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Zhang L, King E, Black WB, Heckmann CM, Wolder A, Cui Y, Nicklen F, Siegel JB, Luo R, Paul CE, Li H. Directed evolution of phosphite dehydrogenase to cycle noncanonical redox cofactors via universal growth selection platform. Nat Commun 2022; 13:5021. [PMID: 36028482 PMCID: PMC9418148 DOI: 10.1038/s41467-022-32727-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/13/2022] [Indexed: 11/09/2022] Open
Abstract
Noncanonical redox cofactors are attractive low-cost alternatives to nicotinamide adenine dinucleotide (phosphate) (NAD(P)+) in biotransformation. However, engineering enzymes to utilize them is challenging. Here, we present a high-throughput directed evolution platform which couples cell growth to the in vivo cycling of a noncanonical cofactor, nicotinamide mononucleotide (NMN+). We achieve this by engineering the life-essential glutathione reductase in Escherichia coli to exclusively rely on the reduced NMN+ (NMNH). Using this system, we develop a phosphite dehydrogenase (PTDH) to cycle NMN+ with ~147-fold improved catalytic efficiency, which translates to an industrially viable total turnover number of ~45,000 in cell-free biotransformation without requiring high cofactor concentrations. Moreover, the PTDH variants also exhibit improved activity with another structurally deviant noncanonical cofactor, 1-benzylnicotinamide (BNA+), showcasing their broad applications. Structural modeling prediction reveals a general design principle where the mutations and the smaller, noncanonical cofactors together mimic the steric interactions of the larger, natural cofactors NAD(P)+.
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Affiliation(s)
- Linyue Zhang
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Edward King
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, 92697, USA
| | - William B Black
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Christian M Heckmann
- Biocatalysis, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, Netherlands
| | - Allison Wolder
- Biocatalysis, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, Netherlands
| | - Youtian Cui
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Francis Nicklen
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Justin B Siegel
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, 2700 Stockton Boulevard, Suite 2102, Sacramento, CA, 95817, USA
- Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA
| | - Ray Luo
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, 92697, USA
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, 92697, USA
- Department Materials Science and Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, Netherlands
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA.
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, 92697, USA.
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Rahuel-Clermont S, Bchini R, Barbe S, Boutserin S, André I, Talfournier F. Enzyme Active Site Loop Revealed as a Gatekeeper for Cofactor Flip by Targeted Molecular Dynamics Simulations and FRET-Based Kinetics. ACS Catal 2019. [DOI: 10.1021/acscatal.8b03951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Raphaël Bchini
- Université de Lorraine, CNRS, IMoPA, Campus Biologie Santé, F-54000 Nancy, France
| | - Sophie Barbe
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France, 135, Avenue de Rangueil, F-31077 Toulouse cedex 04, France
| | - Séverine Boutserin
- Université de Lorraine, CNRS, IMoPA, Campus Biologie Santé, F-54000 Nancy, France
| | - Isabelle André
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France, 135, Avenue de Rangueil, F-31077 Toulouse cedex 04, France
| | - François Talfournier
- Université de Lorraine, CNRS, IMoPA, Campus Biologie Santé, F-54000 Nancy, France
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Do H, Lee CW, Lee SG, Kang H, Park CM, Kim HJ, Park H, Park H, Lee JH. Crystal structure and modeling of the tetrahedral intermediate state of methylmalonate-semialdehyde dehydrogenase (MMSDH) from Oceanimonas doudoroffii. J Microbiol 2016; 54:114-21. [PMID: 26832667 DOI: 10.1007/s12275-016-5549-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/14/2015] [Accepted: 12/18/2015] [Indexed: 11/24/2022]
Abstract
The gene product of dddC (Uniprot code G5CZI2), from the Gram-negative marine bacterium Oceanimonas doudoroffii, is a methylmalonate-semialdehyde dehydrogenase (OdoMMSDH) enzyme. MMSDH is a member of the aldehyde dehydrogenase superfamily, and it catalyzes the NAD-dependent decarboxylation of methylmalonate semialdehyde to propionyl-CoA. We determined the crystal structure of OdoMMSDH at 2.9 Å resolution. Among the twelve molecules in the asymmetric unit, six subunits complexed with NAD, which was carried along the protein purification steps. OdoMMSDH exists as a stable homodimer in solution; each subunit consists of three distinct domains: an NAD-binding domain, a catalytic domain, and an oligomerization domain. Computational modeling studies of the OdoMMSDH structure revealed key residues important for substrate recognition and tetrahedral intermediate stabilization. Two basic residues (Arg103 and Arg279) and six hydrophobic residues (Phe150, Met153, Val154, Trp157, Met281, and Phe449) were found to be important for tetrahedral intermediate binding. Modeling data also suggested that the backbone amide of Cys280 and the side chain amine of Asn149 function as the oxyanion hole during the enzymatic reaction. Our results provide useful insights into the substrate recognition site residues and catalytic mechanism of OdoMMSDH.
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Affiliation(s)
- Hackwon Do
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Republic of Korea
| | - Chang Woo Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Republic of Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, 406-840, Republic of Korea
| | - Sung Gu Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Republic of Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, 406-840, Republic of Korea
| | - Hara Kang
- Division of Life Science, College of Life Science and Bioengineering, Incheon National University, Incheon, 406-772, Republic of Korea
| | - Chul Min Park
- Medicinal Chemistry Research Center, Bio-Organic Division, Korea Research Institute of Chemical Technology, Daejeon, 305-600, Republic of Korea
| | - Hak Jun Kim
- Department of Chemistry, Pukyong National University, Busan, 608-739, Republic of Korea
| | - Hyun Park
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Republic of Korea. .,Department of Polar Sciences, University of Science and Technology, Incheon, 406-840, Republic of Korea.
| | - HaJeung Park
- X-Ray Core, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #1A1, Jupiter, FL, 33458, USA.
| | - Jun Hyuck Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Republic of Korea. .,Department of Polar Sciences, University of Science and Technology, Incheon, 406-840, Republic of Korea.
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Unraveling the function of paralogs of the aldehyde dehydrogenase super family from Sulfolobus solfataricus. Extremophiles 2013; 17:205-16. [PMID: 23296511 DOI: 10.1007/s00792-012-0507-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 12/17/2012] [Indexed: 01/16/2023]
Abstract
Aldehyde dehydrogenases (ALDHs) have been well established in all three domains of life and were shown to play essential roles, e.g., in intermediary metabolism and detoxification. In the genome of Sulfolobus solfataricus, five paralogs of the aldehyde dehydrogenases superfamily were identified, however, so far only the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) and α-ketoglutaric semialdehyde dehydrogenase (α-KGSADH) have been characterized. Detailed biochemical analyses of the remaining three ALDHs revealed the presence of two succinic semialdehyde dehydrogenase (SSADH) isoenzymes catalyzing the NAD(P)(+)-dependent oxidation of succinic semialdehyde. Whereas SSO1629 (SSADH-I) is specific for NAD(+), SSO1842 (SSADH-II) exhibits dual cosubstrate specificity (NAD(P)(+)). Physiological significant activity for both SSO-SSADHs was only detected with succinic semialdehyde and α-ketoglutarate semialdehyde. Bioinformatic reconstructions suggest a major function of both enzymes in γ-aminobutyrate, polyamine as well as nitrogen metabolism and they might additionally also function in pentose metabolism. Phylogenetic studies indicated a close relationship of SSO-SSALDHs to GAPNs and also a convergent evolution with the SSADHs from E. coli. Furthermore, for SSO1218, methylmalonate semialdehyde dehydrogenase (MSDH) activity was demonstrated. The enzyme catalyzes the NAD(+)- and CoA-dependent oxidation of methylmalonate semialdehyde, malonate semialdehyde as well as propionaldehyde (PA). For MSDH, a major function in the degradation of branched chain amino acids is proposed which is supported by the high sequence homology with characterized MSDHs from bacteria. This is the first report of MSDH as well as SSADH isoenzymes in Archaea.
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Bchini R, Vasiliou V, Branlant G, Talfournier F, Rahuel-Clermont S. Retinoic acid biosynthesis catalyzed by retinal dehydrogenases relies on a rate-limiting conformational transition associated with substrate recognition. Chem Biol Interact 2012; 202:78-84. [PMID: 23220587 DOI: 10.1016/j.cbi.2012.11.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 11/15/2012] [Accepted: 11/19/2012] [Indexed: 10/27/2022]
Abstract
Retinoic acid (RA), a metabolite of vitamin A, exerts pleiotropic effects throughout life in vertebrate organisms. Thus, RA action must be tightly regulated through the coordinated action of biosynthetic and degrading enzymes. The last step of retinoic acid biosynthesis is irreversibly catalyzed by the NAD-dependent retinal dehydrogenases (RALDH), which are members of the aldehyde dehydrogenase (ALDH) superfamily. Low intracellular retinal concentrations imply efficient substrate molecular recognition to ensure high affinity and specificity of RALDHs for retinal. This study addresses the molecular basis of retinal recognition in human ALDH1A1 (or RALDH1) and rat ALDH1A2 (or RALDH2), through the comparison of the catalytic behavior of retinal analogs and use of the fluorescence properties of retinol. We show that, in contrast to long chain unsaturated substrates, the rate-limiting step of retinal oxidation by RALDHs is associated with acylation. Use of the fluorescence resonance energy transfer upon retinol interaction with RALDHs provides evidence that retinal recognition occurs in two steps: binding into the substrate access channel, and a slower structural reorganization with a rate constant of the same magnitude as the kcat for retinal oxidation: 0.18 vs. 0.07 and 0.25 vs. 0.1 s(-1) for ALDH1A1 and ALDH1A2, respectively. This suggests that the conformational transition of the RALDH-retinal complex significantly contributes to the rate-limiting step that controls the kinetics of retinal oxidation, as a prerequisite for the formation of a catalytically competent Michaelis complex. This conclusion is consistent with the general notion that structural flexibility within the active site of ALDH enzymes has been shown to be an integral component of catalysis.
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Affiliation(s)
- Raphaël Bchini
- Unité Mixte de Recherche CNRS-Université de Lorraine 7214 AREMS, ARN-RNP Structure-Fonction-Maturation, Enzymologie Moléculaire et Structurale, Faculté de Médecine, Biopôle, Vandœuvre-lès-Nancy, France
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