1
|
Dalal V, Golemi-Kotra D, Kumar P. Quantum Mechanics/Molecular Mechanics Studies on the Catalytic Mechanism of a Novel Esterase (FmtA) of Staphylococcus aureus. J Chem Inf Model 2022; 62:2409-2420. [PMID: 35475370 DOI: 10.1021/acs.jcim.2c00057] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
FmtA is a novel esterase that shares the penicillin-binding protein (PBP) core structural folding but found to hydrolyze the removal of d-Ala from teichoic acids. Molecular docking, dynamics, and MM-GBSA of FmtA and its variants S127A, K130A, Y211A, D213A, and K130AY211A, in the presence or absence of wall teichoic acid (WTA), suggest that active site residues S127, K130, Y211, D213, N343, and G344 play a role in substrate binding. Quantum mechanics (QM)/molecular mechanics (MM) calculations reveal that during WTA catalysis, K130 deprotonates S127, and the nucleophilic S127 attacks the carbonyl carbon of d-Ala bound to WTA. The tetrahedral intermediate (TI) complex is stabilized by hydrogen bonding to the oxyanion holes. The TI complex displays a high energy gap and collapses to an energetically favorable acyl-enzyme complex.
Collapse
Affiliation(s)
- Vikram Dalal
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, Uttrakhand 247667, India
| | - Dasantila Golemi-Kotra
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, Uttrakhand 247667, India
| |
Collapse
|
2
|
Le LTHL, Yoo W, Wang Y, Jeon S, Kim KK, Kim HW, Kim TD. Dual functional roles of a novel bifunctional β-lactamase/esterase from Lactococcus garvieae. Int J Biol Macromol 2022; 206:203-212. [PMID: 35183603 DOI: 10.1016/j.ijbiomac.2022.02.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/27/2022] [Accepted: 02/14/2022] [Indexed: 11/05/2022]
Abstract
A novel bifunctional β-lactamase/esterase (LgLacI), which is capable of hydrolyzing β-lactam-containing antibiotics including ampicillin, oxacillin, and cefotaxime as well as synthesizing biodiesels, was cloned from Lactococcus garvieae. Unlike most bacterial esterases/lipases that have G-x-S-x-G motif, LgLacI, which contains S-x-x-K catalytic motif, has sequence similarities to bacterial family VIII esterase as well as β-lactamases. The catalytic properties of LgLacI were explored using a wide range of biochemical methods including spectroscopy, assays, structural modeling, mutagenesis, and chromatography. We confirmed the bifunctional property of LgLacI hydrolyzing both esters and β-lactam antibiotics. This study provides novel perspectives into a bifunctional enzyme from L. garvieae, which can degrade β-lactam antibiotics with high esterase activity.
Collapse
Affiliation(s)
- Ly Thi Huong Luu Le
- Department of Chemistry, Graduate School of General Studies, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Wanki Yoo
- Department of Chemistry, Graduate School of General Studies, Sookmyung Women's University, Seoul 04310, Republic of Korea; Department of Precision Medicine, Sungkyunkwan University, College of Medicine, Suwon 2066, Republic of Korea
| | - Ying Wang
- Department of Chemistry, Graduate School of General Studies, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Sangeun Jeon
- Department of Chemistry, Graduate School of General Studies, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University, College of Medicine, Suwon 2066, Republic of Korea
| | - Han-Woo Kim
- Unit of Practical Applications, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - T Doohun Kim
- Department of Chemistry, Graduate School of General Studies, Sookmyung Women's University, Seoul 04310, Republic of Korea.
| |
Collapse
|
3
|
Martins PA, Pacheco TF, de Camargo BR, De Marco JL, Salum TFC. Solid-state fermentation production and characterization of an alkaline lipase from a newly isolated Burkholderia gladioli strain. Prep Biochem Biotechnol 2021; 52:70-79. [PMID: 33941018 DOI: 10.1080/10826068.2021.1910959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The newly isolated Burkholderia gladioli BRM58833 strain was shown to secrete an alkaline lipase highly active and stable in organic solvents. Lipase production was optimized through the cultivation of the strain by solid-state fermentation in wheat bran. The lipase extraction conditions were also optimized. The low-cost extract obtained has shown a high hydrolytic activity of 1096.7 ± 39.3 U·gds-1 (units per gram of dry solids) against pNPP and 374.2 ± 20.4 U·gds-1 against triolein. Proteomic analysis revealed the optimized extract is composed of two esterases and three true lipases, showing a preference for long-chain substrates. The highest activity was obtained at 50 °C and pH 9. However, the extract maintained more than 50% of its maximum activity between pH 8.0 and 10.0 and throughout the whole temperature range evaluated (32-70 °C). The enzymes were inhibited by SDS, EDTA, ZnSO4 and FeCl3 and activated by FeSO4, MgCl2 and BaCl2. The lipases conserved their activity when incubated in solvents as acetonitrile, diethyl ether, n-heptane n-hexane, toluene, methanol and t-butanol. The resistance of these lipases to solvents and expressive thermostability when compared to other lipases, reveal their potential both in hydrolysis reactions and in synthesis of esters.
Collapse
Affiliation(s)
- Pedro Alves Martins
- Embrapa Agroenergia, Parque Estação Biológica - PqEB, Brasília-DF, Brazil.,Instituto de Ciências Biológicas, Universidade de Brasília, Brasília-DF, Brazil
| | | | | | | | | |
Collapse
|
4
|
Dalal V, Kumar P, Rakhaminov G, Qamar A, Fan X, Hunter H, Tomar S, Golemi-Kotra D, Kumar P. Repurposing an Ancient Protein Core Structure: Structural Studies on FmtA, a Novel Esterase of Staphylococcus aureus. J Mol Biol 2019; 431:3107-3123. [DOI: 10.1016/j.jmb.2019.06.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 06/15/2019] [Accepted: 06/18/2019] [Indexed: 11/28/2022]
|
5
|
Characterization of phthalate reductase from Ralstonia eutropha CH34 and in silico study of phthalate dioxygenase and phthalate reductase interaction. J Mol Graph Model 2019; 90:161-170. [DOI: 10.1016/j.jmgm.2019.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/03/2019] [Accepted: 05/03/2019] [Indexed: 12/17/2022]
|
6
|
Goins CM, Dajnowicz S, Smith MD, Parks JM, Ronning DR. Mycolyltransferase from Mycobacterium tuberculosis in covalent complex with tetrahydrolipstatin provides insights into antigen 85 catalysis. J Biol Chem 2018; 293:3651-3662. [PMID: 29352107 PMCID: PMC5846135 DOI: 10.1074/jbc.ra117.001681] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Indexed: 01/07/2023] Open
Abstract
Mycobacterium tuberculosis antigen 85 (Ag85) enzymes catalyze the transfer of mycolic acid (MA) from trehalose monomycolate to produce the mycolyl arabinogalactan (mAG) or trehalose dimycolate (TDM). These lipids define the protective mycomembrane of mycobacteria. The current model of substrate binding within the active sites of Ag85s for the production of TDM is not sterically and geometrically feasible; additionally, this model does not account for the production of mAG. Furthermore, this model does not address how Ag85s limit the hydrolysis of the acyl-enzyme intermediate while catalyzing acyl transfer. To inform an updated model, we obtained an Ag85 acyl-enzyme intermediate structure that resembles the mycolated form. Here, we present a 1.45-Å X-ray crystal structure of M. tuberculosis Ag85C covalently modified by tetrahydrolipstatin (THL), an esterase inhibitor that suppresses M. tuberculosis growth and mimics structural attributes of MAs. The mode of covalent inhibition differs from that observed in the reversible inhibition of the human fatty-acid synthase by THL. Similarities between the Ag85-THL structure and previously determined Ag85C structures suggest that the enzyme undergoes structural changes upon acylation, and positioning of the peptidyl arm of THL limits hydrolysis of the acyl-enzyme adduct. Molecular dynamics simulations of the modeled mycolated-enzyme form corroborate the structural analysis. From these findings, we propose an alternative arrangement of substrates that rectifies issues with the previous model and suggest a direct role for the β-hydroxy of MA in the second half-reaction of Ag85 catalysis. This information affords the visualization of a complete mycolyltransferase catalytic cycle.
Collapse
Affiliation(s)
- Christopher M. Goins
- From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606-3390
| | - Steven Dajnowicz
- From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606-3390, ,Biology and Soft Matter Division and
| | - Micholas D. Smith
- University of Tennessee and Oak Ridge National Laboratory (UT/ORNL) Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, and ,Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Jerry M. Parks
- University of Tennessee and Oak Ridge National Laboratory (UT/ORNL) Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, and
| | - Donald R. Ronning
- From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606-3390, , To whom correspondence should be addressed:
Dept. of Chemistry and Biochemistry, University of Toledo, 2801 W. Bancroft St., Toledo, OH 43606-3390. Tel.:
419-530-1585; E-mail:
| |
Collapse
|
7
|
Palló A, Oláh J, Gráczer E, Merli A, Závodszky P, Weiss MS, Vas M. Structural and energetic basis of isopropylmalate dehydrogenase enzyme catalysis. FEBS J 2014; 281:5063-76. [PMID: 25211160 DOI: 10.1111/febs.13044] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/06/2014] [Accepted: 09/08/2014] [Indexed: 01/17/2023]
Abstract
UNLABELLED The three-dimensional structure of the enzyme 3-isopropylmalate dehydrogenase from the bacterium Thermus thermophilus in complex with Mn(2+) , its substrate isopropylmalate and its co-factor product NADH at 2.0 Å resolution features a fully closed conformation of the enzyme. Upon closure of the two domains, the substrate and the co-factor are brought into precise relative orientation and close proximity, with a distance between the C2 atom of the substrate and the C4N atom of the pyridine ring of the co-factor of approximately 3.0 Å. The structure further shows binding of a K(+) ion close to the active site, and provides an explanation for its known activating effect. Hence, this structure is an excellent mimic for the enzymatically competent complex. Using high-level QM/MM calculations, it may be demonstrated that, in the observed arrangement of the reactants, transfer of a hydride from the C2 atom of 3-isopropylmalate to the C4N atom of the pyridine ring of NAD(+) is easily possible, with an activation energy of approximately 15 kcal·mol(-1) . The activation energy increases by approximately 4-6 kcal·mol(-1) when the K(+) ion is omitted from the calculations. In the most plausible scenario, prior to hydride transfer the ε-amino group of Lys185 acts as a general base in the reaction, aiding the deprotonation reaction of 3-isopropylmalate prior to hydride transfer by employing a low-barrier proton shuttle mechanism involving a water molecule. DATABASE Structural data have been submitted to the Protein Data Bank under accession number 4F7I.
Collapse
Affiliation(s)
- Anna Palló
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | | | | | | | | | | | | |
Collapse
|
8
|
Yamabe S, Zeng G, Guan W, Sakaki S. Substrate dependent reaction channels of the Wolff-Kishner reduction reaction: A theoretical study. Beilstein J Org Chem 2014; 10:259-70. [PMID: 24605145 PMCID: PMC3943666 DOI: 10.3762/bjoc.10.21] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/18/2013] [Indexed: 11/23/2022] Open
Abstract
Wolff–Kishner reduction reactions were investigated by DFT calculations for the first time. B3LYP/6-311+G(d,p) SCRF=(PCM, solvent = 1,2-ethanediol) optimizations were carried out. To investigate the role of the base catalyst, the base-free reaction was examined by the use of acetone, hydrazine (H2N–NH2) and (H2O)8. A ready reaction channel of acetone → acetone hydrazine (Me2C=N–NH2) was obtained. The channel involves two likely proton-transfer routes. However, it was found that the base-free reaction was unlikely at the N2 extrusion step from the isopropyl diimine intermediate (Me2C(H)–N=N–H). Two base-catalyzed reactions were investigated by models of the ketone, H2N–NH2 and OH−(H2O)7. Here, ketones are acetone and acetophenone. While routes of the ketone → hydrazone → diimine are similar, those from the diimines are different. From the isopropyl diimine, the N2 extrusion and the C–H bond formation takes place concomitantly. The concomitance leads to the propane product concertedly. From the (1-phenyl)ethyl substituted diimine, a carbanion intermediate is formed. The para carbon of the phenyl ring of the anion is subject to the protonation, which leads to a 3-ethylidene-1,4-cyclohexadiene intermediate. Its [1,5]-hydrogen migration gives the ethylbenzene product. For both ketone substrates, the diimines undergoing E2 reactions were found to be key intermediates.
Collapse
Affiliation(s)
- Shinichi Yamabe
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano-Nishihiraki-cho 34-4, Sakyo-ku, Kyoto 606-8103, JAPAN
| | - Guixiang Zeng
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano-Nishihiraki-cho 34-4, Sakyo-ku, Kyoto 606-8103, JAPAN
| | - Wei Guan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano-Nishihiraki-cho 34-4, Sakyo-ku, Kyoto 606-8103, JAPAN
| | - Shigeyoshi Sakaki
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano-Nishihiraki-cho 34-4, Sakyo-ku, Kyoto 606-8103, JAPAN
| |
Collapse
|
9
|
Krámos B, Oláh J. Enolization as an Alternative Proton Delivery Pathway in Human Aromatase (P450 19A1). J Phys Chem B 2014; 118:390-405. [DOI: 10.1021/jp407365x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Balázs Krámos
- Department of Inorganic and
Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary
| | - Julianna Oláh
- Department of Inorganic and
Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary
| |
Collapse
|
10
|
Kim S, Duc Ngo T, Kim KK, Kim TD. Characterization, crystallization and preliminary X-ray diffraction analysis of an (S)-specific esterase (pfEstA) from Pseudomonas fluorescens KCTC 1767: enantioselectivity for potential industrial applications. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1374-7. [PMID: 23143253 PMCID: PMC3515385 DOI: 10.1107/s1744309112040626] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 09/26/2012] [Indexed: 11/10/2022]
Abstract
The structures and reaction mechanisms of enantioselective hydrolases, which can be used in industrial applications such as biotransformations, are largely unknown. Here, the X-ray crystallographic study of a novel (S)-specific esterase (pfEstA) from Pseudomonas fluorescens KCTC 1767, which can be used in the production of (S)-ketoprofen, is described. Multiple sequence alignments with other hydrolases revealed that pfEstA contains a conserved Ser67 within the S-X-X-K motif as well as a highly conserved Tyr156. Recombinant protein containing an N-terminal His tag was expressed in Escherichia coli, purified to homogeneity and characterized using SDS-PAGE, MALDI-TOF MS and enantioselective analysis. pfEstA was crystallized using a solution consisting of 1 M sodium citrate, 0.1 M CHES pH 9.5, and X-ray diffraction data were collected to a resolution of 1.9 Å with an Rmerge of 7.9%. The crystals of pfEstA belonged to space group P2(1)2(1)2(1), with unit-cell parameters a=65.31, b=82.13, c=100.41 Å, α=β=γ=90°.
Collapse
Affiliation(s)
- Seulgi Kim
- Department of Molecular Science and Technology, Graduate School of Interdisciplinary Programs, Ajou University, Suwon 443-749, Republic of Korea
| | - Tri Duc Ngo
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - T. Doohun Kim
- Department of Molecular Science and Technology, Graduate School of Interdisciplinary Programs, Ajou University, Suwon 443-749, Republic of Korea
| |
Collapse
|