutated to histidine, the enzyme develops a pH dependence corresponding to a loss of catalytic power upon deprotonation of the histidine. Structural data indicate that the change is not due to changes in active site architecture, but due to the difference in charge at this key site. With loss of the positive charge on the K42H side chain at high pH, the enzyme retains lyase activity at ∼100-fold lowered catalytic efficiency but loses detectable mutase activity. We propose that both substrate organization and electrostatic transition state stabilization contribute to catalysis. However, the dominant reaction path for catalysis is dependent on reaction conditions, which influence the electrostatic properties of the enzyme active site amino acid side chains.
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Affiliation(s)
- Jose Olucha
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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28
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Privalov T, Åkermark B, Sun L. The OO Bonding in Water Oxidation: the Electronic Structure Portrayal of a Concerted Oxygen Atom-Proton Transfer Pathway. Chemistry 2011; 17:8313-7. [DOI: 10.1002/chem.201100901] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Indexed: 12/27/2022]
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29
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Luo Q, Meneely KM, Lamb AL. Entropic and enthalpic components of catalysis in the mutase and lyase activities of Pseudomonas aeruginosa PchB. J Am Chem Soc 2011; 133:7229-33. [PMID: 21504201 DOI: 10.1021/ja202091a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The isochorismate-pyruvate lyase from Pseudomonas aeruginosa (PchB) catalyzes two pericyclic reactions, demonstrating the eponymous activity and also chorismate mutase activity. The thermodynamic parameters for these enzyme-catalyzed activities, as well as the uncatalyzed isochorismate decomposition, are reported from temperature dependence of k(cat) and k(uncat) data. The entropic effects do not contribute to enzyme catalysis as expected from previously reported chorismate mutase data. Indeed, an entropic penalty for the enzyme-catalyzed mutase reaction (ΔS(++) = -12.1 ± 0.6 cal/(mol K)) is comparable to that of the previously reported uncatalyzed reaction, whereas that of the enzyme-catalyzed lyase reaction (ΔS(++) = -24.3 ± 0.2 cal/(mol K)) is larger than that of the uncatalyzed lyase reaction (-15.77 ± 0.02 cal/(mol K)) documented here. With the assumption that chemistry is rate-limiting, we propose that a reactive substrate conformation is formed upon loop closure of the active site and that ordering of the loop contributes to the entropic penalty for converting the enzyme substrate complex to the transition state.
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Affiliation(s)
- Qianyi Luo
- Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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30
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Kamerlin SCL, Mavri J, Warshel A. Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues. FEBS Lett 2010; 584:2759-66. [PMID: 20433839 DOI: 10.1016/j.febslet.2010.04.062] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 04/21/2010] [Accepted: 04/22/2010] [Indexed: 10/19/2022]
Abstract
The idea that tunneling is enhanced by the compression of the donor-acceptor distance has attracted significant interest. In particular, recent studies argued that this proposal is consistent with pressure effects on enzymatic reactions, and that the observed pressure effects support the idea of vibrationally enhanced catalysis. However, a careful analysis of the current works reveals serious inconsistencies in the evidence presented to support these hypotheses. Apparently, tunneling decreases upon compression, and external pressure does not lead to the applicable compression of the free energy surface. Additionally, pressure experiments do not provide actual evidence for vibrationally enhanced catalysis. Finally, the temperature dependence of the entropy change in hydride transfer reactions is shown to reflect simple electrostatic effects.
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31
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Ranaghan KE, Mulholland AJ. Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods. INT REV PHYS CHEM 2010. [DOI: 10.1080/01442350903495417] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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32
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Luo Q, Olucha J, Lamb AL. Structure-function analyses of isochorismate-pyruvate lyase from Pseudomonas aeruginosa suggest differing catalytic mechanisms for the two pericyclic reactions of this bifunctional enzyme. Biochemistry 2009; 48:5239-45. [PMID: 19432488 DOI: 10.1021/bi900456e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The isochorismate-pyruvate lyase from Pseudomonas aeruginosa (PchB) catalyzes two pericyclic reactions in a single active site. PchB physiologically produces salicylate and pyruvate from isochorismate for ultimate incorporation of the salicylate into the siderophore pyochelin. PchB also produces prephenate from chorismate, most likely due to structural homology to the Escherchia coli chorismate mutase. The molecular basis of catalysis among enzymatic pericyclic reactions is a matter of debate, one view holding that catalysis may be derived from electrostatic transition state stabilization and the opposing view that catalysis is derived from the generation of a reactive substrate conformation. Mutant forms of PchB were generated by site-directed mutagenesis at the site (K42) hypothesized to be key for electrostatic transition state stabilization (K42A, K42Q, K42E, and K42H). The loop containing K42 is mobile, and a mutant to slow loop dynamics was also designed (A43P). Finally, a previously characterized mutation (I87T) was also produced. Circular dichroism was used to assess the overall effect on secondary structure as a result of the mutations, and X-ray crystallographic structures are reported for K42A with salicylate and pyruvate bound and for apo-I87T. The data illustrate that the active site architecture is maintained in K42A-PchB, which indicates that differences in activity are not caused by secondary structural changes or by differences in active site loop conformation but rather by the chemical nature of this key residue. In contrast, the I87T structure demonstrates considerable mobility, suggesting that loop dynamics and conformational plasticity may be important for efficient catalysis. Finally, the mutational effects on k(cat) provide evidence that the two activities of PchB are not covariant and that a single hypothesis may not provide a sufficient explanation for catalysis.
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Affiliation(s)
- Qianyi Luo
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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33
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34
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Jiménez A, Clapés P, Crehuet R. A dynamic view of enzyme catalysis. J Mol Model 2008; 14:735-46. [DOI: 10.1007/s00894-008-0283-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Accepted: 02/01/2008] [Indexed: 10/22/2022]
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35
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Bruice TC. Computational approaches: reaction trajectories, structures, and atomic motions. Enzyme reactions and proficiency. Chem Rev 2007; 106:3119-39. [PMID: 16895321 DOI: 10.1021/cr050283j] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Thomas C Bruice
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, USA.
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36
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Higashi M, Hayashi S, Kato S. Transition state determination of enzyme reaction on free energy surface: Application to chorismate mutase. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.02.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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Masgrau L, Ranaghan KE, Scrutton NS, Mulholland AJ, Sutcliffe MJ. Tunneling and Classical Paths for Proton Transfer in an Enzyme Reaction Dominated by Tunneling: Oxidation of Tryptamine by Aromatic Amine Dehydrogenase. J Phys Chem B 2007; 111:3032-47. [PMID: 17388439 DOI: 10.1021/jp067898k] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proton tunneling dominates the oxidative deamination of tryptamine catalyzed by the enzyme aromatic amine dehydrogenase. For reaction with the fast substrate tryptamine, a H/D kinetic isotope effect (KIE) of 55 +/- 6 has been reported-one of the largest observed in an enzyme reaction. We present here a computational analysis of this proton-transfer reaction, applying combined quantum mechanics/molecular mechanics (QM/MM) methods (PM3-SRP//PM3/CHARMM22). In particular, we extend our previous computational study (Masgrau et al. Science 2006, 312, 237) by using improved energy corrections, high-level QM/MM methods, and an ensemble of paths to estimate the tunneling contributions. We have carried out QM/MM molecular dynamics simulations and variational transition state theory calculations with small-curvature tunneling corrections. The results provide detailed insight into the processes involved in the reaction. Transfer to the O2 oxygen of the catalytic base, Asp128beta, is found to be the favored reaction both thermodynamically and kinetically, even though O1 is closer in the reactant complex. Comparison of quantum and classical models of proton transfer allows estimation of the contribution of hydrogen tunneling in lowering the barrier to reaction in the enzyme. A reduction of the activation free energy due to tunneling of 3.1 kcal mol-1 is found, which represents a rate enhancement due to tunneling by 2 orders of magnitude. The calculated KIE of 30 is significantly elevated over the semiclassical limit, in agreement with the experimental observations; a semiclassical value of 6 is obtained when tunneling is omitted. A polarization of the C-H bond to be broken is observed due to the close proximity of the catalytic aspartate and the (formally) positively charged imine nitrogen. A comparison is also made with the related quinoprotein methylamine dehydrogenase (MADH)-the much lower KIE of 11 that we obtain for the MADH/methylamine system is found to arise from a more endothermic potential energy surface for the MADH reaction.
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Affiliation(s)
- Laura Masgrau
- Manchester Interdisciplinary Biocentre, School of Chemical Engineering and Analytical Science, and Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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38
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Hediger ME. Design, synthesis, and evaluation of aza inhibitors of chorismate mutase. Bioorg Med Chem 2005; 12:4995-5010. [PMID: 15336279 DOI: 10.1016/j.bmc.2004.06.037] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2003] [Accepted: 06/07/2004] [Indexed: 11/27/2022]
Abstract
A series of aza inhibitors (4-9) of chorismate mutase (E.C. 5.4.99.5) was designed, prepared, and evaluated against the enzyme by monitoring the direct inhibition of the chorismate, 1, to prephenate, 2, conversion. None of these aza inhibitors displayed tighter binding to the enzyme than the native substrate chorismate or greater inhibitory action than the previously reported ether analogue, 3. Furthermore, no time-dependent loss of enzyme activity was observed in the presence of the two potentially reactive aza inhibitors (7 and 9). These results in conjunction with inhibition data from a broader series of chorismate mutase inhibitors allowed a novel proposal for the mechanistic role of chorismate mutase to be developed. This proposed mechanism was computationally verified and correlated with crystallographic studies of various chorismate mutases.
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Affiliation(s)
- Mark E Hediger
- College of Chemistry, Latimer Hall, The University of California, Berkeley, CA 94720-1460, USA.
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39
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Braun-Sand S, Olsson MH, Warshel A. Computer modeling of enzyme catalysis and its relationship to concepts in physical organic chemistry. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2005. [DOI: 10.1016/s0065-3160(05)40005-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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40
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Mazumder-Shivakumar D, Kahn K, Bruice TC. Computational Study of the Ground State of Thermophilic Indole Glycerol Phosphate Synthase: Structural Alterations at the Active Site with Temperature. J Am Chem Soc 2004; 126:5936-7. [PMID: 15137737 DOI: 10.1021/ja049512u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hyperthermophlic indole-3-glycerol phosphate synthase (IGPS) catalyzes the terminal ring-closure step in tryptophan biosynthesis. In this paper, we compare the results from the molecular dynamics (MD) simulation of enzyme-bound substrate at 298 K (E.S298) and 385 K (E.S385) solvated in the TIP3P water box using the CHARMM force field to address the question of the structural change of the Enzyme. Substrate complex with temperature. The population of the reactive Enzyme. Substrate conformers (near attack conformers or NACs) increases by approximately 1100-fold in going from room temperature (E.S298) to high temperature (E.S385). This increased population of NAC conformers in the Michaelis complex correlates well with the increase in rate in going from 298 to 385 K. The positioning of the two active site residues Lys53 and Lys110 controls binding of the substrate in the favorable orientation for general acid-catalyzed intramolecular ring formation reaction. It can be concluded that the NAC formation allowing general acid catalysis has much to do with the temperature dependence of the free energy of reaction.
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Affiliation(s)
- Devleena Mazumder-Shivakumar
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, USA
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Affiliation(s)
- Avital Shurki
- Department of Chemistry, University of Southern California, Los Angeles 90089, USA
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Hur S, Bruice TC. The near attack conformation approach to the study of the chorismate to prephenate reaction. Proc Natl Acad Sci U S A 2003; 100:12015-20. [PMID: 14523243 PMCID: PMC218705 DOI: 10.1073/pnas.1534873100] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Standard free energies (DeltaGN degree) for formation of near attack conformers, those ground state conformers that can convert directly to the transition state, were calculated for the Claisen rearrangement of chorismate to prephenate in six different environments: water, wild-type enzymes from Bacillus subtilis and Escherichia coli, their Arg90Cit and Glu52Ala mutants, and the 1F7 catalytic antibody. Values of the calculated DeltaGN degrees and the experimentally determined activation energies (DeltaG++) are linearly related with the slope of approximately equal to 1. This demonstrates that the relative rate of the chorismate --> prephenate reaction is overwhelmingly dependent on the efficiency of formation of near attack conformers in the ground state.
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Affiliation(s)
- Sun Hur
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
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Bekal S, Niblack TL, Lambert KN. A chorismate mutase from the soybean cyst nematode Heterodera glycines shows polymorphisms that correlate with virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2003; 16:439-46. [PMID: 12744515 DOI: 10.1094/mpmi.2003.16.5.439] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Parasitism genes from phytoparasitic nematodes are thought to be essential for nematode invasion of the host plant, to help the nematode establish feeding sites, and to aid nematodes in the suppression of host plant defenses. One gene that may play several roles in nematode parasitism is chorismate mutase (CM). This secreted enzyme is produced in the nematode's esophageal glands and appears to function within the plant cell to manipulate the plant's shikimate pathway, which controls plant cell growth, development, structure, and pathogen defense. Using degenerate polymerase chain reaction primers, we amplified and cloned a chorismate mutase (Hg-cm-1) from Heterodera glycines, the soybean cyst nematode (SCN), and showed it had CM activity. RNA in situ hybridization of Hg-cm-1 cDNA to SCN sections confirms that it is specifically expressed in the nematodes' esophageal glands. DNA gel blots of genomic DNA isolated from SCN inbred lines that have differing virulence on SCN resistant soybean show Hg-cm-1 is a member of a polymorphic gene family. Some Hg-cm family members predominate in SCN inbred lines that are virulent on certain SCN resistant soybean cultivars. The same polymorphisms and correlation with virulence are seen in the Hg-cm-1 expressed in the SCN second-stage juveniles. Based on the enzymatic activity of Hg-cm-1 and the observation that different forms of the mutase are expressed in virulent nematodes, we hypothesize that the Hg-cm-1 is a virulence gene, some forms of which allow SCN to parasitize certain resistant soybean plants.
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Affiliation(s)
- Sadia Bekal
- Department of Crop Science, University of Illinois, Urbana, IL 61801, USA
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