1
|
Resurrection of ancestral effector caspases identifies novel networks for evolution of substrate specificity. Biochem J 2020; 476:3475-3492. [PMID: 31675069 PMCID: PMC6874516 DOI: 10.1042/bcj20190625] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/30/2019] [Accepted: 11/01/2019] [Indexed: 12/18/2022]
Abstract
Apoptotic caspases evolved with metazoans more than 950 million years ago (MYA), and a series of gene duplications resulted in two subfamilies consisting of initiator and effector caspases. The effector caspase genes (caspases-3, -6, and -7) were subsequently fixed into the Chordata phylum more than 650 MYA when the gene for a common ancestor (CA) duplicated, and the three effector caspases have persisted throughout mammalian evolution. All caspases prefer an aspartate residue at the P1 position of substrates, so each caspase evolved discrete cellular roles through changes in substrate recognition at the P4 position combined with allosteric regulation. We examined the evolution of substrate specificity in caspase-6, which prefers valine at the P4 residue, compared with caspases-3 and -7, which prefer aspartate, by reconstructing the CA of effector caspases (AncCP-Ef1) and the CA of caspase-6 (AncCP-6An). We show that AncCP-Ef1 is a promiscuous enzyme with little distinction between Asp, Val, or Leu at P4. The specificity of caspase-6 was defined early in its evolution, where AncCP-6An demonstrates a preference for Val over Asp at P4. Structures of AncCP-Ef1 and of AncCP-6An show a network of charged amino acids near the S4 pocket that, when combined with repositioning a flexible active site loop, resulted in a more hydrophobic binding pocket in AncCP-6An. The ancestral protein reconstructions show that the caspase-hemoglobinase fold has been conserved for over 650 million years and that only three substitutions in the scaffold are necessary to shift substrate selection toward Val over Asp.
Collapse
|
2
|
Mishra VK, Mishra S. Flipped regiospecificity in L434F mutant of 8-lipoxygenase. Phys Chem Chem Phys 2020; 22:16013-16022. [DOI: 10.1039/d0cp02351e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Conformational change of Phe434 controls regio- and stereospecificity of L434F lipoxygenase catalysis.
Collapse
Affiliation(s)
- Vipin Kumar Mishra
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur
- India
| | - Sabyashachi Mishra
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur
- India
| |
Collapse
|
3
|
Li Q, Yan Y, Liu X, Zhang Z, Tian J, Wu N. Enhancing thermostability of a psychrophilic alpha-amylase by the structural energy optimization in the trajectories of molecular dynamics simulations. Int J Biol Macromol 2020; 142:624-633. [DOI: 10.1016/j.ijbiomac.2019.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/18/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022]
|
4
|
Bilal M, Iqbal HMN. State-of-the-art strategies and applied perspectives of enzyme biocatalysis in food sector - current status and future trends. Crit Rev Food Sci Nutr 2020; 60:2052-2066. [PMID: 31210055 DOI: 10.1080/10408398.2019.1627284] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
With the recent progress in biotechnology, a wide variety of novel enzymes with unique physicochemical properties and diverse applications has been introduced, and new application list continues to extend in the future. Enzymes obtained from microorganisms, including bacteria, fungi, yeast are widely applied in numerous food formulations for intensifying their texture and taste. Owing to several desirable characteristics such as easy, cost-efficient and stable production, microbial-derived enzymes are preferred source in contrast to animals or plants. Enzymatic processes have a considerable impact in controlling the characteristics such as (1) physiochemical properties, (2) rheological functionalities, (3) facile process as compared to the chemical-based processing, (4) no or minimal consumption of harsh chemicals, (5) overall cost-effective ratio, (6) sensory and flavor qualities, and (7) intensifying the stability, shelf life and overall quality of the product, etc. in the food industry. Also, enzyme-catalyzed processing has also been designed for new food applications such as extraction of bioactive compounds, nutrient-rich and texture improved foods production, and eliminating food safety hazards. Herein, we reviewed recent applications of food-processing enzymes and highlighted promising technologies to diversify their application range in food industries. Immobilization technology enabled biocatalysts to be used cost-effectively due to reusability with negligible or no activity loss. Integrated progress in novel enzyme discovery, and recombinant DNA technology, as well as protein engineering and bioprocess engineering strategies, are believed to rapidly propagate biocatalysis at industrial-scale food processing or green and sustainable chemical manufacturing.
Collapse
Affiliation(s)
- Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Hafiz M N Iqbal
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, N.L., Mexico
| |
Collapse
|
5
|
García-López V, Liu D, Tour JM. Light-Activated Organic Molecular Motors and Their Applications. Chem Rev 2019; 120:79-124. [PMID: 31849216 DOI: 10.1021/acs.chemrev.9b00221] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Molecular motors are at the heart of cellular machinery, and they are involved in converting chemical and light energy inputs into efficient mechanical work. From a synthetic perspective, the most advanced molecular motors are rotators that are activated by light wherein a molecular subcomponent rotates unidirectionally around an axis. The mechanical work produced by arrays of molecular motors can be used to induce a macroscopic effect. Light activation offers advantages over biological chemically activated molecular motors because one can direct precise spatiotemporal inputs while conducting reactions in the gas phase, in solution and in vacuum, while generating no chemical byproducts or waste. In this review, we describe the origins of the first light-activated rotary motors and their modes of function, the structural modifications that led to newer motor designs with optimized rotary properties at variable activation wavelengths. Presented are molecular motor attachments to surfaces, their insertion into supramolecular structures and photomodulating materials, their use in catalysis, and their action in biological environments to produce exciting new prospects for biomedicine.
Collapse
|
6
|
Mishra VK, Mishra S. Origin of Regio- and Stereospecific Catalysis by 8-Lipoxygenase. J Phys Chem B 2019; 123:10605-10621. [PMID: 31775504 DOI: 10.1021/acs.jpcb.9b07917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Vipin Kumar Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Sabyashachi Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| |
Collapse
|
7
|
Debnath M, Sasmal S, Podder D, Haldar D. Pentapeptide Nanoreactor as a Platform for Halogenations, Diels-Alder Reaction, and Morita-Baylis-Hillman Reaction. ACS OMEGA 2019; 4:13872-13878. [PMID: 31497704 PMCID: PMC6714524 DOI: 10.1021/acsomega.9b01393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/30/2019] [Indexed: 05/15/2023]
Abstract
A pentapeptide nanoreactor has been designed and synthesized as a platform to carry out the traditional organic reactions such as bromination, iodination, cycloaddition, and condensation reactions. The pentapeptide Boc-Phe-Phe-Aib-Phe-Phe-OMe with a supramolecular helical structure and π-rich channel provides nanoconfinements and thus facilitates the organic reactions. Bromination and iodination of aniline take place without any halogen carrier (Lewis acid) in the pentapeptide platform. Iodination produced p-iodoaniline only. The Diels-Alder reaction between furan and maleic anhydride increased 2-fold in the pentapeptide platform and the Morita-Baylis-Hillman reaction of benzaldehyde and ethyl acrylate in methanol enhanced 1.5-fold.
Collapse
|
8
|
Lee C, Lee H, Lee S, Jeon HG, Jeong KS. Encapsulation of dihydrogenphosphate ions as a cyclic dimer to the cavities of site-specifically modified indolocarbazole-pyridine foldamers. Org Chem Front 2019. [DOI: 10.1039/c8qo01307a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Site-specifically modified aromatic foldamers can encapsulate dihydrogen phosphate ions as a cyclic dimer via the formation of twelve hydrogen bonds.
Collapse
Affiliation(s)
- Chaeeun Lee
- Department of Chemistry
- Yonsei University
- Seoul 03722
- Korea
| | - Hyemi Lee
- Department of Chemistry
- Yonsei University
- Seoul 03722
- Korea
| | - Seungwon Lee
- Department of Chemistry
- Yonsei University
- Seoul 03722
- Korea
| | - Hae-Geun Jeon
- Department of Chemistry
- Yonsei University
- Seoul 03722
- Korea
| | - Kyu-Sung Jeong
- Department of Chemistry
- Yonsei University
- Seoul 03722
- Korea
| |
Collapse
|
9
|
Rational Engineering of a Cold-Adapted α-Amylase from the Antarctic Ciliate Euplotes focardii for Simultaneous Improvement of Thermostability and Catalytic Activity. Appl Environ Microbiol 2017; 83:AEM.00449-17. [PMID: 28455329 PMCID: PMC5478988 DOI: 10.1128/aem.00449-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/18/2017] [Indexed: 12/04/2022] Open
Abstract
The α-amylases are endo-acting enzymes that hydrolyze starch by randomly cleaving the 1,4-α-d-glucosidic linkages between the adjacent glucose units in a linear amylose chain. They have significant advantages in a wide range of applications, particularly in the food industry. The eukaryotic α-amylase isolated from the Antarctic ciliated protozoon Euplotes focardii (EfAmy) is an alkaline enzyme, different from most of the α-amylases characterized so far. Furthermore, EfAmy has the characteristics of a psychrophilic α-amylase, such as the highest hydrolytic activity at a low temperature and high thermolability, which is the major drawback of cold-active enzymes in industrial applications. In this work, we applied site-directed mutagenesis combined with rational design to generate a cold-active EfAmy with improved thermostability and catalytic efficiency at low temperatures. We engineered two EfAmy mutants. In one mutant, we introduced Pro residues on the A and B domains in surface loops. In the second mutant, we changed Val residues to Thr close to the catalytic site. The aim of these substitutions was to rigidify the molecular structure of the enzyme. Furthermore, we also analyzed mutants containing these combined substitutions. Biochemical enzymatic assays of engineered versions of EfAmy revealed that the combination of mutations at the surface loops increased the thermostability and catalytic efficiency of the enzyme. The possible mechanisms responsible for the changes in the biochemical properties are discussed by analyzing the three-dimensional structural model. IMPORTANCE Cold-adapted enzymes have high specific activity at low and moderate temperatures, a property that can be extremely useful in various applications as it implies a reduction in energy consumption during the catalyzed reaction. However, the concurrent high thermolability of cold-adapted enzymes often limits their applications in industrial processes. The α-amylase from the psychrophilic Antarctic ciliate Euplotes focardii (named EfAmy) is a cold-adapted enzyme with optimal catalytic activity in an alkaline environment. These unique features distinguish it from most α-amylases characterized so far. In this work, we engineered a novel EfAmy with improved thermostability, substrate binding affinity, and catalytic efficiency to various extents, without impacting its pH preference. These characteristics can be considered important properties for use in the food, detergent, and textile industries and in other industrial applications. The enzyme engineering strategy developed in this study may also provide useful knowledge for future optimization of molecules to be used in particular industrial applications.
Collapse
|
10
|
Jez JM. Revisiting protein structure, function, and evolution in the genomic era. J Invertebr Pathol 2017; 142:11-15. [DOI: 10.1016/j.jip.2016.07.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 06/04/2016] [Accepted: 07/28/2016] [Indexed: 02/05/2023]
|
11
|
Beier A, Bordewick S, Genz M, Schmidt S, van den Bergh T, Peters C, Joosten HJ, Bornscheuer UT. Switch in Cofactor Specificity of a Baeyer-Villiger Monooxygenase. Chembiochem 2016; 17:2312-2315. [PMID: 27735116 DOI: 10.1002/cbic.201600484] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Indexed: 11/05/2022]
Abstract
Baeyer-Villiger monooxygenases (BVMOs) catalyze the oxidation of ketones to esters or lactones by using molecular oxygen and a cofactor. Type I BVMOs display a strong preference for NADPH. However, for industrial purposes NADH is the preferred cofactor, as it is ten times cheaper and more stable. Thus, we created a variant of the cyclohexanone monooxygenase from Acinetobacter sp. NCIMB 9871 (CHMOAcineto ); this used NADH 4200-fold better than NADPH. By combining structure analysis, sequence alignment, and literature data, 21 residues in proximity of the cofactor were identified and targeted for mutagenesis. Two combinatorial variants bearing three or four mutations showed higher conversions of cyclohexanone with NADH (79 %) compared to NADPH (58 %) as well as specificity. The structural reasons for this switch in cofactor specificity of a type I BVMO are especially a hydrogen-bond network coordinating the two hydroxy groups of NADH through direct interactions and bridging water molecules.
Collapse
Affiliation(s)
- Andy Beier
- Institute of Biochemistry, Department of Biotechnology and Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Sven Bordewick
- Institute of Biochemistry, Department of Biotechnology and Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Maika Genz
- Institute of Biochemistry, Department of Biotechnology and Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Sandy Schmidt
- Institute of Biochemistry, Department of Biotechnology and Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Tom van den Bergh
- Bio-Prodict, Nieuwe Marktstraat 54E, 6511 AA, Nijmegen, The Netherlands
| | - Christin Peters
- Institute of Biochemistry, Department of Biotechnology and Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Henk-Jan Joosten
- Bio-Prodict, Nieuwe Marktstraat 54E, 6511 AA, Nijmegen, The Netherlands
| | - Uwe T Bornscheuer
- Institute of Biochemistry, Department of Biotechnology and Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| |
Collapse
|
12
|
Redesigning alcohol dehydrogenases/reductases for more efficient biosynthesis of enantiopure isomers. Biotechnol Adv 2015; 33:1671-84. [DOI: 10.1016/j.biotechadv.2015.08.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 08/11/2015] [Accepted: 08/12/2015] [Indexed: 11/20/2022]
|
13
|
Mortezaei S, Catarineu NR, Duan X, Hu C, Canary JW. Redox-configurable ambidextrous catalysis: structural and mechanistic insight. Chem Sci 2015; 6:5904-5912. [PMID: 29861915 PMCID: PMC5950827 DOI: 10.1039/c5sc02144h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 07/13/2015] [Indexed: 01/19/2023] Open
Abstract
A helically chiral copper complex is used as a switchable asymmetric catalyst capable of delivering either enantiomer of a Michael addition reaction.
A ligand capable of adopting two pseudo-enantiomeric helically chiral states when bound to copper has been applied as an asymmetric catalyst in the Michael addition of malonate substrates to nitrostyrenes. The absolute configuration of the helically chiral ligand is inverted upon oxidation/reduction of the copper center. In this way, the handedness of the Michael addition product (R/S) can be selected based on the handedness of the catalyst (Λ/Δ). Exciton coupled circular dichroism (ECCD) was used to identify which of the two pseudo-enantiomeric forms the catalyst adopted after reduction/oxidation, with additional support from X-ray crystallographic data. The synthesis of the ligand was achieved in five steps with an overall 61% yield. Enantiomeric excesses of the Michael addition products of up to 72% (S) and 70% (R) were obtained in acetonitrile. The ability to choose the handedness of the product based on the chiral state of the catalyst has been demonstrated with several different solvents, bases, nitrostyrene/malonate substrates, and prochiral malonate substrates. A combination of molecular modelling, crystal structure and kinetic data suggest that one urea moiety of the catalyst ligand likely binds the nitrostyrene substrate while blocking the Re face of the nitrostyrene in the transition state.
Collapse
Affiliation(s)
- Shahab Mortezaei
- Department of Chemistry , New York University , New York , New York 10003 , USA .
| | - Noelle R Catarineu
- Department of Chemistry , New York University , New York , New York 10003 , USA .
| | - Xueyou Duan
- Department of Chemistry , New York University , New York , New York 10003 , USA .
| | - Chunhua Hu
- Department of Chemistry , New York University , New York , New York 10003 , USA .
| | - James W Canary
- Department of Chemistry , New York University , New York , New York 10003 , USA .
| |
Collapse
|
14
|
Identification and characterization of bifunctional proline racemase/hydroxyproline epimerase from archaea: discrimination of substrates and molecular evolution. PLoS One 2015; 10:e0120349. [PMID: 25786142 PMCID: PMC4364671 DOI: 10.1371/journal.pone.0120349] [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] [Received: 10/31/2014] [Accepted: 01/21/2015] [Indexed: 12/14/2022] Open
Abstract
Proline racemase (ProR) is a member of the pyridoxal 5’-phosphate-independent racemase family, and is involved in the Stickland reaction (fermentation) in certain clostridia as well as the mechanisms underlying the escape of parasites from host immunity in eukaryotic Trypanosoma. Hydroxyproline epimerase (HypE), which is in the same protein family as ProR, catalyzes the first step of the trans-4-hydroxy-L-proline metabolism of bacteria. Their substrate specificities were previously considered to be very strict, in spite of similarities in their structures and catalytic mechanisms, and no racemase/epimerase from the ProR superfamily has been found in archaea. We here characterized the ProR-like protein (OCC_00372) from the hyperthermophilic archaeon, Thermococcus litoralis (TlProR). This protein could reversibly catalyze not only the racemization of proline, but also the epimerization of 4-hydroxyproline and 3-hydroxyproline with similar kinetic constants. Among the four (putative) ligand binding sites, one amino acid substitution was detected between TlProR (tryptophan at the position of 241) and natural ProR (phenylalanine). The W241F mutant showed a significant preference for proline over hydroxyproline, suggesting that this (hydrophobic and bulky) tryptophan residue played an importance role in the recognition of hydroxyproline (more hydrophilic and bulky than proline), and substrate specificity for hydroxyproline was evolutionarily acquired separately between natural HypE and ProR. A phylogenetic analysis indicated that such unique broad substrate specificity was derived from an ancestral enzyme of this superfamily.
Collapse
|
15
|
Yang G, Ding Y. Recent advances in biocatalyst discovery, development and applications. Bioorg Med Chem 2014; 22:5604-12. [DOI: 10.1016/j.bmc.2014.06.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/13/2014] [Accepted: 06/17/2014] [Indexed: 12/25/2022]
|
16
|
Watanabe S, Tozawa Y, Watanabe Y. Ornithine cyclodeaminase/μ-crystallin homolog from the hyperthermophilic archaeon Thermococcus litoralis functions as a novel Δ(1)-pyrroline-2-carboxylate reductase involved in putative trans-3-hydroxy-l-proline metabolism. FEBS Open Bio 2014; 4:617-26. [PMID: 25161870 PMCID: PMC4141209 DOI: 10.1016/j.fob.2014.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/25/2014] [Accepted: 07/07/2014] [Indexed: 11/18/2022] Open
Abstract
Ornithine cyclodeaminase homolog from an archeon was characterized biochemically. This protein functions as a novel Δ1-pyrroline-2-carboxylate reductase. This enzyme is probably involved in trans-3-hydroxy-l-proline metabolism as in bacteria and mammals.
l-Ornithine cyclodeaminase (OCD) is involved in l-proline biosynthesis and catalyzes the unique deaminating cyclization of l-ornithine to l-proline via a Δ1-pyrroline-2-carboxyrate (Pyr2C) intermediate. Although this pathway functions in only a few bacteria, many archaea possess OCD-like genes (proteins), among which only AF1665 protein (gene) from Archaeoglobus fulgidus has been characterized as an NAD+-dependent l-alanine dehydrogenase (AfAlaDH). However, the physiological role of OCD-like proteins from archaea has been unclear. Recently, we revealed that Pyr2C reductase, involved in trans-3-hydroxy-l-proline (T3LHyp) metabolism of bacteria, belongs to the OCD protein superfamily and catalyzes only the reduction of Pyr2C to l-proline (no OCD activity) [FEBS Open Bio (2014) 4, 240–250]. In this study, based on bioinformatics analysis, we assumed that the OCD-like gene from Thermococcus litoralis DSM 5473 is related to T3LHyp and/or proline metabolism (TlLhpI). Interestingly, TlLhpI showed three different enzymatic activities: AlaDH; N-methyl-l-alanine dehydrogenase; Pyr2C reductase. Kinetic analysis suggested strongly that Pyr2C is the preferred substrate. In spite of their similar activity, TlLhpI had a poor phylogenetic relationship to the bacterial and mammalian reductases for Pyr2C and formed a close but distinct subfamily to AfAlaDH, indicating convergent evolution. Introduction of several specific amino acid residues for OCD and/or AfAlaDH by site-directed mutagenesis had marked effects on both AlaDH and Pyr2C reductase activities. The OCC_00387 gene, clustered with the TlLhpI gene on the genome, encoded T3LHyp dehydratase, homologous to the bacterial and mammalian enzymes. To our knowledge, this is the first report of T3LHyp metabolism from archaea.
Collapse
Affiliation(s)
- Seiya Watanabe
- Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
- Corresponding author. Tel./fax: +81 89 946 9848.
| | - Yuzuru Tozawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Yasuo Watanabe
- Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
| |
Collapse
|
17
|
Piazzetta P, Marino T, Russo N. Insight into the promiscuous activity of human carbonic anhydrase against the cyanic acid substrate from a combined QM and QM/MM investigation. Phys Chem Chem Phys 2014; 16:16671-6. [DOI: 10.1039/c4cp02363c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
18
|
Alderson RG, De Ferrari L, Mavridis L, McDonagh JL, Mitchell JBO, Nath N. Enzyme informatics. Curr Top Med Chem 2014; 12:1911-23. [PMID: 23116471 DOI: 10.2174/156802612804547353] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 09/12/2012] [Accepted: 09/15/2012] [Indexed: 12/18/2022]
Abstract
Over the last 50 years, sequencing, structural biology and bioinformatics have completely revolutionised biomolecular science, with millions of sequences and tens of thousands of three dimensional structures becoming available. The bioinformatics of enzymes is well served by, mostly free, online databases. BRENDA describes the chemistry, substrate specificity, kinetics, preparation and biological sources of enzymes, while KEGG is valuable for understanding enzymes and metabolic pathways. EzCatDB, SFLD and MACiE are key repositories for data on the chemical mechanisms by which enzymes operate. At the current rate of genome sequencing and manual annotation, human curation will never finish the functional annotation of the ever-expanding list of known enzymes. Hence there is an increasing need for automated annotation, though it is not yet widespread for enzyme data. In contrast, functional ontologies such as the Gene Ontology already profit from automation. Despite our growing understanding of enzyme structure and dynamics, we are only beginning to be able to design novel enzymes. One can now begin to trace the functional evolution of enzymes using phylogenetics. The ability of enzymes to perform secondary functions, albeit relatively inefficiently, gives clues as to how enzyme function evolves. Substrate promiscuity in enzymes is one example of imperfect specificity in protein-ligand interactions. Similarly, most drugs bind to more than one protein target. This may sometimes result in helpful polypharmacology as a drug modulates plural targets, but also often leads to adverse side-effects. Many chemoinformatics approaches can be used to model the interactions between druglike molecules and proteins in silico. We can even use quantum chemical techniques like DFT and QM/MM to compute the structural and energetic course of enzyme catalysed chemical reaction mechanisms, including a full description of bond making and breaking.
Collapse
Affiliation(s)
- Rosanna G Alderson
- Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, Purdie Building, University of St Andrews, North Haugh, St Andrews, Scotland, UK
| | | | | | | | | | | |
Collapse
|
19
|
Paul CE, Arends IWCE, Hollmann F. Is Simpler Better? Synthetic Nicotinamide Cofactor Analogues for Redox Chemistry. ACS Catal 2014. [DOI: 10.1021/cs4011056] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Caroline E. Paul
- Department of Biotechnology, Delft University of Technology, Julianalaan
136, 2628BL Delft, The Netherlands
| | - Isabel W. C. E. Arends
- Department of Biotechnology, Delft University of Technology, Julianalaan
136, 2628BL Delft, The Netherlands
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Julianalaan
136, 2628BL Delft, The Netherlands
| |
Collapse
|
20
|
Marino T, Russo N, Toscano M. Catalytic Mechanism of the Arylsulfatase Promiscuous Enzyme fromPseudomonas Aeruginosa. Chemistry 2012; 19:2185-92. [DOI: 10.1002/chem.201201943] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 11/06/2012] [Indexed: 11/11/2022]
|
21
|
Mortezaei S, Catarineu NR, Canary JW. A Redox-Reconfigurable, Ambidextrous Asymmetric Catalyst. J Am Chem Soc 2012; 134:8054-7. [DOI: 10.1021/ja302283s] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Shahab Mortezaei
- Department of Chemistry, New York University, New York, New York 10003, United
States
| | - Noelle R. Catarineu
- Department of Chemistry, New York University, New York, New York 10003, United
States
| | - James W. Canary
- Department of Chemistry, New York University, New York, New York 10003, United
States
| |
Collapse
|
22
|
Bhave DP, Hong JA, Keller RL, Krebs C, Carroll KS. Iron-sulfur cluster engineering provides insight into the evolution of substrate specificity among sulfonucleotide reductases. ACS Chem Biol 2012; 7:306-15. [PMID: 22023093 PMCID: PMC3288176 DOI: 10.1021/cb200261n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Assimilatory sulfate reduction supplies prototrophic organisms with reduced sulfur that is required for the biosynthesis of all sulfur-containing metabolites, including cysteine and methionine. The reduction of sulfate requires its activation via an ATP-dependent activation to form adenosine-5'-phosphosulfate (APS). Depending on the species, APS can be reduced directly to sulfite by APS reductase (APR) or undergo a second phosphorylation to yield 3'-phosphoadenosine-5'-phosphosulfate (PAPS), the substrate for PAPS reductase (PAPR). These essential enzymes have no human homologue, rendering them attractive targets for the development of novel antibacterial drugs. APR and PAPR share sequence and structure homology as well as a common catalytic mechanism, but the enzymes are distinguished by two features, namely, the amino acid sequence of the phosphate-binding loop (P-loop) and an iron-sulfur cofactor in APRs. On the basis of the crystal structures of APR and PAPR, two P-loop residues are proposed to determine substrate specificity; however, this hypothesis has not been tested. In contrast to this prevailing view, we report here that the P-loop motif has a modest effect on substrate discrimination. Instead, by means of metalloprotein engineering, spectroscopic, and kinetic analyses, we demonstrate that the iron-sulfur cluster cofactor enhances APS reduction by nearly 1000-fold, thereby playing a pivotal role in substrate specificity and catalysis. These findings offer new insights into the evolution of this enzyme family and extend the known functions of protein-bound iron-sulfur clusters.
Collapse
Affiliation(s)
- Devayani P. Bhave
- Chemical Biology Graduate Program, University of Michigan, Ann Arbor, Michigan, 48109-2216
| | - Jiyoung A. Hong
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109-2216
| | - Rebecca L. Keller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Kate S. Carroll
- Chemical Biology Graduate Program, University of Michigan, Ann Arbor, Michigan, 48109-2216
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109-2216
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458
| |
Collapse
|
23
|
Campbell E, Meredith M, Minteer SD, Banta S. Enzymatic biofuel cells utilizing a biomimetic cofactor. Chem Commun (Camb) 2012; 48:1898-900. [PMID: 22227738 DOI: 10.1039/c2cc16156g] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The performance of immobilized enzyme systems is often limited by cofactor diffusion and regeneration. Here, we demonstrate an engineered enzyme capable of utilizing the minimal cofactor nicotinamide mononucleotide (NMN(+)) to address these limitations. Significant gains in performance are observed with NMN(+) in immobilized systems, despite a decreased turnover rate with the minimal cofactor.
Collapse
Affiliation(s)
- Elliot Campbell
- Department of Chemical Engineering, Columbia University in the City of New York, New York, NY 10027, USA
| | | | | | | |
Collapse
|
24
|
Structure and mechanism of a cysteine sulfinate desulfinase engineered on the aspartate aminotransferase scaffold. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1824:339-49. [PMID: 22138634 DOI: 10.1016/j.bbapap.2011.10.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 10/27/2011] [Accepted: 10/28/2011] [Indexed: 11/23/2022]
Abstract
The joint substitution of three active-site residues in Escherichia coli (L)-aspartate aminotransferase increases the ratio of l-cysteine sulfinate desulfinase to transaminase activity 10(5)-fold. This change in reaction specificity results from combining a tyrosine-shift double mutation (Y214Q/R280Y) with a non-conservative substitution of a substrate-binding residue (I33Q). Tyr214 hydrogen bonds with O3 of the cofactor and is close to Arg374 which binds the α-carboxylate group of the substrate; Arg280 interacts with the distal carboxylate group of the substrate; and Ile33 is part of the hydrophobic patch near the entrance to the active site, presumably participating in the domain closure essential for the transamination reaction. In the triple-mutant enzyme, k(cat)' for desulfination of l-cysteine sulfinate increased to 0.5s(-1) (from 0.05s(-1) in wild-type enzyme), whereas k(cat)' for transamination of the same substrate was reduced from 510s(-1) to 0.05s(-1). Similarly, k(cat)' for β-decarboxylation of l-aspartate increased from<0.0001s(-1) to 0.07s(-1), whereas k(cat)' for transamination was reduced from 530s(-1) to 0.13s(-1). l-Aspartate aminotransferase had thus been converted into an l-cysteine sulfinate desulfinase that catalyzes transamination and l-aspartate β-decarboxylation as side reactions. The X-ray structures of the engineered l-cysteine sulfinate desulfinase in its pyridoxal-5'-phosphate and pyridoxamine-5'-phosphate form or liganded with a covalent coenzyme-substrate adduct identified the subtle structural changes that suffice for generating desulfinase activity and concomitantly abolishing transaminase activity toward dicarboxylic amino acids. Apparently, the triple mutation impairs the domain closure thus favoring reprotonation of alternative acceptor sites in coenzyme-substrate intermediates by bulk water.
Collapse
|
25
|
Abstract
An enzyme's substrate specificity is one of its most important characteristics. The quantitative comparison of broad-specificity enzymes requires the selection of a homogenous set of substrates for experimental testing, determination of substrate-specificity data and analysis using multivariate statistics. We describe a systematic analysis of the substrate specificities of nine wild-type and four engineered haloalkane dehalogenases. The enzymes were characterized experimentally using a set of 30 substrates selected using statistical experimental design from a set of nearly 200 halogenated compounds. Analysis of the activity data showed that the most universally useful substrates in the assessment of haloalkane dehalogenase activity are 1-bromobutane, 1-iodopropane, 1-iodobutane, 1,2-dibromoethane and 4-bromobutanenitrile. Functional relationships among the enzymes were explored using principal component analysis. Analysis of the untransformed specific activity data revealed that the overall activity of wild-type haloalkane dehalogenases decreases in the following order: LinB~DbjA>DhlA~DhaA~DbeA~DmbA>DatA~DmbC~DrbA. After transforming the data, we were able to classify haloalkane dehalogenases into four SSGs (substrate-specificity groups). These functional groups are clearly distinct from the evolutionary subfamilies, suggesting that phylogenetic analysis cannot be used to predict the substrate specificity of individual haloalkane dehalogenases. Structural and functional comparisons of wild-type and mutant enzymes revealed that the architecture of the active site and the main access tunnel significantly influences the substrate specificity of these enzymes, but is not its only determinant. The identification of other structural determinants of the substrate specificity remains a challenge for further research on haloalkane dehalogenases.
Collapse
|
26
|
Meyer D, Walter L, Kolter G, Pohl M, Müller M, Tittmann K. Conversion of Pyruvate Decarboxylase into an Enantioselective Carboligase with Biosynthetic Potential. J Am Chem Soc 2011; 133:3609-16. [PMID: 21341803 DOI: 10.1021/ja110236w] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Danilo Meyer
- Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
| | - Lydia Walter
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Geraldine Kolter
- Institute of Biotechnology 2, Research Centre Jülich, 52425 Jülich, Germany
| | - Martina Pohl
- Institute of Biotechnology 2, Research Centre Jülich, 52425 Jülich, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Kai Tittmann
- Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
| |
Collapse
|
27
|
Enhancement of xylitol production by attenuation of intracellular xylitol dehydrogenase activity in Candida tropicalis. Biotechnol Lett 2011; 33:1209-13. [DOI: 10.1007/s10529-011-0558-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2010] [Accepted: 01/31/2011] [Indexed: 10/18/2022]
|
28
|
Wang J, Feringa BL. Dynamic control of chiral space in a catalytic asymmetric reaction using a molecular motor. Science 2011; 331:1429-32. [PMID: 21310964 DOI: 10.1126/science.1199844] [Citation(s) in RCA: 472] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Enzymes and synthetic chiral catalysts have found widespread application to produce single enantiomers, but in situ switching of the chiral preference of a catalytic system is very difficult to achieve. Here, we report on a light-driven molecular motor with integrated catalytic functions in which the stepwise change in configuration during a 360° unidirectional rotary cycle governs the catalyst performance both with respect to activity and absolute stereocontrol in an asymmetric transformation. During one full rotary cycle, catalysts are formed that provide either racemic (R,S) or preferentially the R or the S enantiomer of the chiral product of a conjugate addition reaction. This catalytic system demonstrates how different molecular tasks can be performed in a sequential manner, with the sequence controlled by the directionality of a rotary cycle.
Collapse
Affiliation(s)
- Jiaobing Wang
- Centre for Systems Chemistry, Stratingh Institute for Chemistry and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen, Netherlands
| | | |
Collapse
|
29
|
Jez JM. Toward protein engineering for phytoremediation: possibilities and challenges. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2011; 13 Suppl 1:77-89. [PMID: 22046752 DOI: 10.1080/15226514.2011.568537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The combination of rational protein engineering and directed evolution techniques allow for the redesign of enzymes with tailored properties for use in environmental remediation. This review summarizes current molecular methods for either altering or improving protein function and highlights examples of how these methods can address bioremediation problems. Although much of the protein engineering applied to environmental clean-up employs microbial systems, there is great potential for and significant challenges to translating these approaches to plant systems for phytoremediation purposes. Protein engineering technologies combined with genomic information and metabolic engineering strategies hold promise for the design of plants and microbes to remediate organic and inorganic pollutants.
Collapse
Affiliation(s)
- Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA.
| |
Collapse
|
30
|
Merone L, Mandrich L, Porzio E, Rossi M, Müller S, Reiter G, Worek F, Manco G. Improving the promiscuous nerve agent hydrolase activity of a thermostable archaeal lactonase. BIORESOURCE TECHNOLOGY 2010; 101:9204-9212. [PMID: 20667718 DOI: 10.1016/j.biortech.2010.06.102] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 06/16/2010] [Accepted: 06/24/2010] [Indexed: 05/29/2023]
Abstract
The thermostable Phosphotriesterase-Like Lactonase from Sulfolobus solfataricus (SsoPox) hydrolyzes lactones and, at a lower rate, neurotoxic organophosphorus compounds. The persistent demand of detoxification tools in the field of agricultural wastes and restoring of conditions after terrorist acts prompted us to exploit SsoPox as a "starter" to evolve its ancillary nerve agents hydrolytic capability. A directed evolution strategy yielded, among several variants, the single mutant W263F with k(cat) and specificity constant against paraoxon 16- and 6-fold enhanced, respectively, compared to the wild type. Furthermore, a phenomenon of enzyme activation by SDS has been observed, which allowed to increase those values 150- and 28-fold, respectively. The activity of SsoPox against the deadly nerve gas Cyclosarin has been reported for the first time and proved to be substantially unaffected for variant W263F. Finally, outperforming efficiency of W263F was demonstrated, under severe stressing conditions, with respect to the best known phosphotriesterase PTE from Brevundimonas diminuta.
Collapse
Affiliation(s)
- Luigia Merone
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Wu AC, Wang PY, Lin YS, Kao MF, Chen JR, Ciou JF, Tsai SW. Improvements of enzyme activity and enantioselectivity in lipase-catalyzed alcoholysis of (R,S)-azolides. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.molcatb.2009.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
32
|
Kang TS, Stevens RC. Structural aspects of therapeutic enzymes to treat metabolic disorders. Hum Mutat 2010; 30:1591-610. [PMID: 19790257 DOI: 10.1002/humu.21111] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein therapeutics represents a niche subset of pharmacological agents that is rapidly gaining importance in medicine. In addition to the exceptional specificity that is characteristic of protein therapeutics, several classes of proteins have also been effectively utilized for treatment of conditions that would otherwise lack effective pharmacotherapeutic options. A particularly striking class of protein therapeutics is exogenous enzymes administered for replacement therapy in patients afflicted with metabolic disorders. To date, at least 11 enzymes have either been approved for use, or are in clinical trials for the treatment of selected inherited metabolic disorders. With the recent advancement in structural biology, a significantly larger amount of structural information for several of these enzymes is now available. This article is an overview of the correlation between structural perturbations of these enzymes with the clinical presentation of the respective metabolic conditions, as well as a discussion of the relevant structural modification strategies engaged in improving these enzymes for replacement therapies.
Collapse
Affiliation(s)
- Tse Siang Kang
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | | |
Collapse
|
33
|
Melzer M, Chen JCH, Heidenreich A, Gäb J, Koller M, Kehe K, Blum MM. Reversed enantioselectivity of diisopropyl fluorophosphatase against organophosphorus nerve agents by rational design. J Am Chem Soc 2010; 131:17226-32. [PMID: 19894712 DOI: 10.1021/ja905444g] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Diisopropyl fluorophosphatase (DFPase) from Loligo vulgaris is an efficient and robust biocatalyst for the hydrolysis of a range of highly toxic organophosphorus compounds including the nerve agents sarin, soman, and cyclosarin. In contrast to the substrate diisopropyl fluorophosphate (DFP) the nerve agents possess an asymmetric phosphorus atom, which leads to pairs of enantiomers that display markedly different toxicities. Wild-type DFPase prefers the less toxic stereoisomers of the substrates which leads to slower detoxification despite rapid hydrolysis. Enzyme engineering efforts based on rational design yielded two quadruple enzyme mutants with reversed enantioselectivity and overall enhanced activity against tested nerve agents. The reversed stereochemical preference is explained through modeling studies and the crystal structures of the two mutants. Using the engineered mutants in combination with wild-type DFPase leads to significantly enhanced activity and detoxification, which is especially important for personal decontamination. Our findings may also be of relevance for the structurally related enzyme human paraoxonase (PON), which is of considerable interest as a potential catalytic in vivo scavenger in case of organophosphorus poisoning.
Collapse
Affiliation(s)
- Marco Melzer
- Blum-Scientific Services, Ledererstrasse 23, 80331 Munich, Germany
| | | | | | | | | | | | | |
Collapse
|
34
|
Galant A, Arkus KA, Zubieta C, Cahoon RE, Jez JM. Structural basis for evolution of product diversity in soybean glutathione biosynthesis. THE PLANT CELL 2009; 21:3450-8. [PMID: 19948790 PMCID: PMC2798330 DOI: 10.1105/tpc.109.071183] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2009] [Revised: 10/09/2009] [Accepted: 11/05/2009] [Indexed: 05/05/2023]
Abstract
The redox active peptide glutathione is ubiquitous in nature, but some plants also synthesize glutathione analogs in response to environmental stresses. To understand the evolution of chemical diversity in the closely related enzymes homoglutathione synthetase (hGS) and glutathione synthetase (GS), we determined the structures of soybean (Glycine max) hGS in three states: apoenzyme, bound to gamma-glutamylcysteine (gammaEC), and with hGSH, ADP, and a sulfate ion bound in the active site. Domain movements and rearrangement of active site loops change the structure from an open active site form (apoenzyme and gammaEC complex) to a closed active site form (hGSH*ADP*SO(4)(2-) complex). The structure of hGS shows that two amino acid differences in an active site loop provide extra space to accommodate the longer beta-Ala moiety of hGSH in comparison to the glycinyl group of glutathione. Mutation of either Leu-487 or Pro-488 to an Ala improves catalytic efficiency using Gly, but a double mutation (L487A/P488A) is required to convert the substrate preference of hGS from beta-Ala to Gly. These structures, combined with site-directed mutagenesis, reveal the molecular changes that define the substrate preference of hGS, explain the product diversity within evolutionarily related GS-like enzymes, and reinforce the critical role of active site loops in the adaptation and diversification of enzyme function.
Collapse
Affiliation(s)
- Ashley Galant
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Kiani A.J. Arkus
- Department of Biology, Washington University, St. Louis, Missouri 63130
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Chloe Zubieta
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | | | - Joseph M. Jez
- Department of Biology, Washington University, St. Louis, Missouri 63130
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| |
Collapse
|
35
|
Wang PY, Chen YJ, Wu AC, Lin YS, Kao MF, Chen JR, Ciou JF, Tsai SW. (R,S)-Azolides as Novel Substrates for Lipase-Catalyzed Hydrolytic Resolution in Organic Solvents. Adv Synth Catal 2009. [DOI: 10.1002/adsc.200900391] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
36
|
Kotormán M, Cseri A, Laczkó I, Simon LM. Stabilization of α-chymotrypsin in aqueous organic solvents by chemical modification with organic acid anhydrides. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2009.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
37
|
Wang PY, Tsai SW. Modification of enzyme surface negative charges via covalent immobilization for tailoring the activity and enantioselectivity. J Taiwan Inst Chem Eng 2009. [DOI: 10.1016/j.jtice.2008.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
38
|
Spadiut O, Radakovits K, Pisanelli I, Salaheddin C, Yamabhai M, Tan TC, Divne C, Haltrich D. A thermostable triple mutant of pyranose 2-oxidase fromTrametes multicolorwith improved properties for biotechnological applications. Biotechnol J 2009; 4:525-34. [DOI: 10.1002/biot.200800260] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
39
|
Spadiut O, Pisanelli I, Maischberger T, Peterbauer C, Gorton L, Chaiyen P, Haltrich D. Engineering of pyranose 2-oxidase: Improvement for biofuel cell and food applications through semi-rational protein design. J Biotechnol 2009; 139:250-7. [DOI: 10.1016/j.jbiotec.2008.11.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Revised: 11/03/2008] [Accepted: 11/20/2008] [Indexed: 10/21/2022]
|
40
|
Mizuno T, Hasegawa C, Tanabe Y, Hamajima K, Muto T, Nishi Y, Oda M, Kobayashi Y, Tanaka T. Organic ligand binding by a hydrophobic cavity in a designed tetrameric coiled-coil protein. Chemistry 2008; 15:1491-8. [PMID: 19115294 DOI: 10.1002/chem.200800855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The design and characterization of a hydrophobic cavity in de novo designed proteins provides a wide range of information about the functions of de novo proteins. We designed a de novo tetrameric coiled-coil protein with a hydrophobic pocketlike cavity. Tetrameric coiled coils with hydrophobic cavities have previously been reported. By replacing one Leu residue at the a position with Ala, hydrophobic cavities that did not flatten out due to loose peptide chains were reliably created. To perform a detailed examination of the ligand-binding characteristics of the cavities, we originally designed two other coiled-coil proteins: AM2, with eight Ala substitutions at the adjacent a and d positions at the center of a bundled structure, and AM2W, with one Trp and seven Ala substitutions at the same positions. To increase the association of the helical peptides, each helical peptide was connected with flexible linkers, which resulted in a single peptide chain. These proteins exhibited CD spectra corresponding to superhelical structures, despite weakened hydrophobic packing. AM2W exhibited binding affinity for size-complementary organic compounds. The dissociation constants, K(d), of AM2W were 220 nM for adamantane, 81 microM for 1-adamantanol, and 294 microM for 1-adamantaneacetic acid, as measured by fluorescence titration analyses. Although it was contrary to expectations, AM2 did not exhibit any binding affinity, probably due to structural defects around the designed hydrophobic cavity. Interestingly, AM2W exhibited incremental structure stability through ligand binding. Plugging of structural defects with organic ligands would be expected to facilitate protein folding.
Collapse
Affiliation(s)
- Toshihisa Mizuno
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Nagoya, Aichi, 466-8555, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Wang PY, Tsai SW, Chen TL. Improvements of enzyme activity and enantioselectivity via combined substrate engineering and covalent immobilization. Biotechnol Bioeng 2008; 101:460-9. [PMID: 18435484 DOI: 10.1002/bit.21916] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Esterases, lipases, and serine proteases have been applied as versatile biocatalysts for preparing a variety of chiral compounds in industry via the kinetic resolution of their racemates. In order to meet this requirement, three approaches of enzyme engineering, medium engineering, and substrate engineering are exploited to improve the enzyme activity and enantioselectivity. With the hydrolysis of (R,S)-mandelates in biphasic media consisting of isooctane and pH 6 buffer at 55 degrees C as the model system, the strategy of combined substrate engineering and covalent immobilization leads to an increase of enzyme activity and enantioselectivity from V(S)/(E(t)) = 1.62 mmol/h g and V(S)/V(R) = 43.6 of (R,S)-ethyl mandelate (1) for a Klebsiella oxytoca esterase (named as SNSM-87 from the producer) to 16.7 mmol/h g and 867 of (R,S)-2-methoxyethyl mandelate (4) for the enzyme immobilized on Eupergit C 250L. The analysis is then extended to other (R,S)-2-hydroxycarboxylic acid esters, giving improvements of the enzyme performance from V(S)/(E(t)) = 1.56 mmol/h g and V(S)/V(R) = 41.9 of (R,S)-ethyl 3-chloromandelate (9) for the free esterase to 39.4 mmol/h g and 401 of (R,S)-2-methoxyethyl 3-chloromandelate (16) for the immobilized enzyme, V(S)/(E(t)) = 5.46 mmol/h g and V(S)/V(R) = 8.27 of (R,S)-ethyl 4-chloromandelate (10) for free SNSM-87 to 33.5 mmol/h g and 123 of (R,S)-methyl 4-chloromandelate (14) for the immobilized enzyme, as well as V(S)/(E(t)) = 3.0 mmol/h g and V(S)/V(R) = 7.94 of (R,S)-ethyl 3-phenyllactate (11) for the free esterase to 40.7 mmol/h g and 158 of (R,S)-2-methoxyethyl 3-phenyllactate (18) for the immobilized enzyme. The great enantioselectivty enhancement is rationalized from the alteration of ionization constants of imidazolium moiety of catalytic histidine for both enantiomers and conformation distortion of active site after the covalent immobilization, as well as the selection of leaving alcohol moiety via substrate engineering approach.
Collapse
Affiliation(s)
- Pei-Yun Wang
- Institute of Biochemical and Biomedical Engineering, Chang Gung University, Kwei-Shan, Tao-Yuan 33302, Taiwan
| | | | | |
Collapse
|
42
|
Wu TK, Wang TT, Chang CH, Liu YT, Shie WS. Importance of Saccharomyces cerevisiae Oxidosqualene-Lanosterol Cyclase Tyrosine 707 Residue for Chair-Boat Bicyclic Ring Formation and Deprotonation Reactions. Org Lett 2008; 10:4959-62. [DOI: 10.1021/ol802036c] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tung-Kung Wu
- Department of Biological Science and Technology, National Chiao Tung University, 300, Hsin-Chu, Taiwan (Republic of China)
| | - Tsai-Ting Wang
- Department of Biological Science and Technology, National Chiao Tung University, 300, Hsin-Chu, Taiwan (Republic of China)
| | - Cheng-Hsiang Chang
- Department of Biological Science and Technology, National Chiao Tung University, 300, Hsin-Chu, Taiwan (Republic of China)
| | - Yuan-Ting Liu
- Department of Biological Science and Technology, National Chiao Tung University, 300, Hsin-Chu, Taiwan (Republic of China)
| | - Wen-Shiang Shie
- Department of Biological Science and Technology, National Chiao Tung University, 300, Hsin-Chu, Taiwan (Republic of China)
| |
Collapse
|
43
|
Rejasse B, Lamare S, Legoy MD, Besson T. Influence of microwave irradiation on enzymatic properties: applications in enzyme chemistry. J Enzyme Inhib Med Chem 2008; 22:518-26. [DOI: 10.1080/14756360701424959] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
44
|
Liu JQ, Wulff G. Functional Mimicry of Carboxypeptidase A by a Combination of Transition State Stabilization and a Defined Orientation of Catalytic Moieties in Molecularly Imprinted Polymers. J Am Chem Soc 2008; 130:8044-54. [DOI: 10.1021/ja8012648] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jun-qiu Liu
- Institute of Organic and Macromolecular Chemistry, Heinrich Heine University, 40225 Düsseldorf, Germany and the State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, 130012, P. R. China
| | - Günter Wulff
- Institute of Organic and Macromolecular Chemistry, Heinrich Heine University, 40225 Düsseldorf, Germany and the State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, 130012, P. R. China
| |
Collapse
|
45
|
Wu TK, Wen HY, Chang CH, Liu YT. Protein Plasticity: A Single Amino Acid Substitution in the Saccharomyces cerevisiae Oxidosqualene−Lanosterol Cyclase Generates Protosta-13(17),24-dien-3β-ol, a Rearrangement Product. Org Lett 2008; 10:2529-32. [DOI: 10.1021/ol800799n] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tung-Kung Wu
- Department of Biological Science and Technology, Institute of Molecular Science and Department of Applied Chemistry, National Chiao Tung University, 300, Hsin-Chu, Taiwan, Republic of China
| | - Hao-Yu Wen
- Department of Biological Science and Technology, Institute of Molecular Science and Department of Applied Chemistry, National Chiao Tung University, 300, Hsin-Chu, Taiwan, Republic of China
| | - Cheng-Hsiang Chang
- Department of Biological Science and Technology, Institute of Molecular Science and Department of Applied Chemistry, National Chiao Tung University, 300, Hsin-Chu, Taiwan, Republic of China
| | - Yuan-Ting Liu
- Department of Biological Science and Technology, Institute of Molecular Science and Department of Applied Chemistry, National Chiao Tung University, 300, Hsin-Chu, Taiwan, Republic of China
| |
Collapse
|
46
|
Yu O, Jez JM. Nature's assembly line: biosynthesis of simple phenylpropanoids and polyketides. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 54:750-62. [PMID: 18476876 DOI: 10.1111/j.1365-313x.2008.03436.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants produce large amounts of phenylpropanoids, both in terms of molecular diversity and absolute quantity of these compounds. The phenylpropanoids, and the related plant polyketides, have multiple biological functions. They serve to attract pollinators, support secondary cell-wall growth, provide protection against various plant diseases, and interact with beneficial soil microbes. Their basic chemical properties also make them useful in the biofuel and biomaterial industries. Phenylpropanoid metabolism begins with the amino acid phenylalanine, which feeds into various biosynthetic pathways that generate a wide range of structurally related polyphenolic compounds. This review focuses on four sub-groups of these polyphenolic compounds - polyketides, stilbenes, isoflavones and catechins. We discuss the biosynthesis of these molecules, their physiological role in plants, and their striking pharmacological and physiological effects on humans. This review also highlights metabolic engineering efforts aimed at increasing or decreasing the amounts of each class of compound in various model plants and crops.
Collapse
Affiliation(s)
- Oliver Yu
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO 63132, USA.
| | | |
Collapse
|
47
|
Tan XH, Yang R, Wirjo A, Liu CF. Subtiligase as a hydrothiolase for the synthesis of peptide thioacids. Tetrahedron Lett 2008. [DOI: 10.1016/j.tetlet.2008.03.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
48
|
Zubieta C, Arkus KAJ, Cahoon RE, Jez JM. A single amino acid change is responsible for evolution of acyltransferase specificity in bacterial methionine biosynthesis. J Biol Chem 2008; 283:7561-7. [PMID: 18216013 DOI: 10.1074/jbc.m709283200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacteria and yeast rely on either homoserine transsuccinylase (HTS, metA) or homoserine transacetylase (HTA; met2) for the biosynthesis of methionine. Although HTS and HTA catalyze similar chemical reactions, these proteins are typically unrelated in both sequence and three-dimensional structure. Here we present the 2.0 A resolution x-ray crystal structure of the Bacillus cereus metA protein in complex with homoserine, which provides the first view of a ligand bound to either HTA or HTS. Surprisingly, functional analysis of the B. cereus metA protein shows that it does not use succinyl-CoA as a substrate. Instead, the protein catalyzes the transacetylation of homoserine using acetyl-CoA. Therefore, the B. cereus metA protein functions as an HTA despite greater than 50% sequence identity with bona fide HTS proteins. This result emphasizes the need for functional confirmation of annotations of enzyme function based on either sequence or structural comparisons. Kinetic analysis of site-directed mutants reveals that the B. cereus metA protein and the E. coli HTS share a common catalytic mechanism. Structural and functional examination of the B. cereus metA protein reveals that a single amino acid in the active site determines acetyl-CoA (Glu-111) versus succinyl-CoA (Gly-111) specificity in the metA-like of acyltransferases. Switching of this residue provides a mechanism for evolving substrate specificity in bacterial methionine biosynthesis. Within this enzyme family, HTS and HTA activity likely arises from divergent evolution in a common structural scaffold with conserved catalytic machinery and homoserine binding sites.
Collapse
Affiliation(s)
- Chloe Zubieta
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | | | | | | |
Collapse
|
49
|
Rasmussen BS, Pedersen JM, Sørensen J, Egebjerg J, Schiøtt B, Mortensen KK, Skrydstrup T. Enantioselective proteins: selection, binding studies and molecular modeling of antibodies with affinity towards hydrophobic BINOL derivatives. Chembiochem 2008; 8:1974-80. [PMID: 17924375 DOI: 10.1002/cbic.200700295] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In this paper, the initial steps towards the design of novel artificial metalloenzymes that exploit proteins as a second coordination sphere for traditional metal-ligand catalysis are described. Phage display was employed to select and study antibody fragments capable of recognizing hydrophobic BINOL derivatives designed to mimic BINAP, a widely used ligand in asymmetric metal-catalyzed reactions. The binding affinities of the selected antibodies towards a series of haptens were evaluated by using ELISA assays. A homology model of one of the most selective antibodies was constructed, and a computer-assisted ligand-docking study was carried out to elucidate the binding of the hapten. It was shown that, due to the hydrophobic nature of the haptens, a higher level of theoretical treatment was required to identify the correct binding modes. A small selection of the antibodies was found to discriminate between enantiomers and small structural modifications of the BINOL derivatives. The selectivities arise from hydrophobic interactions, and we propose that the identified set of antibodies provides a foundation for a novel route to artificial metalloenzymes.
Collapse
Affiliation(s)
- Brian Schou Rasmussen
- Department of Chemistry and Interdisciplinary Nanoscience Center, University of Aarhus, Langelandsgade 140, 8000 Aarhus C, Denmark.
| | | | | | | | | | | | | |
Collapse
|
50
|
Pastor JJ, Granados G, Carulla N, Rabanal F, Giralt E. Redesign of Protein Domains Using One-Bead-One-Compound Combinatorial Chemistry. J Am Chem Soc 2007; 129:14922-32. [DOI: 10.1021/ja073969x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jose J. Pastor
- Contribution from the Institute for Biomedical Research, Barcelona Science Park, 08028 Barcelona, Spain, and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona Spain
| | - Giovanna Granados
- Contribution from the Institute for Biomedical Research, Barcelona Science Park, 08028 Barcelona, Spain, and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona Spain
| | - Natàlia Carulla
- Contribution from the Institute for Biomedical Research, Barcelona Science Park, 08028 Barcelona, Spain, and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona Spain
| | - Francesc Rabanal
- Contribution from the Institute for Biomedical Research, Barcelona Science Park, 08028 Barcelona, Spain, and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona Spain
| | - Ernest Giralt
- Contribution from the Institute for Biomedical Research, Barcelona Science Park, 08028 Barcelona, Spain, and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona Spain
| |
Collapse
|