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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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Muñoz-Bacasehua C, Santacruz-Ortega H, Valenzuela-Soto EM. BADH-NAD +-K + Complex Interaction Studies Reveal a New Possible Mechanism between Potassium and Glutamic 254 at the Coenzyme Binding Site. Cell Biochem Biophys 2022; 80:39-44. [PMID: 34981410 DOI: 10.1007/s12013-021-01051-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/23/2021] [Indexed: 11/26/2022]
Abstract
Betaine aldehyde dehydrogenase (BADH EC 1.2.1.8) catalyzes the irreversible oxidation of betaine aldehyde to glycine betaine using NAD+ as a coenzyme. Incubation of porcine kidney BADH (pkBADH) with NAD+ decreases the catalytic cysteine (C288) reactivity. Potassium ion increases the pkBADH affinity by the coenzyme. This work aimed to analyze pkBADH and NAD+ interaction in the presence and absence of K+ using 1H NMR to identify the amino acids that interact with NAD+ and/or K+ to understand the regulation process of pkBADH-NAD+ complex formation mediated by the K+ ion and their impact on the substrate binding and catalysis. Nuclear magnetic resonance spectra of pkBADH were obtained in the presence and absence of NAD+ and K+. The results show a chemical shift of the signals corresponding to the catalytic glutamic that participates in the transfer of H+ in the reaction of the pkBADH-NAD+-K+ complex formation. Furthermore, there is a widening of the signal that belongs to the catalytic cysteine indicating higher rigidity or less grade of rotation of the structure, which is consistent with the possible conformations of C288 in the catalytic process; in addition, there is evidence of changes in the chemical environment that surrounds NAD+.
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Affiliation(s)
- César Muñoz-Bacasehua
- Centro de Investigación en Alimentación y Desarrollo A.C., Apartado Postal 1735, Hermosillo, 83304, Sonora, México
| | - Hisila Santacruz-Ortega
- División de Ingeniería, Departamento de Investigación en Polímeros y Materiales, Universidad de Sonora, Hermosillo, 83000, Sonora, México
| | - Elisa M Valenzuela-Soto
- Centro de Investigación en Alimentación y Desarrollo A.C., Apartado Postal 1735, Hermosillo, 83304, Sonora, México.
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Muñoz-Bacasehua C, Rosas-Rodríguez JA, Arvizu-Flores AA, Valenzuela-Soto EM. Role of potassium levels in pkBADH heterogeneity of NAD + binding site. J Bioenerg Biomembr 2020; 52:61-70. [PMID: 32128683 DOI: 10.1007/s10863-020-09827-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/26/2020] [Indexed: 12/20/2022]
Abstract
Betaine aldehyde dehydrogenase (BADH) catalyzes the oxidation of betaine aldehyde to glycine betaine using NAD+ as a coenzyme. Studies in porcine kidney BADH (pkBADH) suggested that the enzyme exhibits heterogeneity of active sites and undergoes potassium-induced conformational changes. This study aimed to analyze if potassium concentration plays a role in the heterogeneity of pkBADH active sites through changes in NAD+ affinity constants, in its secondary structure content and stability. The enzyme was titrated with NAD+ 1 mM at fixed-variable KCl concentration, and the interaction measured by Isothermal Titration Calorimetry (ITC) and Circular Dichroism (CD). ITC data showed that K+ increased the first active site affinity in a manner dependent on its concentration; KD values to the first site were 14.4, 13.1, and 10.4 μM, at 25, 50, and 75 mM KCl. ΔG values showed that the coenzyme binding is a spontaneous reaction without changes between active sites or depending on KCl concentration. ΔH and TΔSb values showed that NAD+ binding to the active site is an endothermic process and is carried out at the expense of changes in entropy. α-Helix content increased as KCl increased, enzyme (Tm)app values were 2.6 °C and 3.3 °C higher at 20 mM and 200 mM K+. PkBADH molecular model showed three different interaction K+ sites. Results suggested K+ can interact with pkBADH and cause changes in the secondary structure, it provokes changes in the enzyme affinity by the coenzyme, and in the thermostability.
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Affiliation(s)
- César Muñoz-Bacasehua
- Centro de Investigación en Alimentación y Desarrollo A.C, GE Astiazaran Rosas 46, 83304, Hermosillo, Sonora, Mexico
| | | | - Aldo A Arvizu-Flores
- Departamento de Ciencias Químico-Biológicas, Universidad de Sonora, Apartado Postal, 83000, Hermosillo, Sonora, Mexico
| | - Elisa M Valenzuela-Soto
- Centro de Investigación en Alimentación y Desarrollo A.C, GE Astiazaran Rosas 46, 83304, Hermosillo, Sonora, Mexico.
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Cloning and molecular characterization of the betaine aldehyde dehydrogenase involved in the biosynthesis of glycine betaine in white shrimp (Litopenaeus vannamei). Chem Biol Interact 2017; 276:65-74. [PMID: 28212821 DOI: 10.1016/j.cbi.2017.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 01/09/2017] [Accepted: 02/13/2017] [Indexed: 11/21/2022]
Abstract
The enzyme betaine aldehyde dehydrogenase (BADH) catalyzes the irreversible oxidation of betaine aldehyde to glycine betaine (GB), a very efficient osmolyte accumulated during osmotic stress. In this study, we determined the nucleotide sequence of the cDNA for the BADH from the white shrimp Litopenaeus vannamei (LvBADH). The cDNA was 1882 bp long, with a complete open reading frame of 1524 bp, encoding 507 amino acids with a predicted molecular mass of 54.15 kDa and a pI of 5.4. The predicted LvBADH amino acid sequence shares a high degree of identity with marine invertebrate BADHs. Catalytic residues (C-298, E-264 and N-167) and the decapeptide VTLELGGKSP involved in nucleotide binding and highly conserved in BADHs were identified in the amino acid sequence. Phylogenetic analyses classified LvBADH in a clade that includes ALDH9 sequences from marine invertebrates. Molecular modeling of LvBADH revealed that the protein has amino acid residues and sequence motifs essential for the function of the ALDH9 family of enzymes. LvBADH modeling showed three potential monovalent cation binding sites, one site is located in an intra-subunit cavity; other in an inter-subunit cavity and a third in a central-cavity of the protein. The results show that LvBADH shares a high degree of identity with BADH sequences from marine invertebrates and enzymes that belong to the ALDH9 family. Our findings suggest that the LvBADH has molecular mechanisms of regulation similar to those of other BADHs belonging to the ALDH9 family, and that BADH might be playing a role in the osmoregulation capacity of L. vannamei.
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Zhao C, Wang D, Feng B, Gou M, Liu X, Li Q. Identification and characterization of aldehyde dehydrogenase 9 from Lampetra japonica and its protective role against cytotoxicity. Comp Biochem Physiol B Biochem Mol Biol 2015; 187:102-9. [DOI: 10.1016/j.cbpb.2015.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 12/16/2014] [Accepted: 05/07/2015] [Indexed: 11/16/2022]
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Halavaty AS, Rich RL, Chen C, Joo JC, Minasov G, Dubrovska I, Winsor JR, Myszka DG, Duban M, Shuvalova L, Yakunin AF, Anderson WF. Structural and functional analysis of betaine aldehyde dehydrogenase from Staphylococcus aureus. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1159-75. [PMID: 25945581 PMCID: PMC4427200 DOI: 10.1107/s1399004715004228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/01/2015] [Indexed: 02/02/2023]
Abstract
When exposed to high osmolarity, methicillin-resistant Staphylococcus aureus (MRSA) restores its growth and establishes a new steady state by accumulating the osmoprotectant metabolite betaine. Effective osmoregulation has also been implicated in the acquirement of a profound antibiotic resistance by MRSA. Betaine can be obtained from the bacterial habitat or produced intracellularly from choline via the toxic betaine aldehyde (BA) employing the choline dehydrogenase and betaine aldehyde dehydrogenase (BADH) enzymes. Here, it is shown that the putative betaine aldehyde dehydrogenase SACOL2628 from the early MRSA isolate COL (SaBADH) utilizes betaine aldehyde as the primary substrate and nicotinamide adenine dinucleotide (NAD(+)) as the cofactor. Surface plasmon resonance experiments revealed that the affinity of NAD(+), NADH and BA for SaBADH is affected by temperature, pH and buffer composition. Five crystal structures of the wild type and three structures of the Gly234Ser mutant of SaBADH in the apo and holo forms provide details of the molecular mechanisms of activity and substrate specificity/inhibition of this enzyme.
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Affiliation(s)
- Andrei S. Halavaty
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | | | - Chao Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Jeong Chan Joo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - George Minasov
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - Ievgeniia Dubrovska
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - James R. Winsor
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | | | - Mark Duban
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - Ludmilla Shuvalova
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Wayne F. Anderson
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
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Garza-Ramos G, Mújica-Jiménez C, Muñoz-Clares RA. Potassium and ionic strength effects on the conformational and thermal stability of two aldehyde dehydrogenases reveal structural and functional roles of K⁺-binding sites. PLoS One 2013; 8:e54899. [PMID: 23365686 PMCID: PMC3554688 DOI: 10.1371/journal.pone.0054899] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 12/17/2012] [Indexed: 11/18/2022] Open
Abstract
Many aldehyde dehydrogenases (ALDHs) have potential potassium-binding sites of as yet unknown structural or functional roles. To explore possible K(+)-specific effects, we performed comparative structural studies on the tetrameric betaine aldehyde dehydrogenase from Pseudomonas aeruginosa (PaBADH) and on the dimeric BADH from spinach (SoBADH), whose activities are K(+)-dependent and K(+)-independent, respectively, although both enzymes contain potassium-binding sites. Size exclusion chromatography, dynamic light scattering, far- and near-UV circular dichroism, and extrinsic fluorescence results indicated that in the absence of K(+) ions and at very low ionic strength, PaBADH remained tetrameric but its tertiary structure was significantly altered, accounting for its inactivation, whereas SoBADH formed tetramers that maintained the native tertiary structure. The recovery of PaBADH native tertiary-structure was hyperbolically dependent on KCl concentration, indicating potassium-specific structuring effects probably arising from binding to a central-cavity site present in PaBADH but not in SoBADH. K(+) ions stabilized the native structure of both enzymes against thermal denaturation more than did tetraethylammonium (TEA(+)) ions. This indicated specific effects of potassium on both enzymes, particularly on PaBADH whose apparent T(m) values showed hyperbolical dependence on potassium concentration, similar to that observed with the tertiary structure changes. Interestingly, we also found that thermal denaturation of both enzymes performed in low ionic-strength buffers led to formation of heat-resistant, inactive soluble aggregates that retain 80% secondary structure, have increased β-sheet content and bind thioflavin T. These structured aggregates underwent further thermal-induced aggregation and precipitation when the concentrations of KCl or TEACl were raised. Given that PaBADH and SoBADH belong to different ALDH families and differ not only in amino acid composition but also in association state and surface electrostatic potential, the formation of this kind of β-sheet pre-fibrillar aggregates, not described before for any ALDH enzyme, appear to be a property of the ALDH fold.
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Affiliation(s)
- Georgina Garza-Ramos
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México, Distrito Federal, México
| | - Carlos Mújica-Jiménez
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, México, Distrito Federal, México
| | - Rosario A. Muñoz-Clares
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, México, Distrito Federal, México
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