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Ruickoldt J, Jeoung JH, Rudolph MA, Lennartz F, Kreibich J, Schomäcker R, Dobbek H. Coupling CO2 Reduction and Acetyl-CoA Formation: The Role of a CO Capturing Tunnel in Enzymatic Catalysis. Angew Chem Int Ed Engl 2024:e202405120. [PMID: 38743001 DOI: 10.1002/anie.202405120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
The bifunctional CO-dehydrogenase/acetyl-CoA synthase (CODH/ACS) complex couples the reduction of CO2 to the condensation of CO with a methyl-moiety and CoA to acetyl-CoA. Catalysis occurs at two sites connected by a tunnel transporting the CO. Here, we investigated how the bifunctional complex and its tunnel support catalysis using the CODH/ACS from Carboxydothermus hydrogenoformans as a model. Although CODH/ACS adapted to form a stable bifunctional complex with a secluded substrate tunnel, catalysis and CO transport is even more efficient when two monofunctional enzymes are coupled. Efficient CO channeling appears to be ensured by hydrophobic binding sites for CO, which act in a bucket-brigade fashion rather than as a simple tube. Tunnel remodeling showed that opening the tunnel increased activity but impaired directed transport of CO. Constricting the tunnel impaired activity and CO transport, suggesting that the tunnel evolved to sequester CO rather than to maximize turnover.
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Affiliation(s)
| | | | | | - Frank Lennartz
- Helmholtz Zentrum Berlin, Macromolecular Crystallography, GERMANY
| | | | | | - Holger Dobbek
- Humboldt-Universitaet zu Berlin, Structural Biology and Biochemistry, Unter den Linden 6, 10099, Berlin, GERMANY
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Chi B, Li F, Wang X, Pan H, Yi X, Liu Y, Zhan J, Zhang X, Zhou H, Wang W. DMF mineralization and substrate specificity mechanism of Aminobacter ciceronei DMFA1. Environ Res 2024; 245:117980. [PMID: 38142731 DOI: 10.1016/j.envres.2023.117980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/04/2023] [Accepted: 12/16/2023] [Indexed: 12/26/2023]
Abstract
N,N-dimethylformamide (DMF) is widely used in various industries, but its direct release into water poses high risks to human beings. Although a lot of DMF-degrading bacteria has been isolated, limited studies focus on the degradation preference among DMF and its analogues. In this study, an efficient DMF mineralization bacterium designated Aminobacter ciceronei DMFA1 was isolated from marine sediment. When exposed to a 0.2% DMF (∼1900 mg/L), strain DMFA1 exhibited a degradation efficiency of 100% within 4 days. The observed growth using formamide as the sole carbon source implied the possible DMF degradation pathway of strain DMFA1. Meanwhile,the strain DMFA1 possesses a broad-spectrum substrate degradation, which could effectively degraded 0.2% N,N-dimethylacetamide (DMAC) and N-methylformamide (NMF). Genomic analysis further confirmed the supposed pathway through annotating the genes encoding N, N-dimethylformamidase (DMFase), formamidase, and formate dehydrogenase. The existence of sole DMFase indicating its substrate specificity controlled the preference of DMAc of strain DMFA1. By integrating multiple sequence alignment, homology modeling and molecular docking, the preference of the DMFase in strain DMFA1 towards DMAc are related to: 1) Mutations in key active site residues; 2) the absence of small subunit; and 3) no energy barrier for substrates entering the active site.
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Affiliation(s)
- Baihui Chi
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Fei Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Xukang Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Haixia Pan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Xianliang Yi
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Yang Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Jingjing Zhan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Xuwang Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Hao Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China.
| | - Wenyuan Wang
- State Key Laboratory of Coastal and Offshore Engineering, Dalian University of Technology, Dalian, 116024, China.
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Xia B, Li Z, Wei J, Hu G, Yang J, Zhang H, Hu X. Modification of the Loop Region Near the Substrate Tunnel to Alter the Hydrolytic Process of Dextranase. J Biotechnol 2024; 381:57-66. [PMID: 38185430 DOI: 10.1016/j.jbiotec.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
Dextranases are hydrolases that exclusively catalyze the disruption of α-1,6 glycosidic bonds. A series of variant enzymes were obtained by comparing the sequences of dextranases from different sources and introducing sequence substitutions. A correlation was found between the number of amino acids in the 397-401 region and the hydrolytic process. When there were no more than 5 amino acids in the 397-401 region, the enzyme first hydrolyzed the dextran T70 to a low molecular weight dextran with a molecular weight of about 5000, then IMOs1 appeared in the system if the degradation continued, showing a clear sequential relationship. And when there are more than 5 amino acids in the 397-401 region, IMOs were produced at the beginning of hydrolysis and continue to increase throughout the hydrolytic process. At the same time, we investigated the enzymatic properties of the variants and found that the hydrolytic rate of A-Ca was 11 times higher than that of the original enzyme. The proportion of IMOs produced by A-Ca was 80.68%, which was nearly10% higher than the original enzyme, providing a new enzyme for the industrial preparation of IMOs.
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Affiliation(s)
- Bingbing Xia
- School of Food and Biological Engineering, Hefei University of Technology, Anhui 230000, China
| | - Zhiwei Li
- School of Food and Biological Engineering, Hefei University of Technology, Anhui 230000, China
| | - Jinao Wei
- School of Food and Biological Engineering, Hefei University of Technology, Anhui 230000, China
| | - Ganpeng Hu
- School of Food and Biological Engineering, Hefei University of Technology, Anhui 230000, China
| | - Jingwen Yang
- School of Food and Biological Engineering, Hefei University of Technology, Anhui 230000, China
| | - Hongbin Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Anhui 230000, China.
| | - Xueqin Hu
- School of Food and Biological Engineering, Hefei University of Technology, Anhui 230000, China.
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Guo J, Berdychowska J, Lai Q, Meng Y, Cheng Z, Peplowski L, Zhou Z. "Toolbox" construction of an extremophilic nitrile hydratase from Streptomyces thermoautotrophicus for the promising industrial production of various amides. Int J Biol Macromol 2022; 221:1103-11. [PMID: 36108746 DOI: 10.1016/j.ijbiomac.2022.09.071] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/23/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022]
Abstract
Nitrile hydratase (NHase; EC 4.2.1.84) is widely used to synthesize the corresponding amides from nitriles, which is the most successful green biocatalyst. However, the limited acceptability of substrates and instability under harsh reaction conditions have hindered its widespread industrial application. Here, a gene encoding an extremophilic NHase from Streptomyces thermoautotrophicus (S.t NHase) was successfully overexpressed in Escherichia coli. The enzyme exhibited excellent thermostability, retaining >50 % of residual activity after heat treatment at 65 °C for 252 min. To further improve the catalytic performance of S.t NHase, semi-rational engineering of its substrate access tunnel was performed. A mutant βL48D showed a specific activity of 566.18 ± 18.86 U/mg towards 3-cyanopyridine, which was 7.7 times higher than its parent enzyme (73.80 ± 5.76 U/mg). Molecular dynamics simulation showed that the introduction of aspartic acid into βLeu48 resulted in a larger and more frequent opening of the substrate access tunnel entrance. On this basis, a "toolbox" containing various mutants on the substrate access tunnel was further established, whose catalytic activity towards various nitrile substrates was extensively improved, showing great potential for efficient synthesis of multiple high-value amides.
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Sun BY, Sui HL, Liu ZW, Tao XY, Gao B, Zhao M, Ma YS, Zhao J, Liu M, Wang FQ, Wei DZ. Structure-guided engineering of a flavin-containing monooxygenase for the efficient production of indirubin. BIORESOUR BIOPROCESS 2022; 9:70. [PMID: 38647553 PMCID: PMC10991670 DOI: 10.1186/s40643-022-00559-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/10/2022] [Indexed: 11/10/2022] Open
Abstract
Indirubin is a bisindole compound for the treatment of chronic myelocytic leukemia. Here, we presented a structure-guided method to improve the activity of a flavin-containing monooxygenase (bFMO) for the efficient production of indirubin in Escherichia coli. A flexible loop interlocked with the active pocket through a helix and the substrate tunnel rather than the active pocket in bFMO were identified to be two reconfigurable structures to improve its activity, resulting in K223R and N291T mutants with enhanced catalytic activity by 2.5- and 2.0-fold, respectively. A combined modification at the two regions (K223R/D317S) achieved a 6.6-fold improvement in catalytic efficiency (kcat/Km) due to enhancing π-π stacking interactions stabilization. Finally, an engineered E. coli strain was constructed by metabolic engineering, which could produce 860.7 mg/L (18 mg/L/h) indirubin, the highest yield ever reported. This work provides new insight into the redesign of FMOs to boost their activities and an efficient approach to produce indirubin.
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Affiliation(s)
- Bing-Yao Sun
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Hua-Lu Sui
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Zi-Wei Liu
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Xin-Yi Tao
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Bei Gao
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Ming Zhao
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Yu-Shu Ma
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Jian Zhao
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Min Liu
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Feng-Qing Wang
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Dong-Zhi Wei
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
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Dostál J, Brynda J, Blaha J, Macháček S, Heidingsfeld O, Pichová I. Crystal structure of carbonic anhydrase CaNce103p from the pathogenic yeast Candida albicans. BMC Struct Biol 2018; 18:14. [PMID: 30367660 PMCID: PMC6203986 DOI: 10.1186/s12900-018-0093-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/02/2018] [Indexed: 01/27/2023]
Abstract
Background The pathogenic yeast Candida albicans can proliferate in environments with different carbon dioxide concentrations thanks to the carbonic anhydrase CaNce103p, which accelerates spontaneous conversion of carbon dioxide to bicarbonate and vice versa. Without functional CaNce103p, C. albicans cannot survive in atmospheric air. CaNce103p falls into the β-carbonic anhydrase class, along with its ortholog ScNce103p from Saccharomyces cerevisiae. The crystal structure of CaNce103p is of interest because this enzyme is a potential target for surface disinfectants. Results Recombinant CaNce103p was prepared in E. coli, and its crystal structure was determined at 2.2 Å resolution. CaNce103p forms a homotetramer organized as a dimer of dimers, in which the dimerization and tetramerization surfaces are perpendicular. Although the physiological role of CaNce103p is similar to that of ScNce103p from baker’s yeast, on the structural level it more closely resembles carbonic anhydrase from the saprophytic fungus Sordaria macrospora, which is also tetrameric. Dimerization is mediated by two helices in the N-terminal domain of the subunits. The N-terminus of CaNce103p is flexible, and crystals were obtained only upon truncation of the first 29 amino acids. Analysis of CaNce103p variants truncated by 29, 48 and 61 amino acids showed that residues 30–48 are essential for dimerization. Each subunit contains a zinc atom in the active site and displays features characteristic of type I β-carbonic anhydrases. Zinc is tetrahedrally coordinated by one histidine residue, two cysteine residues and a molecule of β-mercaptoethanol originating from the crystallization buffer. The active sites are accessible via substrate tunnels, which are slightly longer and narrower than those observed in other fungal carbonic anhydrases. Conclusions CaNce103p is a β-class homotetrameric metalloenzyme composed of two homodimers. Its structure closely resembles those of other β-type carbonic anhydrases, in particular CAS1 from Sordaria macrospora. The main differences occur in the N-terminal part and the substrate tunnel. Detailed knowledge of the CaNce103p structure and the properties of the substrate tunnel in particular will facilitate design of selective inhibitors of this enzyme.
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Affiliation(s)
- Jiří Dostál
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague, Czech Republic
| | - Jan Blaha
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague, Czech Republic
| | - Stanislav Macháček
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague, Czech Republic
| | - Olga Heidingsfeld
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague, Czech Republic.,Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentská 95, 532 10, Pardubice, Czech Republic
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague, Czech Republic.
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Tsai CL, Tainer JA. Robust Production, Crystallization, Structure Determination, and Analysis of [Fe-S] Proteins: Uncovering Control of Electron Shuttling and Gating in the Respiratory Metabolism of Molybdopterin Guanine Dinucleotide Enzymes. Methods Enzymol 2017; 599:157-196. [PMID: 29746239 DOI: 10.1016/bs.mie.2017.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
[Fe-S] clusters are essential cofactors in all domains of life. They play many biological roles due to their unique abilities for electron transfer and conformational control. Yet, producing and analyzing Fe-S proteins can be difficult and even misleading if not done anaerobically. Due to unique redox properties of [Fe-S] clusters and their oxygen sensitivity, they pose multiple challenges and can lose enzymatic activity or cause their component proteins to be structurally disordered due to [Fe-S] cluster oxidation and loss in air. Here we highlight tested protocols and strategies enabling efficient and stable [Fe-S] protein production, purification, crystallization, X-ray diffraction data collection, and structure determination. From multiple high-resolution anaerobic crystal structures, we furthermore analyze exemplary data defining [Fe-S] clusters, substrate entry, and product exit for the functional oxidation states of type II molybdo-bis(molybdopterin guanine dinucleotide) (Mo-bisMGD) enzymes. Notably, these enzymes perform electron shuttling between quinone pools and specific substrates to catalyze respiratory metabolism. The identified structure-activity relationships for this enzyme class have broad implications germane to perchlorate environments on Earth and Mars extending to an alternative mechanism underlying metabolic origins for the evolution of the oxygen atmosphere. Integrated structural analyses of type II Mo-bisMGD enzymes unveil novel distinctive shared molecular mechanisms for dynamic control of substrate entry and product release gated by hydrophobic residues. Collective findings support a prototypic model for type II Mo-bisMGD enzymes including insights for a fundamental molecular mechanistic understanding of selectivity and regulation by a conformationally gated channel with general implications for [Fe-S] cluster respiratory enzymes.
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Affiliation(s)
- Chi-Lin Tsai
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States
| | - John A Tainer
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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