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Zhan P, Liu X, Zhang S, Zhu Q, Zhao H, Ren C, Zhang J, Lu L, Cai D, Qin P. Electroenzymatic Reduction of Furfural to Furfuryl Alcohol by an Electron Mediator and Enzyme Orderly Assembled Biocathode. ACS APPLIED MATERIALS & INTERFACES 2023; 15:12855-12863. [PMID: 36859767 DOI: 10.1021/acsami.3c00320] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The electroenzymatic valorization of biomass derivatives into valuable biochemicals has a promising outlook. However, bottlenecks including poor electron transfer between the electrode surface and oxidoreductase, inefficient regeneration of cofactors, and high cost of enzymes and electron mediators hindered the realistic applications of the technique. Herein, to address the above technical barriers, a novel bio-electrocatalytic system that integrates the electrochemical NADH regeneration and enzymatic reaction was constructed, using an orderly assembled composite bioelectrode consisting of an outer immobilized enzyme layer and a sandwiched redox mediator rhodium complex layer. The as-prepared composite bioelectrode was further applied for the highly selective hydrogenation of furfural into furfural alcohol. Results indicated that the enzyme activity was significantly improved, while the furfural valorization was promoted by effective interfacial electron transition and co-factor regeneration on the composite bioelectrode. Considerable high furfural conversion (96.4%) can be achieved accompanied by a furfural alcohol selectivity of 90.0% at -1.2 V (vs Ag/AgCl). The novel composite bioelectrode also showed good stability and reusability. Up to 85.1% of the original furfural alcohol selectivity can be preserved after 10 times of recycling. This work presents a promising green alternative for the valorization of furfural, which also shows great potential extending to the valorization of other biomass compounds.
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Affiliation(s)
- Peng Zhan
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Xiangshi Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Shiding Zhang
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Qian Zhu
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Hongqing Zhao
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Cong Ren
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Jiawen Zhang
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Lu Lu
- Paris Curie Engineer School, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Di Cai
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Peiyong Qin
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P. R. China
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2
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Li Y, Wang R, Pei Y, Yu W, Wu W, Li D, Hu Z. Phylogeny and functional characterization of the cinnamyl alcohol dehydrogenase gene family in Phryma leptostachya. Int J Biol Macromol 2022; 217:407-416. [PMID: 35841957 DOI: 10.1016/j.ijbiomac.2022.07.063] [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: 01/15/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/05/2022]
Abstract
Phryma leptostachya has attracted increasing attention because it is rich in furofuran lignans with a wide range of biological activities. Biosynthesis of furofuran lignans begins with the dimerization of coniferyl alcohol, one of the monolignol. Cinnamyl alcohol dehydrogenase (CAD) catalyzes the final step of monolignol biosynthesis, reducing cinnamyl aldehydes to cinnamyl alcohol. As it is in the terminal position of monolignol biosynthesis, its type and activity can cause significant changes in the total amount and composition of lignans. Herein, combined with bioinformatics analysis and in vitro enzyme assays, we clarified that CAD in P. leptostachya belonged to a multigene family, and identified nearly the entire CAD gene family. Our in-depth characterization about the functions and structures of two major CAD isoforms, PlCAD2 and PlCAD3, showed that PlCAD2 exhibited the highest catalytic activity, and coniferyl aldehyde was its preferred substrate, followed by PlCAD3, and sinapyl aldehyde was its preferred substrate. Considering the accumulation patterns of furofuran lignans and expression patterns of PlCADs, we speculated that PlCAD2 was the predominant CAD isoform responsible for furofuran lignans biosynthesis in P. leptostachya. Moreover, these CADs found here can also provide effective biological parts for lignans and lignins biosynthesis.
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Affiliation(s)
- Yankai Li
- Institute of Pesticide Science, College of Plant Protection, Northwest A & F University, Yangling, Shaanxi 712100, China; Key Laboratory for Botanical Pesticide R & D of Shaanxi Province, Yangling, Shaanxi 712100, China
| | - Rui Wang
- Institute of Pesticide Science, College of Plant Protection, Northwest A & F University, Yangling, Shaanxi 712100, China; Key Laboratory for Botanical Pesticide R & D of Shaanxi Province, Yangling, Shaanxi 712100, China
| | - Yakun Pei
- Institute of Pesticide Science, College of Plant Protection, Northwest A & F University, Yangling, Shaanxi 712100, China; Key Laboratory for Botanical Pesticide R & D of Shaanxi Province, Yangling, Shaanxi 712100, China
| | - Wenwen Yu
- Institute of Pesticide Science, College of Plant Protection, Northwest A & F University, Yangling, Shaanxi 712100, China; Key Laboratory for Botanical Pesticide R & D of Shaanxi Province, Yangling, Shaanxi 712100, China
| | - Wenjun Wu
- Institute of Pesticide Science, College of Plant Protection, Northwest A & F University, Yangling, Shaanxi 712100, China; Key Laboratory for Botanical Pesticide R & D of Shaanxi Province, Yangling, Shaanxi 712100, China
| | - Ding Li
- College of Chemistry & Pharmacy, Northwest A & F University, Yangling, Shaanxi 712100, China.
| | - Zhaonong Hu
- Institute of Pesticide Science, College of Plant Protection, Northwest A & F University, Yangling, Shaanxi 712100, China; Key Laboratory for Botanical Pesticide R & D of Shaanxi Province, Yangling, Shaanxi 712100, China; Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture, Yangling, Shaanxi 712100, China.
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Characterization of Two Dehydrogenases from Gluconobacter oxydans Involved in the Transformation of Patulin to Ascladiol. Toxins (Basel) 2022; 14:toxins14070423. [PMID: 35878161 PMCID: PMC9323132 DOI: 10.3390/toxins14070423] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/03/2022] [Accepted: 06/20/2022] [Indexed: 01/25/2023] Open
Abstract
Patulin is a mycotoxin that primarily contaminate apples and apple products. Whole cell or cell-free extracts of Gluconobacter oxydans ATCC 621 were able to transform patulin to E-ascladiol. Proteins from cell-free extracts were separated by anion exchange chromatography and fractions with patulin transformation activity were subjected to peptide mass fingerprinting, enabling the identification of two NADPH dependent short chain dehydrogenases, GOX0525 and GOX1899, with the requisite activity. The genes encoding these enzymes were expressed in E. coli and purified. Kinetic parameters for patulin reduction, as well as pH profiles and thermostability were established to provide further insight on the potential application of these enzymes for patulin detoxification.
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Luan P, Li Y, Huang C, Dong L, Ma T, Liu J, Gao J, Liu Y, Jiang Y. Design of De Novo Three-Enzyme Nanoreactors for Stereodivergent Synthesis of α-Substituted Cyclohexanols. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Pengqian Luan
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Yongxing Li
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Chen Huang
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Lele Dong
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Teng Ma
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Jianqiao Liu
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Jing Gao
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Yunting Liu
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Yanjun Jiang
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
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Zhang T, Bao F, Ding A, Yang Y, Cheng T, Wang J, Zhang Q. Comprehensive Analysis of Endogenous Volatile Compounds, Transcriptome, and Enzyme Activity Reveals PmCAD1 Involved in Cinnamyl Alcohol Synthesis in Prunus mume. FRONTIERS IN PLANT SCIENCE 2022; 13:820742. [PMID: 35251090 PMCID: PMC8894765 DOI: 10.3389/fpls.2022.820742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Floral scent is an important economic and ornamental trait of Prunus mume. The floral volatiles from most cultivars of P. mume in composition exist significant differences. Cinnamyl alcohol was one of the main floral volatile compounds with distinct abundances in different cultivars, namely, 'Zaohua Lve,' 'Zao Yudie,' 'Fenpi Gongfen,' 'Jiangsha Gongfen,' and 'Fenhong Zhusha.' Based on the determination of endogenous volatiles of full-blooming flowers, vital enzyme activity and transcriptomes were comprehensively analyzed to screen the key potential genes involved in cinnamyl alcohol synthesis. Transcriptome combining with enzyme activity level analysis suggested that the expression levels of three PmCADs were highly correlated with the cinnamyl alcohol dehydrogenase (CAD) enzyme activities in six cultivars. Furthermore, phylogenetic tree and transcriptome analysis suggested that PmCAD1 and PmCAD2 might contribute to the cinnamyl alcohol synthesis. Relative expression analyses and enzyme activity assays showed that PmCAD1 played an important role in cinnamyl alcohol biosynthesis in vitro. Overall, this research lays a theoretical foundation for clarifying comprehensively the molecular biosynthesis mechanism of floral volatiles in P. mume.
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Design of a Microbial Remediation Inoculation Program for Petroleum Hydrocarbon Contaminated Sites Based on Degradation Pathways. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18168794. [PMID: 34444543 PMCID: PMC8395025 DOI: 10.3390/ijerph18168794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 11/24/2022]
Abstract
This paper analyzed the degradation pathways of petroleum hydrocarbon degradation bacteria, screened the main degradation pathways, and found the petroleum hydrocarbon degradation enzymes corresponding to each step of the degradation pathway. Through the Copeland method, the best inoculation program of petroleum hydrocarbon degradation bacteria in a polluted site was selected as follows: single oxygenation path was dominated by Streptomyces avermitilis, hydroxylation path was dominated by Methylosinus trichosporium OB3b, secondary oxygenation path was dominated by Pseudomonas aeruginosa, secondary hydroxylation path was dominated by Methylococcus capsulatus, double oxygenation path was dominated by Acinetobacter baylyi ADP1, hydrolysis path was dominated by Rhodococcus erythropolis, and CoA path was dominated by Geobacter metallireducens GS-15 to repair petroleum hydrocarbon contaminated sites. The Copeland method score for this solution is 22, which is the highest among the 375 solutions designed in this paper, indicating that it has the best degradation effect. Meanwhile, we verified its effect by the Cdocker method, and the Cdocker energy of this solution is −285.811 kcal/mol, which has the highest absolute value. Among the inoculation programs of the top 13 petroleum hydrocarbon degradation bacteria, the effect of the best inoculation program of petroleum hydrocarbon degradation bacteria was 18% higher than that of the 13th group, verifying that this solution has the best overall degradation effect. The inoculation program of petroleum hydrocarbon degradation bacteria designed in this paper considered the main pathways of petroleum hydrocarbon pollutant degradation, especially highlighting the degradability of petroleum hydrocarbon intermediate degradation products, and enriching the theoretical program of microbial remediation of petroleum hydrocarbon contaminated sites.
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Prototyping of microbial chassis for the biomanufacturing of high-value chemical targets. Biochem Soc Trans 2021; 49:1055-1063. [PMID: 34100907 DOI: 10.1042/bst20200017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/06/2021] [Accepted: 05/10/2021] [Indexed: 12/19/2022]
Abstract
Metabolic engineering technologies have been employed with increasing success over the last three decades for the engineering and optimization of industrial host strains to competitively produce high-value chemical targets. To this end, continued reductions in the time taken from concept, to development, to scale-up are essential. Design-Build-Test-Learn pipelines that are able to rapidly deliver diverse chemical targets through iterative optimization of microbial production strains have been established. Biofoundries are employing in silico tools for the design of genetic parts, alongside combinatorial design of experiments approaches to optimize selection from within the potential design space of biological circuits based on multi-criteria objectives. These genetic constructs can then be built and tested through automated laboratory workflows, with performance data analysed in the learn phase to inform further design. Successful examples of rapid prototyping processes for microbially produced compounds reveal the potential role of biofoundries in leading the sustainable production of next-generation bio-based chemicals.
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Guntupalli SR, Li Z, Chang L, Plapp BV, Subramanian R. Cryo-Electron Microscopy Structures of Yeast Alcohol Dehydrogenase. Biochemistry 2021; 60:663-677. [PMID: 33620215 DOI: 10.1021/acs.biochem.0c00921] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structures of yeast alcohol dehydrogenase determined by X-ray crystallography show that the subunits have two different conformational states in each of the two dimers that form the tetramer. Apoenzyme and holoenzyme complexes relevant to the catalytic mechanism were described, but the asymmetry led to questions about the cooperativity of the subunits in catalysis. This study used cryo-electron microscopy (cryo-EM) to provide structures for the apoenzyme, two different binary complexes with NADH, and a ternary complex with NAD+ and 2,2,2-trifluoroethanol. All four subunits in each of these complexes are identical, as the tetramers have D2 symmetry, suggesting that there is no preexisting asymmetry and that the subunits can be independently active. The apoenzyme and one enzyme-NADH complex have "open" conformations and the inverted coordination of the catalytic zinc with Cys-43, His-66, Glu-67, and Cys-153, whereas another enzyme-NADH complex and the ternary complex have closed conformations with the classical coordination of the zinc with Cys-43, His-66, Cys-153, and a water or the oxygen of trifluoroethanol. The conformational change involves interactions of Arg-340 with the pyrophosphate group of the coenzyme and Glu-67. The cryo-EM and X-ray crystallography studies provide structures relevant for the catalytic mechanism.
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Affiliation(s)
- Sai Rohit Guntupalli
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.,Manipal University, Manipal, India.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhuang Li
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Leifu Chang
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Bryce V Plapp
- Department of Biochemistry, Bowen Science Building, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Ramaswamy Subramanian
- Department of Biological Sciences and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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Hu X, Han X, Wu L, Wang H, Ouyang Y, Li Q, Kuang X, Xiang Q, Yu X, Li X, Gu Y, Zhao K, Chen Q, Ma M. The open reading frame 02797 from Candida tropicalis encodes a novel NADH-dependent aldehyde reductase. Protein Expr Purif 2020; 171:105625. [PMID: 32173567 DOI: 10.1016/j.pep.2020.105625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 12/17/2022]
Abstract
Owing to its high-temperature tolerance, robustness, and wide use of carbon sources, Candida tropicalis is considered a good candidate microorganism for bioconversion of lignocellulose to ethanol. It also has the intrinsic ability to in situ detoxify aldehydes derived from lignocellulosic hydrolysis. However, the aldehyde reductases that catalyze this bioconversion in C. tropicalis remain unknown. Herein, we found that the uncharacterized open reading frame (ORF), CTRG_02797, from C. tropicalis encodes a novel and broad substrate-specificity aldehyde reductase that reduces at least seven aldehydes. This enzyme strictly depended on NADH rather than NADPH as the co-factor for catalyzing the reduction reaction. Its highest affinity (Km), maximum velocity (Vmax), catalytic rate constant (Kcat), and catalytic efficiency (Kcat/Km) were observed when reducing acetaldehyde (AA) and its enzyme activity was influenced by different concentrations of salts, metal ions, and chemical protective additives. Protein localization assay demonstrated that Ctrg_02797p was localized in the cytoplasm in C. tropicalis cells, which ensures an effective enzymatic reaction. Finally, Ctrg_02797p was grouped into the cinnamyl alcohol dehydrogenase (CADH) subfamily of the medium-chain dehydrogenase/reductase family. This research provides guidelines for exploring more uncharacterized genes with reduction activity for detoxifying aldehydes.
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Affiliation(s)
- Xiangdong Hu
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, PR China
| | - Xuebing Han
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, PR China
| | - Lan Wu
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, PR China
| | - Hanyu Wang
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, PR China
| | - Yidan Ouyang
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, PR China
| | - Qian Li
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, PR China
| | - Xiaolin Kuang
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, PR China
| | - Quanju Xiang
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, PR China
| | - Xiumei Yu
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, PR China
| | - Xi Li
- College of Landscape Architecture, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, PR China
| | - Yunfu Gu
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, PR China
| | - Ke Zhao
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, PR China
| | - Qiang Chen
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, PR China
| | - Menggen Ma
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, PR China; Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, PR China.
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Stomberski CT, Hess DT, Stamler JS. Protein S-Nitrosylation: Determinants of Specificity and Enzymatic Regulation of S-Nitrosothiol-Based Signaling. Antioxid Redox Signal 2019; 30:1331-1351. [PMID: 29130312 PMCID: PMC6391618 DOI: 10.1089/ars.2017.7403] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SIGNIFICANCE Protein S-nitrosylation, the oxidative modification of cysteine by nitric oxide (NO) to form protein S-nitrosothiols (SNOs), mediates redox-based signaling that conveys, in large part, the ubiquitous influence of NO on cellular function. S-nitrosylation regulates protein activity, stability, localization, and protein-protein interactions across myriad physiological processes, and aberrant S-nitrosylation is associated with diverse pathophysiologies. Recent Advances: It is recently recognized that S-nitrosylation endows S-nitroso-protein (SNO-proteins) with S-nitrosylase activity, that is, the potential to trans-S-nitrosylate additional proteins, thereby propagating SNO-based signals, analogous to kinase-mediated signaling cascades. In addition, it is increasingly appreciated that cellular S-nitrosylation is governed by dynamically coupled equilibria between SNO-proteins and low-molecular-weight SNOs, which are controlled by a growing set of enzymatic denitrosylases comprising two main classes (high and low molecular weight). S-nitrosylases and denitrosylases, which together control steady-state SNO levels, may be identified with distinct physiology and pathophysiology ranging from cardiovascular and respiratory disorders to neurodegeneration and cancer. CRITICAL ISSUES The target specificity of protein S-nitrosylation and the stability and reactivity of protein SNOs are determined substantially by enzymatic machinery comprising highly conserved transnitrosylases and denitrosylases. Understanding the differential functionality of SNO-regulatory enzymes is essential, and is amenable to genetic and pharmacological analyses, read out as perturbation of specific equilibria within the SNO circuitry. FUTURE DIRECTIONS The emerging picture of NO biology entails equilibria among potentially thousands of different SNOs, governed by denitrosylases and nitrosylases. Thus, to elucidate the operation and consequences of S-nitrosylation in cellular contexts, studies should consider the roles of SNO-proteins as both targets and transducers of S-nitrosylation, functioning according to enzymatically governed equilibria.
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Affiliation(s)
- Colin T Stomberski
- 1 Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, Ohio.,2 Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio
| | - Douglas T Hess
- 1 Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, Ohio.,3 Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Jonathan S Stamler
- 2 Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio.,3 Department of Medicine, Case Western Reserve University, Cleveland, Ohio.,4 Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio
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Aggarwal N, Ananthathamula R, Karanam VK, Doble M, Chadha A. Understanding substrate specificity and enantioselectivity of carbonyl reductase from Candida parapsilosis ATCC 7330 (CpCR): Experimental and modeling studies. MOLECULAR CATALYSIS 2018. [DOI: 10.1016/j.mcat.2018.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Wang H, Li Q, Kuang X, Xiao D, Han X, Hu X, Li X, Ma M. Functions of aldehyde reductases from Saccharomyces cerevisiae in detoxification of aldehyde inhibitors and their biotechnological applications. Appl Microbiol Biotechnol 2018; 102:10439-10456. [PMID: 30306200 DOI: 10.1007/s00253-018-9425-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 09/28/2018] [Accepted: 09/28/2018] [Indexed: 11/25/2022]
Abstract
Bioconversion of lignocellulosic biomass to high-value bioproducts by fermentative microorganisms has drawn extensive attentions worldwide. Lignocellulosic biomass cannot be efficiently utilized by microorganisms, such as Saccharomyces cerevisiae, but has to be pretreated prior to fermentation. Aldehyde compounds, as the by-products generated in the pretreatment process of lignocellulosic biomass, are considered as the most important toxic inhibitors to S. cerevisiae cells for their growth and fermentation. Aldehyde group in the aldehyde inhibitors, including furan aldehydes, aliphatic aldehydes, and phenolic aldehydes, is identified as the toxic factor. It has been demonstrated that S. cerevisiae has the ability to in situ detoxify aldehydes to their corresponding less or non-toxic alcohols. This reductive reaction is catalyzed by the NAD(P)H-dependent aldehyde reductases. In recent years, detoxification of aldehyde inhibitors by S. cerevisiae has been extensively studied and a huge progress has been made. This mini-review summarizes the classifications and structural features of the characterized aldehyde reductases from S. cerevisiae, their catalytic abilities to exogenous and endogenous aldehydes and effects of metal ions, chemical protective additives, and salts on enzyme activities, subcellular localization of the aldehyde reductases and their possible roles in protection of the subcellular organelles, and transcriptional regulation of the aldehyde reductase genes by the key stress-response transcription factors. Cofactor preference of the aldehyde reductases and their molecular mechanisms and efficient supply pathways of cofactors, as well as biotechnological applications of the aldehyde reductases in the detoxification of aldehyde inhibitors derived from pretreatment of lignocellulosic biomass, are also included or supplemented in this mini-review.
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Affiliation(s)
- Hanyu Wang
- Institute of Natural Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Qian Li
- Institute of Natural Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Xiaolin Kuang
- Institute of Natural Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Difan Xiao
- Institute of Natural Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Xuebing Han
- Institute of Natural Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Xiangdong Hu
- Institute of Natural Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Xi Li
- College of Landscape Architecture, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Menggen Ma
- Institute of Natural Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China.
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China.
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Wielgus-Kutrowska B, Grycuk T, Bzowska A. Part-of-the-sites binding and reactivity in the homooligomeric enzymes - facts and artifacts. Arch Biochem Biophys 2018; 642:31-45. [PMID: 29408402 DOI: 10.1016/j.abb.2018.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/13/2018] [Accepted: 01/17/2018] [Indexed: 01/18/2023]
Abstract
For a number of enzymes composed of several subunits with the same amino acid sequence, it was documented, or suggested, that binding of a ligand, or catalysis, is carried out by a single subunit. This phenomenon may be the result of a pre-existent asymmetry of subunits or a limiting case of the negative cooperativity, and is sometimes called "half-of-the-sites binding (or reactivity)" for dimers and could be called "part-of-the-sites binding (or reactivity)" for higher oligomers. In this article, we discuss molecular mechanisms that may result in "part-of-the-sites binding (and reactivity)", offer possible explanations why it may have a beneficial role in enzyme function, and point to experimental problems in documenting this behaviour. We describe some cases, for which such a mechanism was first reported and later disproved. We also give several examples of enzymes, for which this mechanism seems to be well documented, and profitable. A majority of enzymes identified in this study as half-of-the-sites binding (or reactive) use it in the flip-flop version, in which "half-of-the-sites" refers to a particular moment in time. In general, the various variants of the mechanism seems to be employed often by oligomeric enzymes for allosteric regulation to enhance the efficiency of enzymatic reactions in many key metabolic pathways.
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Affiliation(s)
- Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Department of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland.
| | - Tomasz Grycuk
- Division of Biophysics, Institute of Experimental Physics, Department of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Department of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland.
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14
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Chen L, Krol ES, Sakharkar MK, Khan HA, Alhomida AS, Yang J. Residues His172 and Lys238 are Essential for the Catalytic Activity of the Maleylacetate Reductase from Sphingobium chlorophenolicum Strain L-1. Sci Rep 2017; 7:18097. [PMID: 29273747 PMCID: PMC5741723 DOI: 10.1038/s41598-017-18475-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/12/2017] [Indexed: 02/08/2023] Open
Abstract
Maleylacetate reductase (PcpE), the last enzyme in the pentachlorophenol biodegradation pathway in Sphingobium chlorophenolicum L-1, catalyzes two consecutive reductive reactions, reductive dehalogenation of 2-chloromaleylacetate (2-CMA) to maleylacetate (MA) and subsequent reduction of MA to 3-oxoadipate (3-OXO). In each reaction, one molecule of NADH is consumed. To better understand its catalytic function, we undertook a structural model-based site-directed mutagenesis and steady-state kinetics study of PcpE. Our results showed that the putative catalytic site of PcpE is located in a positively charged solvent channel at the interface of the two domains and the binding of 2-CMA/MA involves seven basic amino acids, His172, His236, His237, His241 and His251, Lys140 and Lys238. Mutagenesis studies showed that His172 and Lys238 are essential for the catalytic activity of PcpE. However, the mutation of His236 to an alanine can increase the catalytic efficiency (k cat /K m ) of PcpE by more than 2-fold, implying that PcpE is still in an early stage of molecular evolution. Similar to tetrachlorobenzoquinone reductase (PcpD), PcpE is also inhibited by pentachlorophenol in a concentration-dependent manner. Furthermore, our studies showed that PcpE exhibits an extremely low but detectable level of alcohol dehalogenase activity toward ethanol and supports the notion that it is evolved from an iron-containing alcohol dehydrogenase.
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Affiliation(s)
- Lifeng Chen
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
- Agrisoma Biosciences Inc., 4410-110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Ed S Krol
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Meena K Sakharkar
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Haseeb A Khan
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah S Alhomida
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Jian Yang
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada.
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15
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Kwak J, Kim MC, Lee SY. An enzyme-coupled artificial photosynthesis system prepared from antenna protein-mimetic tyrosyl bolaamphiphile self-assembly. NANOSCALE 2016; 8:15064-70. [PMID: 27480074 DOI: 10.1039/c6nr04711d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
An artificial photosynthesis system coupled with an enzyme was constructed using the nanospherical self-assembly of tyrosyl bolaamphiphiles, which worked as a host matrix exhibiting an antenna effect that allowed enhanced energy transfer to the ZnDPEG photosensitizer. The excited electrons from the photosensitizer were transferred to NAD+ to produce NADH, which subsequently initiated the conversion of an aldehyde to ethanol by alcohol dehydrogenase. Production of NADH and ethanol was enhanced by increasing the concentration of tyrosyl bolaamphiphiles. Spectroscopic investigations proved that the photosensitizer closely associated with the surface of the bolaamphiphile assembly through hydrogen bonds that allowed energy transfer between the host matrix and the photosensitizer. This study demonstrates that the self-assembly of bolaamphiphiles could be applicable to the construction of biomimetic energy systems exploiting biochemical activity.
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Affiliation(s)
- Jinyoung Kwak
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea..
| | - Min-Chul Kim
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea..
| | - Sang-Yup Lee
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea..
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16
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Plapp BV, Charlier HA, Ramaswamy S. Mechanistic implications from structures of yeast alcohol dehydrogenase complexed with coenzyme and an alcohol. Arch Biochem Biophys 2016; 591:35-42. [PMID: 26743849 DOI: 10.1016/j.abb.2015.12.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/18/2015] [Accepted: 12/21/2015] [Indexed: 11/27/2022]
Abstract
Yeast alcohol dehydrogenase I is a homotetramer of subunits with 347 amino acid residues, catalyzing the oxidation of alcohols using NAD(+) as coenzyme. A new X-ray structure was determined at 3.0 Å where both subunits of an asymmetric dimer bind coenzyme and trifluoroethanol. The tetramer is a pair of back-to-back dimers. Subunit A has a closed conformation and can represent a Michaelis complex with an appropriate geometry for hydride transfer between coenzyme and alcohol, with the oxygen of 2,2,2-trifluoroethanol ligated at 2.1 Å to the catalytic zinc in the classical tetrahedral coordination with Cys-43, Cys-153, and His-66. Subunit B has an open conformation, and the coenzyme interacts with amino acid residues from the coenzyme binding domain, but not with residues from the catalytic domain. Coenzyme appears to bind to and dissociate from the open conformation. The catalytic zinc in subunit B has an alternative, inverted coordination with Cys-43, Cys-153, His-66 and the carboxylate of Glu-67, while the oxygen of trifluoroethanol is 3.5 Å from the zinc. Subunit B may represent an intermediate in the mechanism after coenzyme and alcohol bind and before the conformation changes to the closed form and the alcohol oxygen binds to the zinc and displaces Glu-67.
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Affiliation(s)
- Bryce V Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA.
| | - Henry A Charlier
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA.
| | - S Ramaswamy
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA.
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17
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Cahn JKB, Baumschlager A, Brinkmann-Chen S, Arnold FH. Mutations in adenine-binding pockets enhance catalytic properties of NAD(P)H-dependent enzymes. Protein Eng Des Sel 2016; 29:31-8. [PMID: 26512129 PMCID: PMC4678007 DOI: 10.1093/protein/gzv057] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 09/28/2015] [Indexed: 11/14/2022] Open
Abstract
NAD(P)H-dependent enzymes are ubiquitous in metabolism and cellular processes and are also of great interest for pharmaceutical and industrial applications. Here, we present a structure-guided enzyme engineering strategy for improving catalytic properties of NAD(P)H-dependent enzymes toward native or native-like reactions using mutations to the enzyme's adenine-binding pocket, distal to the site of catalysis. Screening single-site saturation mutagenesis libraries identified mutations that increased catalytic efficiency up to 10-fold in 7 out of 10 enzymes. The enzymes improved in this study represent three different cofactor-binding folds (Rossmann, DHQS-like, and FAD/NAD binding) and utilize both NADH and NADPH. Structural and biochemical analyses show that the improved activities are accompanied by minimal changes in other properties (cooperativity, thermostability, pH optimum, uncoupling), and initial tests on two enzymes (ScADH6 and EcFucO) show improved functionality in Escherichia coli.
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Affiliation(s)
- J K B Cahn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd, MC 210-41, Pasadena, CA 91125, USA
| | - A Baumschlager
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd, MC 210-41, Pasadena, CA 91125, USA
| | - S Brinkmann-Chen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd, MC 210-41, Pasadena, CA 91125, USA
| | - F H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd, MC 210-41, Pasadena, CA 91125, USA
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18
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Zhao X, Tang J, Wang X, Yang R, Zhang X, Gu Y, Li X, Ma M. YNL134C from Saccharomyces cerevisiae encodes a novel protein with aldehyde reductase activity for detoxification of furfural derived from lignocellulosic biomass. Yeast 2015; 32:409-22. [PMID: 25656244 DOI: 10.1002/yea.3068] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/28/2014] [Accepted: 01/28/2015] [Indexed: 02/03/2023] Open
Abstract
Furfural and 5-hydroxymethylfurfural (HMF) are the two main aldehyde compounds derived from pentoses and hexoses, respectively, during lignocellulosic biomass pretreatment. These two compounds inhibit microbial growth and interfere with subsequent alcohol fermentation. Saccharomyces cerevisiae has the in situ ability to detoxify furfural and HMF to the less toxic 2-furanmethanol (FM) and furan-2,5-dimethanol (FDM), respectively. Herein, we report that an uncharacterized gene, YNL134C, was highly up-regulated under furfural or HMF stress and Yap1p and Msn2/4p transcription factors likely controlled its up-regulated expression. Enzyme activity assays showed that YNL134C is an NADH-dependent aldehyde reductase, which plays a role in detoxification of furfural to FM. However, no NADH- or NADPH-dependent enzyme activity was observed for detoxification of HMF to FDM. This enzyme did not catalyse the reverse reaction of FM to furfural or FDM to HMF. Further studies showed that YNL134C is a broad-substrate aldehyde reductase, which can reduce multiple aldehydes to their corresponding alcohols. Although YNL134C is grouped into the quinone oxidoreductase family, no quinone reductase activity was observed using 1,2-naphthoquinone or 9,10-phenanthrenequinone as a substrate, and phylogenetic analysis indicates that it is genetically distant to quinone reductases. Proteins similar to YNL134C in sequence from S. cerevisiae and other microorganisms were phylogenetically analysed.
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Affiliation(s)
- Xianxian Zhao
- Institute of Ecological and Environmental Sciences, College of Resources and Environmental Sciences, Sichuan Agricultural University, Wenjiang, Sichuan, People's Republic of China
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19
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Raj S, Ramaswamy S, Plapp BV. Yeast alcohol dehydrogenase structure and catalysis. Biochemistry 2014; 53:5791-803. [PMID: 25157460 PMCID: PMC4165444 DOI: 10.1021/bi5006442] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 08/22/2014] [Indexed: 11/30/2022]
Abstract
Yeast (Saccharomyces cerevisiae) alcohol dehydrogenase I (ADH1) is the constitutive enzyme that reduces acetaldehyde to ethanol during the fermentation of glucose. ADH1 is a homotetramer of subunits with 347 amino acid residues. A structure for ADH1 was determined by X-ray crystallography at 2.4 Å resolution. The asymmetric unit contains four different subunits, arranged as similar dimers named AB and CD. The unit cell contains two different tetramers made up of "back-to-back" dimers, AB:AB and CD:CD. The A and C subunits in each dimer are structurally similar, with a closed conformation, bound coenzyme, and the oxygen of 2,2,2-trifluoroethanol ligated to the catalytic zinc in the classical tetrahedral coordination with Cys-43, Cys-153, and His-66. In contrast, the B and D subunits have an open conformation with no bound coenzyme, and the catalytic zinc has an alternative, inverted coordination with Cys-43, Cys-153, His-66, and the carboxylate of Glu-67. The asymmetry in the dimeric subunits of the tetramer provides two structures that appear to be relevant for the catalytic mechanism. The alternative coordination of the zinc may represent an intermediate in the mechanism of displacement of the zinc-bound water with alcohol or aldehyde substrates. Substitution of Glu-67 with Gln-67 decreases the catalytic efficiency by 100-fold. Previous studies of structural modeling, evolutionary relationships, substrate specificity, chemical modification, and site-directed mutagenesis are interpreted more fully with the three-dimensional structure.
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Affiliation(s)
| | | | - Bryce V. Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, Iowa 52242, United States
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20
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Pan H, Zhou R, Louie GV, Mühlemann JK, Bomati EK, Bowman ME, Dudareva N, Dixon RA, Noel JP, Wang X. Structural studies of cinnamoyl-CoA reductase and cinnamyl-alcohol dehydrogenase, key enzymes of monolignol biosynthesis. THE PLANT CELL 2014; 26:3709-27. [PMID: 25217505 PMCID: PMC4213152 DOI: 10.1105/tpc.114.127399] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 07/27/2014] [Accepted: 08/08/2014] [Indexed: 05/18/2023]
Abstract
The enzymes cinnamoyl-CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) catalyze the two key reduction reactions in the conversion of cinnamic acid derivatives into monolignol building blocks for lignin polymers in plant cell walls. Here, we describe detailed functional and structural analyses of CCRs from Medicago truncatula and Petunia hybrida and of an atypical CAD (CAD2) from M. truncatula. These enzymes are closely related members of the short-chain dehydrogenase/reductase (SDR) superfamily. Our structural studies support a reaction mechanism involving a canonical SDR catalytic triad in both CCR and CAD2 and an important role for an auxiliary cysteine unique to CCR. Site-directed mutants of CAD2 (Phe226Ala and Tyr136Phe) that enlarge the phenolic binding site result in a 4- to 10-fold increase in activity with sinapaldehyde, which in comparison to the smaller coumaraldehyde and coniferaldehyde substrates is disfavored by wild-type CAD2. This finding demonstrates the potential exploitation of rationally engineered forms of CCR and CAD2 for the targeted modification of monolignol composition in transgenic plants. Thermal denaturation measurements and structural comparisons of various liganded and unliganded forms of CCR and CAD2 highlight substantial conformational flexibility of these SDR enzymes, which plays an important role in the establishment of catalytically productive complexes of the enzymes with their NADPH and phenolic substrates.
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Affiliation(s)
- Haiyun Pan
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Rui Zhou
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Gordon V Louie
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Joëlle K Mühlemann
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Erin K Bomati
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037 Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92037
| | - Marianne E Bowman
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Richard A Dixon
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203-5017
| | - Joseph P Noel
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037 Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92037
| | - Xiaoqiang Wang
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
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21
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Purification and characterization of a zinc-dependent cinnamyl alcohol dehydrogenase from Leucaena leucocephala, a tree legume. Appl Biochem Biotechnol 2014; 172:3414-23. [PMID: 24532464 DOI: 10.1007/s12010-014-0776-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 02/03/2014] [Indexed: 10/25/2022]
Abstract
A cinnamyl alcohol dehydrogenase (CAD) from the secondary xylem of Leucaena leucocephala has been purified to homogeneity through successive steps of ammonium sulfate fractionation, DEAE cellulose, Sephadex G-75, and Blue Sepharose CL-6B affinity column chromatographies. CAD was purified to 514.2 folds with overall recovery of 13 % and specific activity of 812. 5 nkat/mg. Native and subunit molecular masses of the purified enzyme were found to be ∼76 and ∼38 kDa, respectively, suggesting it to be a homodimer. The enzyme exhibited highest catalytic efficiency (Kcat/Km 3.75 μM(-1) s(-1)) with cinnamyl aldehyde among all the substrates investigated. The pH and temperature optima of the purified CAD were pH 8.8 and 40 °C, respectively. The enzyme activity was enhanced in the presence of 2.0 mM Mg(2+), while Zn(2+) at the same concentration exerted an inhibitory effect. The inclusion of 2.0 mM EDTA in the assay system activated the enzyme. The enzyme was inhibited with caffeic acid and ferulic acid in a concentration-dependent manner, while no inhibition was observed with salicylic acid. Peptide mass analysis of the purified CAD by MALDI-TOF showed a significant homology to alcohol dehydrogenases of MDR superfamily.
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22
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Lee C, Bedgar DL, Davin LB, Lewis NG. Assessment of a putative proton relay in Arabidopsis cinnamyl alcohol dehydrogenase catalysis. Org Biomol Chem 2013; 11:1127-34. [PMID: 23296200 DOI: 10.1039/c2ob27189c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Extended proton relay systems have been proposed for various alcohol dehydrogenases, including the Arabidopsis thaliana cinnamyl alcohol dehydrogenases (AtCADs). Following a previous structural biology investigation of AtCAD5, the potential roles of three amino acid residues in a putative proton relay system, namely Thr49, His52 and Asp57, in AtCAD5, were investigated herein. Using site-directed mutagenesis, kinetic and isothermal titration calorimetry (ITC) analyses, it was established that the Thr49 residue was essential for overall catalytic conversion, whereas His52 and Asp57 residues were not. Mutation of the Thr49 residue to Ala resulted in near abolition of catalysis, with thermodynamic data indicating a negative enthalpic change (ΔH), as well as a significant decrease in binding affinity with NADPH, in contrast to wild type AtCAD5. Mutation of His52 and Asp57 residues by Ala did not significantly change either catalytic efficiency or thermodynamic parameters. Therefore, only the Thr49 residue is demonstrably essential for catalytic function. ITC analyses also suggested that for AtCAD5 catalysis, NADPH was bound first followed by p-coumaryl aldehyde.
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Affiliation(s)
- Choonseok Lee
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
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23
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Alcohol dehydrogenases from Scheffersomyces stipitis involved in the detoxification of aldehyde inhibitors derived from lignocellulosic biomass conversion. Appl Microbiol Biotechnol 2013; 97:8411-25. [PMID: 23912116 DOI: 10.1007/s00253-013-5110-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/03/2013] [Accepted: 07/07/2013] [Indexed: 10/26/2022]
Abstract
Aldehyde inhibitors such as furfural and 5-hydroxymethylfurfural (HMF) are generated from biomass pretreatment. Scheffersomyces stipitis is able to reduce furfural and HMF to less toxic furanmethanol and furan-2,5-dimethanol; however, the enzymes involved in the reductive reaction still remain unknown. In this study, transcription responses of two known and five putative alcohol dehydrogenase genes from S. stipitis were analyzed under furfural and HMF stress conditions. All the seven alcohol dehydrogenase genes were also cloned and overexpressed for their activity analyses. Our results indicate that transcriptions of SsADH4 and SsADH6 were highly induced under furfural and HMF stress conditions, and the proteins encoded by them exhibited NADH- and/or NADPH-dependent activities for furfural and HMF reduction, respectively. For furfural reduction, NADH-dependent activity was also observed in SsAdh1p and NAD(P)H-dependent activities were also observed in SsAdh5p and SsAdh7p. For HMF reduction, NADPH-dependent activities were also observed in SsAdh5p and SsAdh7p. SsAdh4p displayed the highest NADPH-dependent specific activity and catalytic efficiency for reduction of both furfural and HMF among the seven alcohol dehydrogenases. Enzyme activities of all SsADH proteins were more stable under acidic condition. For most SsADH proteins, the optimum temperature for enzyme activities was 30 °C and more than 50 % enzyme activities remained at 60 °C. Reduction activities of formaldehyde, acetaldehyde, isovaleraldehyde, benzaldehyde, and phenylacetaldehyde were also observed in some SsADH proteins. Our results indicate that multiple alcohol dehydrogenases in S. stipitis are involved in the detoxification of aldehyde inhibitors derived from lignocellulosic biomass conversion.
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Aggarwal N, Mandal PK, Gautham N, Chadha A. Expression, purification, crystallization and preliminary X-ray diffraction analysis of carbonyl reductase from Candida parapsilosis ATCC 7330. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:313-5. [PMID: 23519811 PMCID: PMC3606581 DOI: 10.1107/s1744309113003667] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 02/05/2013] [Indexed: 11/10/2022]
Abstract
The NAD(P)H-dependent carbonyl reductase from Candida parapsilosis ATCC 7330 catalyses the asymmetric reduction of ethyl 4-phenyl-2-oxobutanoate to ethyl (R)-4-phenyl-2-hydroxybutanoate, a precursor of angiotensin-converting enzyme inhibitors such as Cilazapril and Benazepril. The carbonyl reductase was expressed in Escherichia coli and purified by GST-affinity and size-exclusion chromatography. Crystals were obtained by the hanging-drop vapour-diffusion method and diffracted to 1.86 Å resolution. The asymmetric unit contained two molecules of carbonyl reductase, with a solvent content of 48%. The structure was solved by molecular replacement using cinnamyl alcohol dehydrogenase from Saccharomyces cerevisiae as a search model.
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Affiliation(s)
- Nidhi Aggarwal
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, India
| | - P. K. Mandal
- CAS in Crystallography and Biophysics, University of Madras, Guindy, Chennai 600 025, India
| | - Namasivayam Gautham
- CAS in Crystallography and Biophysics, University of Madras, Guindy, Chennai 600 025, India
| | - Anju Chadha
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, India
- National Center for Catalysis Research, Indian Institute of Technology Madras, Chennai 600 036, India
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25
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Leiros HKS, Fedøy AE, Leiros I, Steen IH. The complex structures of isocitrate dehydrogenase from Clostridium thermocellum and Desulfotalea psychrophila suggest a new active site locking mechanism. FEBS Open Bio 2012; 2:159-72. [PMID: 23650595 PMCID: PMC3642140 DOI: 10.1016/j.fob.2012.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 06/28/2012] [Accepted: 06/28/2012] [Indexed: 11/29/2022] Open
Abstract
Isocitrate dehydrogenase (IDH) catalyzes the oxidative NAD(P)+-dependent decarboxylation of isocitrate into α-ketoglutarate and CO2 and is present in organisms spanning the biological range of temperature. We have solved two crystal structures of the thermophilic Clostridium thermocellum IDH (CtIDH), a native open apo CtIDH to 2.35 Å and a quaternary complex of CtIDH with NADP+, isocitrate and Mg2+ to 2.5 Å. To compare to these a quaternary complex structure of the psychrophilic Desulfotalea psychrophila IDH (DpIDH) was also resolved to 1.93 Å. CtIDH and DpIDH showed similar global thermal stabilities with melting temperatures of 67.9 and 66.9 °C, respectively. CtIDH represents a typical thermophilic enzyme, with a large number of ionic interactions and hydrogen bonds per residue combined with stabilization of the N and C termini. CtIDH had a higher activity temperature optimum, and showed greater affinity for the substrates with an active site that was less thermolabile compared to DpIDH. The uncompensated negative surface charge and the enlarged methionine cluster in the hinge region both of which are important for cold activity in DpIDH, were absent in CtIDH. These structural comparisons revealed that prokaryotic IDHs in subfamily II have a unique locking mechanism involving Arg310, Asp251′ and Arg255 (CtIDH). These interactions lock the large domain to the small domain and direct NADP+ into the correct orientation, which together are important for NADP+ selectivity.
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Key Words
- CtIDH, Clostridium thermocellum IDH
- DSC, differential scanning calorimetry
- DhIDH, Desulfitobacterium hafniense IDH
- Domain movement
- DpIDH, Desulfotalea psychrophila IDH
- EcIDH, Escherichia coli IDH
- HcIDH, human cytosolic IDH
- IDH, isocitrate dehydrogenase
- NADP+ selectivity
- PcIDH, porcine heart mitochondrial IDH
- Psychrophilic
- ScIDH, Saccharomyces cerevesiae mitochondrial IDH
- Temperature adaptation
- Thermophilic
- Tm, apparent melting temperature
- TmIDH, Thermotoga maritima
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Affiliation(s)
- Hanna-Kirsti S Leiros
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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Seo KH, Zhuang N, Chen C, Song JY, Kang HL, Rhee KH, Lee KH. Unusual NADPH conformation in the crystal structure of a cinnamyl alcohol dehydrogenase from Helicobacter pylori in complex with NADP(H) and substrate docking analysis. FEBS Lett 2012; 586:337-43. [PMID: 22269576 DOI: 10.1016/j.febslet.2012.01.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 12/31/2011] [Accepted: 01/12/2012] [Indexed: 11/26/2022]
Abstract
Cinnamyl alcohol dehydrogenase is a zinc- and NADPH-dependent dehydrogenase catalyzing the reversible conversion of p-hydroxycinnamaldehydes to their corresponding hydroxycinnamyl alcohols. A CAD homolog from Helicobacter pylori (HpCAD) possesses broad substrate specificities like the plant CADs and additionally a dismutation activity converting benzaldehyde to benzyl alcohol and benzoic acid. We have determined the crystal structure of HpCAD complexed with NADP(H) at 2.18Å resolution to get a better understanding of this class of CAD outside of plants. The structure of HpCAD is highly homologous to the sinapyl alcohol dehydrogenase and the plant CAD with well-conserved residues involved in catalysis and zinc binding. However, the NADP(H) binding mode of the HpCAD has been found to be significantly different from those of plant CADs.
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Affiliation(s)
- Kyung Hye Seo
- Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju, Republic of Korea
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Pandey B, Pandey VP, Dwivedi UN. Cloning, expression, functional validation and modeling of cinnamyl alcohol dehydrogenase isolated from xylem of Leucaena leucocephala. Protein Expr Purif 2011; 79:197-203. [DOI: 10.1016/j.pep.2011.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2011] [Revised: 06/05/2011] [Accepted: 06/07/2011] [Indexed: 10/18/2022]
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Badawi HM, Förner W. Vibrational spectra and assignments of 3-phenylprop-2-en-1-ol (cinnamyl alcohol) and 3-phenyl-1-propanol. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.07.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Evolution of the Cinnamyl/Sinapyl Alcohol Dehydrogenase (CAD/SAD) gene family: the emergence of real lignin is associated with the origin of Bona Fide CAD. J Mol Evol 2010; 71:202-18. [PMID: 20721545 DOI: 10.1007/s00239-010-9378-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 07/26/2010] [Indexed: 10/19/2022]
Abstract
Lignin plays a vital role in plant adaptation to terrestrial environments. The cinnamyl alcohol dehydrogenase (CAD) catalyzes the last step in monolignol biosynthesis and might have contributed to the lignin diversity in plants. To investigate the evolutionary history and functional differentiation of the CAD gene family, we made a comprehensive evolutionary analysis of this gene family from 52 species, including bacteria, early eukaryotes and green plants. The phylogenetic analysis, together with gene structure and function, indicates that all members of land plants, except two of moss, could be divided into three classes. Members of Class I (bona fide CAD), generally accepted as the primary genes involved in the monolignol biosynthesis, are all from vascular plants, and form a robustly supported monophyletic group with the lycophyte CADs at the basal position. This class is also conserved in the predicted three-dimensional structure and the residues constituting the substrate-binding pocket of the proteins. Given that Selaginella has real lignin, the above evidence strongly suggests that the earliest occurrence of the bona fide CAD in the lycophyte could be directly correlated with the origin of lignin. Class II comprises members more similar to the aspen sinapyl alcohol dehydrogenase gene, and includes three groups corresponding to lycophyte, gymnosperm, and angiosperm. Class III is conserved in land plants. The three classes differ in patterns of evolution and expression, implying that functional divergence has occurred among them. Our study also supports the hypothesis of convergent evolution of lignin biosynthesis between red algae and vascular plants.
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Ehsani M, Fernández MR, Biosca JA, Dequin S. Reversal of coenzyme specificity of 2,3-butanediol dehydrogenase fromSaccharomyces cerevisaeand in vivo functional analysis. Biotechnol Bioeng 2009; 104:381-9. [DOI: 10.1002/bit.22391] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Atsumi S, Wu TY, Eckl EM, Hawkins SD, Buelter T, Liao JC. Engineering the isobutanol biosynthetic pathway in Escherichia coli by comparison of three aldehyde reductase/alcohol dehydrogenase genes. Appl Microbiol Biotechnol 2009; 85:651-7. [PMID: 19609521 PMCID: PMC2802489 DOI: 10.1007/s00253-009-2085-6] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2009] [Revised: 06/02/2009] [Accepted: 06/06/2009] [Indexed: 11/29/2022]
Abstract
Biofuels synthesized from renewable resources are of increasing interest because of global energy and environmental problems. We have previously demonstrated production of higher alcohols from Escherichia coli using a 2-keto acid-based pathway. Here, we have compared the effect of various alcohol dehydrogenases (ADH) for the last step of the isobutanol production. E. coli has the yqhD gene which encodes a broad-range ADH. Isobutanol production significantly decreased with the deletion of yqhD, suggesting that the yqhD gene on the genome contributed to isobutanol production. The adh genes of two bacteria and one yeast were also compared in E. coli harboring the isobutanol synthesis pathway. Overexpression of yqhD or adhA in E. coli showed better production than ADH2, a result confirmed by activity measurements with isobutyraldehyde.
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Affiliation(s)
- Shota Atsumi
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
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Porté S, Valencia E, Yakovtseva EA, Borràs E, Shafqat N, Debreczeny JÉ, Pike ACW, Oppermann U, Farrés J, Fita I, Parés X. Three-dimensional structure and enzymatic function of proapoptotic human p53-inducible quinone oxidoreductase PIG3. J Biol Chem 2009; 284:17194-17205. [PMID: 19349281 PMCID: PMC2719357 DOI: 10.1074/jbc.m109.001800] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Revised: 03/31/2009] [Indexed: 01/10/2023] Open
Abstract
Tumor suppressor p53 regulates the expression of p53-induced genes (PIG) that trigger apoptosis. PIG3 or TP53I3 is the only known member of the medium chain dehydrogenase/reductase superfamily induced by p53 and is used as a proapoptotic marker. Although the participation of PIG3 in the apoptotic pathway is proven, the protein and its mechanism of action were never characterized. We analyzed human PIG3 enzymatic function and found NADPH-dependent reductase activity with ortho-quinones, which is consistent with the classification of PIG3 in the quinone oxidoreductase family. However, the activity is much lower than that of zeta-crystallin, a better known quinone oxidoreductase. In addition, we report the crystallographic structure of PIG3, which allowed the identification of substrate- and cofactor-binding sites, with residues fully conserved from bacteria to human. Tyr-59 in zeta-crystallin (Tyr-51 in PIG3) was suggested to participate in the catalysis of quinone reduction. However, kinetics of Tyr/Phe and Tyr/Ala mutants of both enzymes demonstrated that the active site Tyr is not catalytic but may participate in substrate binding, consistent with a mechanism based on propinquity effects. It has been proposed that PIG3 contribution to apoptosis would be through oxidative stress generation. We found that in vitro activity and in vivo overexpression of PIG3 accumulate reactive oxygen species. Accordingly, an inactive PIG3 mutant (S151V) did not produce reactive oxygen species in cells, indicating that enzymatically active protein is necessary for this function. This supports that PIG3 action is through oxidative stress produced by its enzymatic activity and provides essential knowledge for eventual control of apoptosis.
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Affiliation(s)
- Sergio Porté
- From the Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Eva Valencia
- Institut de Biologia Molecular (IBMB-Consejo Superior de Investigaciones Científicas) and IRB Barcelona, Parc Científic de Barcelona, Josep-Samitier 1-5, 08028 Barcelona, Spain
| | - Evgenia A Yakovtseva
- From the Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Emma Borràs
- From the Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Naeem Shafqat
- Structural Genomics Consortium, Old Road Research Campus, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Judit É Debreczeny
- Structural Genomics Consortium, Old Road Research Campus, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Ashley C W Pike
- Structural Genomics Consortium, Old Road Research Campus, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Udo Oppermann
- Structural Genomics Consortium, Old Road Research Campus, University of Oxford, Oxford OX3 7DQ, United Kingdom; Botnar Research Center, Oxford Biomedical Research Unit, Oxford OX3 7LD, United Kingdom
| | - Jaume Farrés
- From the Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Ignacio Fita
- Institut de Biologia Molecular (IBMB-Consejo Superior de Investigaciones Científicas) and IRB Barcelona, Parc Científic de Barcelona, Josep-Samitier 1-5, 08028 Barcelona, Spain
| | - Xavier Parés
- From the Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
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Purification, characterization, and potential bacterial wax production role of an NADPH-dependent fatty aldehyde reductase from Marinobacter aquaeolei VT8. Appl Environ Microbiol 2009; 75:2758-64. [PMID: 19270127 DOI: 10.1128/aem.02578-08] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Wax esters, ester-linked fatty acids and long-chain alcohols, are important energy storage compounds in select bacteria. The synthesis of wax esters from fatty acids is proposed to require the action of a four-enzyme pathway. An essential step in the pathway is the reduction of a fatty aldehyde to the corresponding fatty alcohol, although the enzyme responsible for catalyzing this reaction has yet to be identified in bacteria. We report here the purification and characterization of an enzyme from the wax ester-accumulating bacterium Marinobacter aquaeolei VT8, which is a proposed fatty aldehyde reductase in this pathway. The enzyme, a 57-kDa monomer, was expressed in Escherichia coli as a fusion protein with the maltose binding protein on the N terminus and was purified to near homogeneity by using amylose affinity chromatography. The purified enzyme was found to reduce a number of long-chain aldehydes to the corresponding alcohols coupled to the oxidation of NADPH. The highest specific activity was observed for the reduction of decanal (85 nmol decanal reduced/min/mg). Short-chain and aromatic aldehydes were not substrates. The enzyme showed no detectable catalysis of the reverse reaction, the oxidation of decanol by NADP(+). The mechanism of the enzyme was probed with several site-specific chemical probes. The possible uses of this enzyme in the production of wax esters are discussed.
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Nakamura S, Oda M, Kataoka S, Ueda S, Uchiyama S, Yoshida T, Kobayashi Y, Ohkubo T. Apo- and Holo-structures of 3α-Hydroxysteroid Dehydrogenase from Pseudomonas sp. B-0831. J Biol Chem 2006. [DOI: 10.1016/s0021-9258(19)84102-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Nakamura S, Oda M, Kataoka S, Ueda S, Uchiyama S, Yoshida T, Kobayashi Y, Ohkubo T. Apo- and holo-structures of 3alpha-hydroxysteroid dehydrogenase from Pseudomonas sp. B-0831. Loop-helix transition induced by coenzyme binding. J Biol Chem 2006; 281:31876-84. [PMID: 16905772 DOI: 10.1074/jbc.m604226200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial 3alpha-hydroxysteroid dehydrogenase, which belongs to a short-chain dehydrogenase/reductase family and forms a dimer composed of two 26-kDa subunits, catalyzes the oxidoreduction of hydroxysteroids in a coenzyme-dependent manner. This enzyme also catalyzes the oxidoreduction of nonsteroid compounds that play an important role in xenobiotic metabolism of bacteria. We performed an x-ray analysis on the crystal of Ps3alphaHSD, the enzyme from Pseudomonas sp. B-0831 complexed with NADH. The resulting crystal structure at 1.8A resolution showed that Ps3alphaHSD exists as a structural heterodimer composed of apo- and holo-subunits. A distinct structural difference between them was found in the 185-207-amino acid region, where the structure in the apo-subunit is disordered whereas that in the holo-subunit consists of two alpha-helices. This fact proved that the NADH binding allows the helical structures to form the substrate binding pocket even in the absence of the substrate, although the region corresponds to the so-called "substrate-binding loop." The induction of alpha-helices in solution by the coenzyme binding was also confirmed by the CD experiment. In addition, the CD experiment revealed that the helix-inducing ability of NADH is stronger than that of NAD. We discuss the negative cooperativity for the coenzyme binding, which is caused by the effect of the structural change transferred between the subunits of the heterodimer.
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Affiliation(s)
- Shota Nakamura
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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Youn B, Camacho R, Moinuddin SGA, Lee C, Davin LB, Lewis NG, Kang C. Crystal structures and catalytic mechanism of the Arabidopsis cinnamyl alcohol dehydrogenases AtCAD5 and AtCAD4. Org Biomol Chem 2006; 4:1687-97. [PMID: 16633561 DOI: 10.1039/b601672c] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cinnamyl alcohol dehydrogenase (CAD) multigene family in planta encodes proteins catalyzing the reductions of various phenylpropenyl aldehyde derivatives in a substrate versatile manner, and whose metabolic products are the precursors of structural lignins, health-related lignans, and various other metabolites. In Arabidopsis thaliana, the two isoforms, AtCAD5 and AtCAD4, are the catalytically most active being viewed as mainly involved in the formation of guaiacyl/syringyl lignins. In this study, we determined the crystal structures of AtCAD5 in the apo-form and as a binary complex with NADP+, respectively, and modeled that of AtCAD4. Both AtCAD5 and AtCAD4 are dimers with two zinc ions per subunit and belong to the Zn-dependent medium chain dehydrogenase/reductase (MDR) superfamily, on the basis of their overall 2-domain structures and distribution of secondary structural elements. The catalytic Zn2+ ions in both enzymes are tetrahedrally coordinated, but differ from those in horse liver alcohol dehydrogenase since the carboxyl side-chain of Glu70 is ligated to Zn2+ instead of water. Using AtCAD5, site-directed mutagenesis of Glu70 to alanine resulted in loss of catalytic activity, thereby indicating that perturbation of the Zn2+ coordination was sufficient to abolish catalytic activity. The substrate-binding pockets of both AtCAD5 and AtCAD4 were also examined, and found to be significantly different and smaller compared to that of a putative aspen sinapyl alcohol dehydrogenase (SAD) and a putative yeast CAD. While the physiological roles of the aspen SAD and the yeast CAD are uncertain, they nevertheless have a high similarity in the overall 3D structures to AtCAD5 and 4. With the bona fide CAD's from various species, nine out of the twelve residues which constitute the proposed substrate-binding pocket were, however, conserved. This is provisionally considered as indicative of a characteristic fingerprint for the CAD family.
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Affiliation(s)
- Buhyun Youn
- School of Molecular Biosciences, Washington State University, Pullman, 99164-4660, USA
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Current awareness on yeast. Yeast 2005. [PMID: 15773059 PMCID: PMC7169799 DOI: 10.1002/yea.1158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to keep subscribers up‐to‐date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly‐published material on yeasts. Each bibliography is divided into 10 sections. 1 Books, Reviews & Symposia; 2 General; 3 Biochemistry; 4 Biotechnology; 5 Cell Biology; 6 Gene Expression; 7 Genetics; 8 Physiology; 9 Medical Mycology; 10 Recombinant DNA Technology. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted. (4 weeks journals ‐ search completed 10th. Nov. 2004)
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