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Dong X, Zhang T, Gui C, Fei S, Xu H, Chang J, Lian C, Tang W. The critical role of residues Phe120 and Val161 of (2 R,3 R)‑2,3‑butanediol dehydrogenase from Neisseria gonorrhoeae as probed by molecular docking and site-directed mutagenesis. J Basic Microbiol 2024; 64:e2300751. [PMID: 38644586 DOI: 10.1002/jobm.202300751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/01/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024]
Abstract
NAD+-dependent (2 R,3 R)‑2,3‑butanediol dehydrogenase (BDH) from Neisseria gonorrhoeae (NgBDH) is a representative member of the medium-chain dehydrogenase/reductase (MDR) superfamily. To date, little information is available on the substrate binding sites and catalytic residues of BDHs from this superfamily. In this work, according to molecular docking studies, we found that conserved residues Phe120 and Val161 form strong hydrophobic interactions with both (2 R,3 R)‑2,3‑butanediol (RR-BD) and meso-2,3‑butanediol (meso-BD) and that mutations of these residues to alanine or threonine impair substrate binding. To further evaluate the roles of these two residues, Phe120 and Val161 were mutated to alanine or threonine. Kinetic analysis revealed that, relative to those of wild type, the apparent KM values of the Phe120Ala mutant for RR-BD and meso-BD increased 36- and 369-fold, respectively; the catalytic efficiencies of this mutant with RR-BD and meso-BD decreased approximately 586- and 3528-fold, respectively; and the apparent KM values of the Val161Ala mutant for RR-BD and meso-BD increased 4- and 37-fold, respectively, the catalytic efficiencies of this mutant with RR-BD and meso-BD decreased approximately 3- and 28-fold, respectively. Additionally, the Val161Thr mutant slightly decreased catalytic efficiencies (twofold with RR-BD; 7.3-fold with meso-BD) due to an increase in KM (sixfold for RR-BD; 24-fold for meso-BD) and a slight increase (2.8-fold with RR-BD; 3.3-fold with meso-BD) in kcat. These findings validate the critical roles of Phe120 and Val161 of NgBDH in substrate binding and catalysis. Overall, the current study provides a better understanding of the substrate binding and catalysis of BDHs within the MDR superfamily.
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Affiliation(s)
- Xue Dong
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
| | - Tingting Zhang
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
| | - Chuanyue Gui
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
| | - Shuping Fei
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
| | - Haonan Xu
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
| | - Jianrong Chang
- Scientific Research Center, Bengbu Medical University, Bengbu, China
| | - Chaoqun Lian
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
| | - Wanggang Tang
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
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Fernández-Silva A, Juárez-Vázquez AL, González-Segura L, Juárez-Díaz JA, Muñoz-Clares RA. The uncharacterized Pseudomonas aeruginosa PA4189 is a novel and efficient aminoacetaldehyde dehydrogenase. Biochem J 2023; 480:259-281. [PMID: 36727473 DOI: 10.1042/bcj20220567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/03/2023]
Abstract
Neither the Pseudomonas aeruginosa aldehyde dehydrogenase encoded by the PA4189 gene nor its ortholog proteins have been biochemically or structurally characterized and their physiological function is unknown. We cloned the PA4189 gene, obtained the PA4189 recombinant protein, and studied its structure-function relationships. PA4189 is an NAD+-dependent aminoaldehyde dehydrogenase highly efficient with protonated aminoacetaldehyde and 3-aminopropionaldehyde, which are much more preferred to the non-protonated species as indicated by pH studies. Based on the higher activity with aminoacetaldehyde than with 3-aminopropionaldehyde, we propose that aminoacetaldehyde might be the PA4189 physiological substrate. Even though at the physiological pH of P. aeruginosa cells the non-protonated aminoacetaldehyde species will be predominant, and despite the competition of these species with the protonated ones, PA4189 would very efficiently oxidize ACTAL in vivo, producing glycine. To our knowledge, PA4189 is the first reported enzyme that might metabolize ACTAL, which is considered a dead-end metabolite because its consuming reactions are unknown. The PA4189 crystal structure reported here suggested that the charge and size of the active-site residue Glu457, which narrows the aldehyde-entrance tunnel, greatly define the specificity for small positively charged aldehydes, as confirmed by the kinetics of the E457G and E457Q variants. Glu457 and the residues that determine Glu457 conformation inside the active site are conserved in the PA4189 orthologs, which we only found in proteobacteria species. Also is conserved the PA4189 genomic neighborhood, which suggests that PA4189 participates in an uncharacterized metabolic pathway. Our results open the door to future efforts to characterize this pathway.
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Affiliation(s)
- Arline Fernández-Silva
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Ana L Juárez-Vázquez
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Lilian González-Segura
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Javier Andrés Juárez-Díaz
- Departamento de Biología Comparada, Facultad de Ciencias, Ciudad Universitaria, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Rosario A Muñoz-Clares
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
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3
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Glenn KC, Silvanovich A, Lee SG, Allen A, Park S, Dunn SE, Kessenich C, Meng C, Vicini JL, Jez JM. Biochemical and clinical studies of putative allergens to assess what distinguishes them from other non-allergenic proteins in the same family. Transgenic Res 2022; 31:507-524. [PMID: 35939227 PMCID: PMC9489553 DOI: 10.1007/s11248-022-00316-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 07/21/2022] [Indexed: 10/26/2022]
Abstract
Many protein families have numerous members listed in databases as allergens; however, some allergen database entries, herein called "orphan allergens", are members of large families of which all other members are not allergens. These orphan allergens provide an opportunity to assess whether specific structural features render a protein allergenic. Three orphan allergens [Cladosporium herbarum aldehyde dehydrogenase (ChALDH), Alternaria alternata ALDH (AaALDH), and C. herbarum mannitol dehydrogenase (ChMDH)] were recombinantly produced and purified for structure characterization and for clinical skin prick testing (SPT) in mold allergic participants. Examination of the X-ray crystal structures of ChALDH and ChMDH and a homology structure model of AaALDH did not identify any discernable epitopes that distinguish these putative orphan allergens from their non-allergenic protein relatives. SPT results were aligned with ChMDH being an allergen, 53% of the participants were SPT (+). AaALDH did not elicit SPT reactivity above control proteins not in allergen databases (i.e., Psedomonas syringae indole-3-acetaldehyde dehydrogenase and Zea mays ALDH). Although published results showed consequential human IgE reactivity with ChALDH, no SPT reactivity was observed in this study. With only one of these three orphan allergens, ChMDH, eliciting SPT(+) reactions consistent with the protein being included in allergen databases, this underscores the complicated nature of how bioinformatics is used to assess the potential allergenicity of food proteins that could be newly added to human diets and, when needed, the subsequent clinical testing of that bioinformatic assessment.Trial registration number and date of registration AAC-2017-0467, approved as WIRB protocol #20172536 on 07DEC2017 by WIRB-Copernicus (OHRP/FDA Registration #: IRB00000533, organization #: IORG0000432).
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Affiliation(s)
- Kevin C Glenn
- Bayer Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA
| | - Andre Silvanovich
- Bayer Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA
| | - Soon Goo Lee
- Department of Biology, Washington University, CB 1137, One Brookings Dr., St. Louis, MO, 63130, USA.,Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC, 28403, USA
| | - Aron Allen
- Department of Biology, Washington University, CB 1137, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Stephanie Park
- Allergy and Asthma Care of St. Louis, 8888 Ladue Road, Suite 105, St. Louis, MO, 63124, USA
| | - S Eliza Dunn
- Bayer Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA
| | - Colton Kessenich
- Bayer Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA
| | - Chen Meng
- Bayer Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA
| | - John L Vicini
- Bayer Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA.
| | - Joseph M Jez
- Department of Biology, Washington University, CB 1137, One Brookings Dr., St. Louis, MO, 63130, USA
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4
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Optimal Secretory Expression of Acetaldehyde Dehydrogenase from Issatchenkia terricola in Bacillus subtilis through a Combined Strategy. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030747. [PMID: 35164011 PMCID: PMC8838704 DOI: 10.3390/molecules27030747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 01/20/2023]
Abstract
Acetaldehyde dehydrogenases are potential enzyme preparations that can be used to detoxify acetaldehyde and other exogenous aldehydes from pharmaceuticals, food, and biofuel production. In this study, we enhanced the expression of acetaldehyde dehydrogenase sourced from Issatchenkia terricola (istALDH) in Bacillus subtilis using a combinatorial strategy for the optimization of signal peptides, promoters, and growth conditions. First, a library of various signal peptides was constructed to identify the optimal signal peptides for efficient istALDH secretion. The signal peptide yqzG achieved the highest extracellular istALDH activity (204.85 ± 3.31 U/mL). Second, the aprE promoter was replaced by a constitutive promoter (i.e., P43) and an inducible promoter (i.e., Pglv), resulting in 12.40% and 19.97% enhanced istALDH, respectively. Furthermore, the tandem promoter P43-Pglv provided a better performance, resulting in 30.96% enhanced istALDH activity. Third, the production of istALDH was optimized by testing one factor at a time. Physical parameters were optimized including the inducer (e.g., maltose) concentrations, incubation temperatures, and inoculation amounts, and the results were 2.0%, 35 °C, and 2.0%, respectively. The optimized medium results were 2.0% glucose, 1.5% peptone, 2.5% yeast extract, 1% NaCl, and 0.5% (NH4)2SO4. The extracellular istALDH activity was 331.19 ± 4.19 U/mL, yielding the highest production reported in the literature to date.
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5
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Lin GH, Hsieh MC, Shu HY. Role of Iron-Containing Alcohol Dehydrogenases in Acinetobacter baumannii ATCC 19606 Stress Resistance and Virulence. Int J Mol Sci 2021; 22:ijms22189921. [PMID: 34576087 PMCID: PMC8465190 DOI: 10.3390/ijms22189921] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 11/21/2022] Open
Abstract
Most bacteria possess alcohol dehydrogenase (ADH) genes (Adh genes) to mitigate alcohol toxicity, but these genes have functions beyond alcohol degradation. Previous research has shown that ADH can modulate quorum sensing in Acinetobacter baumannii, a rising opportunistic pathogen. However, the number and nature of Adh genes in A. baumannii have not yet been fully characterized. We identified seven alcohol dehydrogenases (NAD+-ADHs) from A. baumannii ATCC 19606, and examined the roles of three iron-containing ADHs, ADH3, ADH4, and ADH6. Marker-less mutation was used to generate Adh3, Adh4, and Adh6 single, double, and triple mutants. Disrupted Adh4 mutants failed to grow in ethanol-, 1-butanol-, or 1-propanol-containing mediums, and recombinant ADH4 exhibited strongest activity against ethanol. Stress resistance assays with inorganic and organic hydroperoxides showed that Adh3 and Adh6 were key to oxidative stress resistance. Virulence assays performed on the Galleria mellonella model organism revealed that Adh4 mutants had comparable virulence to wild-type, while Adh3 and Adh6 mutants had reduced virulence. The results suggest that ADH4 is primarily involved in alcohol metabolism, while ADH3 and ADH6 are key to stress resistance and virulence. Further investigation into the roles of other ADHs in A. baumannii is warranted.
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Affiliation(s)
- Guang-Huey Lin
- Master Program of Microbiology and Immunology, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan; (G.-H.L.); (M.-C.H.)
- Department of Microbiology, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan
- International College, Tzu Chi University, Hualien 97004, Taiwan
| | - Ming-Chuan Hsieh
- Master Program of Microbiology and Immunology, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan; (G.-H.L.); (M.-C.H.)
| | - Hung-Yu Shu
- Department of Bioscience Technology, Chang Jung Christian University, Tainan 71101, Taiwan
- Correspondence: ; Tel.: +886-6-278-5123 (ext. 3211); Fax: +886-6-278-5010
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6
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A critical assessment of the potential of pharmacological modulation of aldehyde dehydrogenases to treat the diseases of bone loss. Eur J Pharmacol 2020; 886:173541. [PMID: 32896553 DOI: 10.1016/j.ejphar.2020.173541] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 12/19/2022]
Abstract
Chronic alcoholism (CA) decreases bone mass and increases the risk of hip fracture. Alcohol and its main metabolite, acetaldehyde impairs osteoblastogenesis by increasing oxidative stress. Aldehyde dehydrogenase (ALDH) is the rate-limiting enzyme in clearing acetaldehyde from the body. The clinical relevance of ALDH in skeletal function has been established by the discovery of single nucleotide polymorphism, SNP (rs671) in the ALDH2 gene giving rise to an inactive form of the enzyme (ALDH2*2) that causes increased serum acetaldehyde and osteoporosis in the affected individuals. Subsequent mouse genetics studies have replicated human phenotype in mice and confirmed the non-redundant role of ALDH2 in bone homeostasis. The activity of ALDH2 is amenable to pharmacological modulation. ALDH2 inhibition by disulfiram (DSF) and activation by alda-1 cause reduction and induction of bone formation, respectively. DSF also inhibits peak bone mass accrual in growing rats. On the other hand, DSF showed an anti-osteoclastogenic effect and protected mice from alcohol-induced osteopenia by inhibiting ALDH1a1 in bone marrow monocytes. Besides DSF, there are several classes of ALDH inhibitors with disparate skeletal effects. Alda-1, the ALDH2 activator induced osteoblast differentiation by increasing bone morphogenic protein 2 (BMP2) expression via ALDH2 activation. Alda-1 also restored ovariectomy-induced bone loss. The scope of structure-activity based studies with ALDH2 and the alda-1-like molecule could lead to the discovery of novel osteoanabolic molecules. This review will critically discuss the molecular mechanism of the ethanol and its principal metabolite, acetaldehyde in the context of ALDH2 in bone cells, and skeletal homeostasis.
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Lee SG, Harline K, Abar O, Akadri SO, Bastian AG, Chen HYS, Duan M, Focht CM, Groziak AR, Kao J, Kottapalli JS, Leong MC, Lin JJ, Liu R, Luo JE, Meyer CM, Mo AF, Pahng SH, Penna V, Raciti CD, Srinath A, Sudhakar S, Tang JD, Cox BR, Holland CK, Cascella B, Cruz W, McClerkin SA, Kunkel BN, Jez JM. The plant pathogen enzyme AldC is a long-chain aliphatic aldehyde dehydrogenase. J Biol Chem 2020; 295:13914-13926. [PMID: 32796031 DOI: 10.1074/jbc.ra120.014747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
Aldehyde dehydrogenases are versatile enzymes that serve a range of biochemical functions. Although traditionally considered metabolic housekeeping enzymes because of their ability to detoxify reactive aldehydes, like those generated from lipid peroxidation damage, the contributions of these enzymes to other biological processes are widespread. For example, the plant pathogen Pseudomonas syringae strain PtoDC3000 uses an indole-3-acetaldehyde dehydrogenase to synthesize the phytohormone indole-3-acetic acid to elude host responses. Here we investigate the biochemical function of AldC from PtoDC3000. Analysis of the substrate profile of AldC suggests that this enzyme functions as a long-chain aliphatic aldehyde dehydrogenase. The 2.5 Å resolution X-ray crystal of the AldC C291A mutant in a dead-end complex with octanal and NAD+ reveals an apolar binding site primed for aliphatic aldehyde substrate recognition. Functional characterization of site-directed mutants targeting the substrate- and NAD(H)-binding sites identifies key residues in the active site for ligand interactions, including those in the "aromatic box" that define the aldehyde-binding site. Overall, this study provides molecular insight for understanding the evolution of the prokaryotic aldehyde dehydrogenase superfamily and their diversity of function.
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Affiliation(s)
- Soon Goo Lee
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA; Department of Chemistry and Biochemistry, University of North Carolina-Wilmington, Wilmington, North Carolina, USA
| | - Kate Harline
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Orchid Abar
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Sakirat O Akadri
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Alexander G Bastian
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Hui-Yuan S Chen
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael Duan
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Caroline M Focht
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Amanda R Groziak
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jesse Kao
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | | | - Matthew C Leong
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Joy J Lin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Regina Liu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Joanna E Luo
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Christine M Meyer
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Albert F Mo
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Seong Ho Pahng
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Vinay Penna
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Chris D Raciti
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Abhinav Srinath
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Shwetha Sudhakar
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Joseph D Tang
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Brian R Cox
- Department of Chemistry and Biochemistry, University of North Carolina-Wilmington, Wilmington, North Carolina, USA
| | - Cynthia K Holland
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA; Department of Biology, Williams College, Williamstown, Massachusetts, USA
| | - Barrie Cascella
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Wilhelm Cruz
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Sheri A McClerkin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA; Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, USA
| | - Barbara N Kunkel
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA.
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Altered Cofactor Preference of Thermostable StDAPDH by a Single Mutation at K159. Int J Mol Sci 2020; 21:ijms21051788. [PMID: 32150965 PMCID: PMC7084900 DOI: 10.3390/ijms21051788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 11/16/2022] Open
Abstract
D-amino acid production from 2-keto acid by reductive amination is an attractive pathway because of its high yield and environmental safety. StDAPDH, a meso-diaminopimelate dehydrogenase (meso-DAPDH) from Symbiobacterium thermophilum, was the first meso-DAPDH to show amination of 2-keto acids. Furthermore, StDAPDH shows excellent thermostability compared to other meso-DAPDHs. However, the cofactor of StDAPDH is NADP(H), which is less common than NAD(H) in industrial applications. Therefore, cofactor engineering for StDAPDH is needed. In this study, the highly conserved cofactor binding sites around the adenosine moiety of NADPH were targeted to determine cofactor specificity. Lysine residues within a loop were found to be critical for the cofactor specificity of StDAPDH. Replacement of lysine with arginine resulted in the activity of pyruvic acid with NADH as the cofactor. The affinity of K159R to pyruvic acid was equal with NADH or NADPH as the cofactor, regardless of the mutation. Molecular dynamics simulations revealed that the large steric hindrance of arginine and the interaction of the salt bridge between NADH and arginine may have restricted the free movement of NADH, which prompted the formation of a stable active conformation of mutant K159R. These results provide further understanding of the catalytic mechanism of StDAPDH and guidance for the cofactor engineering of StDAPDH.
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9
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Hanukoglu I. Conservation of the Enzyme-Coenzyme Interfaces in FAD and NADP Binding Adrenodoxin Reductase-A Ubiquitous Enzyme. J Mol Evol 2017; 85:205-218. [PMID: 29177972 DOI: 10.1007/s00239-017-9821-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/21/2017] [Indexed: 10/18/2022]
Abstract
FAD and NAD(P) together represent an ideal pair for coupled redox reactions in their capacity to accept two electrons and their redox potentials. Enzymes that bind both NAD(P) and FAD represent large superfamilies that fulfill essential roles in numerous metabolic pathways. Adrenodoxin reductase (AdxR) shares Rossmann fold features with some of these superfamilies but remains in a group of its own in the absence of sequence homology. This article documents the phylogenetic distribution of AdxR by examining whole genome databases for Metazoa, Plantae, Fungi, and Protista, and determines the conserved structural features of AdxR. Scanning these databases showed that most organisms have a single gene coding for an AdxR ortholog. The sequence identity between AdxR orthologs is correlated with the phylogenetic distance among metazoan species. The NADP binding site of all AdxR orthologs showed a modified Rossmann fold motif with a GxGxxA consensus instead of the classical GxGxxG at the edge of the first βα-fold. To examine the hypothesis that enzyme-coenzyme interfaces represent the conserved regions of AdxR, the residues interfacing FAD and NADP were identified and compared with multiple-sequence alignment results. Most conserved residues were indeed found at sites that surround the interfacing residues between the enzyme and the two coenzymes. In contrast to protein-protein interaction hot-spots that may appear in isolated patches, in AdxR the conserved regions show strict preservation of the overall structure. This structure maintains the precise positioning of the two coenzymes for optimal electron transfer between NADP and FAD without electron leakage to other acceptors.
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Affiliation(s)
- Israel Hanukoglu
- Laboratory of Cell Biology, Ariel University, 40700, Ariel, Israel.
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10
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Zahniser MPD, Prasad S, Kneen MM, Kreinbring CA, Petsko GA, Ringe D, McLeish MJ. Structure and mechanism of benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633, a member of the Class 3 aldehyde dehydrogenase superfamily. Protein Eng Des Sel 2017; 30:271-278. [PMID: 28338942 DOI: 10.1093/protein/gzx015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/23/2017] [Indexed: 11/14/2022] Open
Abstract
Benzaldehyde dehydrogenase from Pseudomonas putida (PpBADH) belongs to the Class 3 aldehyde dehydrogenase (ALDH) family. The Class 3 ALDHs are unusual in that they are generally dimeric (rather than tetrameric), relatively non-specific and utilize both NAD+ and NADP+. To date, X-ray structures of three Class 3 ALDHs have been determined, of which only two have cofactor bound, both in the NAD+ form. Here we report the crystal structure of PpBADH in complex with NADP+ and a thioacyl intermediate adduct. The overall architecture of PpBADH resembles that of most other members of the ALDH superfamily, and the cofactor binding residues are well conserved. Conversely, the pattern of cofactor binding for the rat Class 3 ALDH differs from that of PpBADH and other ALDHs. This has been interpreted in terms of a different mechanism for the rat enzyme. Comparison with the PpBADH structure, as well as multiple sequence alignments, suggest that one of two conserved glutamates, at positions 215 (209 in rat) and 337 (333 in rat), would act as the general base necessary to hydrolyze the thioacyl intermediate. While the latter is the general base in the rat Class 3 ALDH, site-specific mutagenesis indicates that Glu215 is the likely candidate for PpBADH, a result more typical of the Class 1 and 2 ALDH families. Finally, this study shows that hydride transfer is not rate limiting, lending further credence to the suggestion that PpBADH is more similar to the Class 1 and 2 ALDHs than it is to other Class 3 ALDHs.
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Affiliation(s)
- Megan P D Zahniser
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454,USA
| | - Shreenath Prasad
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N. Blackford Street, Indianapolis, IN 46202,USA
| | - Malea M Kneen
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N. Blackford Street, Indianapolis, IN 46202,USA
| | - Cheryl A Kreinbring
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.,Rosenstiel Basic Medical Sciences Research Center, MS029, 415 South Street, Waltham, MA 02454, USA
| | - Gregory A Petsko
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.,Rosenstiel Basic Medical Sciences Research Center, MS029, 415 South Street, Waltham, MA 02454, USA
| | - Dagmar Ringe
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.,Rosenstiel Basic Medical Sciences Research Center, MS029, 415 South Street, Waltham, MA 02454, USA.,Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Michael J McLeish
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N. Blackford Street, Indianapolis, IN 46202,USA
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In vitro activity and stability of pure human salivary aldehyde dehydrogenase. Int J Biol Macromol 2017; 96:798-806. [DOI: 10.1016/j.ijbiomac.2016.12.084] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/28/2016] [Accepted: 12/31/2016] [Indexed: 11/22/2022]
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Mechanisms of protection against irreversible oxidation of the catalytic cysteine of ALDH enzymes: Possible role of vicinal cysteines. Chem Biol Interact 2017; 276:52-64. [PMID: 28216341 DOI: 10.1016/j.cbi.2017.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 12/29/2016] [Accepted: 02/13/2017] [Indexed: 01/22/2023]
Abstract
The catalytic mechanism of the NAD(P)+-dependent aldehyde dehydrogenases (ALDHs) involves the nucleophilic attack of the essential cysteine (Cys302, mature HsALDH2 numbering) on the aldehyde substrate. Although oxidation of Cys302 will inactivate these enzymes, it is not yet well understood how this oxidation is prevented. In this work we explore possible mechanisms of protection by systematically analyzing the reported three-dimensional structures and amino acid sequences of the enzymes of the ALDH superfamily. Specifically, we considered the Cys302 conformational space, the structure and residues conservation of the catalytic loop where Cys302 is located, the observed oxidation states of Cys302, the ability of physiological reductants to revert its oxidation, and the presence of vicinal Cys in the catalytic loop. Our analyses suggested that: 1) In the apo-enzyme, the thiol group of Cys302 is quite resistant to oxidation by ambient O2 or mild oxidative conditions, because the protein environment promotes its high pKa. 2) NAD(P)+ bound in the "hydride transfer" conformation afforded total protection against Cys302 oxidation by an unknown mechanism. 3) If formed, the Cys302-sulfenic acid is protected against irreversible oxidation. 4) Of the physiological reductant agents, the dithiol lipoic acid could reduce a sulfenic or a disulfide bond in the ALDHs active site; glutathione cannot because its thiol group cannot reach Cys302, and other physiological monothiols may be ineffective in those ALDHs where their active site cannot sterically accommodate two molecules of the monothiols. 5) Formation of the disulfides Cys301-Cys302, Cys302-Cys304, Cys302-Cys305 and Cys-302-Cys306 in those ALDHs that have these Cys residues is not probable, because of the permitted Cys conformers as well as the conserved structure and low flexibility of the catalytic loop. 6) Only in some ALDH2, ALDH9, ALDH16 and ALDH23 enzymes, Cys303, alone or in conjunction with Cys301, allows disulfide formation. Interestingly, several of these enzymes are mitochondrial.
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Gaona-López C, Julián-Sánchez A, Riveros-Rosas H. Diversity and Evolutionary Analysis of Iron-Containing (Type-III) Alcohol Dehydrogenases in Eukaryotes. PLoS One 2016; 11:e0166851. [PMID: 27893862 PMCID: PMC5125639 DOI: 10.1371/journal.pone.0166851] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/05/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Alcohol dehydrogenase (ADH) activity is widely distributed in the three domains of life. Currently, there are three non-homologous NAD(P)+-dependent ADH families reported: Type I ADH comprises Zn-dependent ADHs; type II ADH comprises short-chain ADHs described first in Drosophila; and, type III ADH comprises iron-containing ADHs (FeADHs). These three families arose independently throughout evolution and possess different structures and mechanisms of reaction. While types I and II ADHs have been extensively studied, analyses about the evolution and diversity of (type III) FeADHs have not been published yet. Therefore in this work, a phylogenetic analysis of FeADHs was performed to get insights into the evolution of this protein family, as well as explore the diversity of FeADHs in eukaryotes. PRINCIPAL FINDINGS Results showed that FeADHs from eukaryotes are distributed in thirteen protein subfamilies, eight of them possessing protein sequences distributed in the three domains of life. Interestingly, none of these protein subfamilies possess protein sequences found simultaneously in animals, plants and fungi. Many FeADHs are activated by or contain Fe2+, but many others bind to a variety of metals, or even lack of metal cofactor. Animal FeADHs are found in just one protein subfamily, the hydroxyacid-oxoacid transhydrogenase (HOT) subfamily, which includes protein sequences widely distributed in fungi, but not in plants), and in several taxa from lower eukaryotes, bacteria and archaea. Fungi FeADHs are found mainly in two subfamilies: HOT and maleylacetate reductase (MAR), but some can be found also in other three different protein subfamilies. Plant FeADHs are found only in chlorophyta but not in higher plants, and are distributed in three different protein subfamilies. CONCLUSIONS/SIGNIFICANCE FeADHs are a diverse and ancient protein family that shares a common 3D scaffold with a patchy distribution in eukaryotes. The majority of sequenced FeADHs from eukaryotes are distributed in just two subfamilies, HOT and MAR (found mainly in animals and fungi). These two subfamilies comprise almost 85% of all sequenced FeADHs in eukaryotes.
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Affiliation(s)
- Carlos Gaona-López
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM). Cd. Universitaria, Ciudad de México, México
| | - Adriana Julián-Sánchez
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM). Cd. Universitaria, Ciudad de México, México
| | - Héctor Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM). Cd. Universitaria, Ciudad de México, México
- * E-mail:
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