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Nigro M, Sánchez-Moreno I, Benito-Arenas R, Valino AL, Iribarren AM, Veiga N, García-Junceda E, Lewkowicz ES. Synthesis of Chiral Acyclic Pyrimidine Nucleoside Analogues from DHAP-Dependent Aldolases. Biomolecules 2024; 14:750. [PMID: 39062466 PMCID: PMC11274987 DOI: 10.3390/biom14070750] [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: 05/23/2024] [Revised: 06/14/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
Dihydroxyacetone phosphate (DHAP)-dependent aldolases catalyze the aldol addition of DHAP to a variety of aldehydes and generate compounds with two stereocenters. This reaction is useful to synthesize chiral acyclic nucleosides, which constitute a well-known class of antiviral drugs currently used. In such compounds, the chirality of the aliphatic chain, which mimics the open pentose residue, is crucial for activity. In this work, three DHAP-dependent aldolases: fructose-1,6-biphosphate aldolase from rabbit muscle, rhanmulose-1-phosphate aldolase from Thermotoga maritima, and fuculose-1-phosphate aldolase from Escherichia coli, were used as biocatalysts. Aldehyde derivatives of thymine and cytosine were used as acceptor substrates, generating new acyclic nucleoside analogues containing two new stereocenters with conversion yields between 70% and 90%. Moreover, structural analyses by molecular docking were carried out to gain insights into the diasteromeric excess observed.
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Affiliation(s)
- Mariano Nigro
- Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, Universidad Nacional de Quilmes, Bernal 1876, Argentina; (M.N.); (A.L.V.); (A.M.I.)
| | - Israél Sánchez-Moreno
- Departamento de Química Bio-Orgánica, Instituto de Química Orgánica General, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain; (I.S.-M.); (R.B.-A.)
| | - Raúl Benito-Arenas
- Departamento de Química Bio-Orgánica, Instituto de Química Orgánica General, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain; (I.S.-M.); (R.B.-A.)
| | - Ana L. Valino
- Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, Universidad Nacional de Quilmes, Bernal 1876, Argentina; (M.N.); (A.L.V.); (A.M.I.)
| | - Adolfo M. Iribarren
- Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, Universidad Nacional de Quilmes, Bernal 1876, Argentina; (M.N.); (A.L.V.); (A.M.I.)
| | - Nicolás Veiga
- Química Inorgánica, Departamento Estrella Campos, Facultad de Química, Universidad de la República (UdelaR), Av. Gral. Flores 2124, Montevideo 11800, Uruguay;
| | - Eduardo García-Junceda
- Departamento de Química Bio-Orgánica, Instituto de Química Orgánica General, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain; (I.S.-M.); (R.B.-A.)
| | - Elizabeth S. Lewkowicz
- Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, Universidad Nacional de Quilmes, Bernal 1876, Argentina; (M.N.); (A.L.V.); (A.M.I.)
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Hagedoorn PL, Pabst M, Hanefeld U. The metal cofactor: stationary or mobile? Appl Microbiol Biotechnol 2024; 108:391. [PMID: 38910188 PMCID: PMC11194214 DOI: 10.1007/s00253-024-13206-2] [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: 03/11/2024] [Revised: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 06/25/2024]
Abstract
Metal cofactors are essential for catalysis and enable countless conversions in nature. Interestingly, the metal cofactor is not always static but mobile with movements of more than 4 Å. These movements of the metal can have different functions. In the case of the xylose isomerase and medium-chain dehydrogenases, it clearly serves a catalytic purpose. The metal cofactor moves during substrate activation and even during the catalytic turnover. On the other hand, in class II aldolases, the enzymes display resting states and active states depending on the movement of the catalytic metal cofactor. This movement is caused by substrate docking, causing the metal cofactor to take the position essential for catalysis. As these metal movements are found in structurally and mechanistically unrelated enzymes, it has to be expected that this metal movement is more common than currently perceived. KEY POINTS: • Metal ions are essential cofactors that can move during catalysis. • In class II aldolases, the metal cofactors can reside in a resting state and an active state. • In MDR, the movement of the metal cofactor is essential for substrate docking.
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Affiliation(s)
- Peter-Leon Hagedoorn
- Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Martin Pabst
- Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Ulf Hanefeld
- Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands.
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Catalytic and structural insights into a stereospecific and thermostable Class II aldolase HpaI from Acinetobacter baumannii. J Biol Chem 2021; 297:101280. [PMID: 34624314 PMCID: PMC8560999 DOI: 10.1016/j.jbc.2021.101280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 11/21/2022] Open
Abstract
Aldolases catalyze the reversible reactions of aldol condensation and cleavage and have strong potential for the synthesis of chiral compounds, widely used in pharmaceuticals. Here, we investigated a new Class II metal aldolase from the p-hydroxyphenylacetate degradation pathway in Acinetobacter baumannii, 4-hydroxy-2-keto-heptane-1,7-dioate aldolase (AbHpaI), which has various properties suitable for biocatalysis, including stereoselectivity/stereospecificity, broad aldehyde utilization, thermostability, and solvent tolerance. Notably, the use of Zn2+ by AbHpaI as a native cofactor is distinct from other enzymes in this class. AbHpaI can also use other metal ion (M2+) cofactors, except Ca2+, for catalysis. We found that Zn2+ yielded the highest enzyme complex thermostability (Tm of 87 °C) and solvent tolerance. All AbHpaI•M2+ complexes demonstrated preferential cleavage of (4R)-2-keto-3-deoxy-D-galactonate ((4R)-KDGal) over (4S)-2-keto-3-deoxy-D-gluconate ((4S)-KDGlu), with AbHpaI•Zn2+ displaying the highest R/S stereoselectivity ratio (sixfold higher than other M2+ cofactors). For the aldol condensation reaction, AbHpaI•M2+ only specifically forms (4R)-KDGal and not (4S)-KDGlu and preferentially catalyzes condensation rather than cleavage by ∼40-fold. Based on 11 X-ray structures of AbHpaI complexed with M2+ and ligands at 1.85 to 2.0 Å resolution, the data clearly indicate that the M2+ cofactors form an octahedral geometry with Glu151 and Asp177, pyruvate, and water molecules. Moreover, Arg72 in the Zn2+-bound form governs the stereoselectivity/stereospecificity of AbHpaI. X-ray structures also show that Ca2+ binds at the trimer interface via interaction with Asp51. Hence, we conclude that AbHpaI•Zn2+ is distinctive from its homologues in substrate stereospecificity, preference for aldol formation over cleavage, and protein robustness, and is attractive for biocatalytic applications.
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Pirovich DB, Da’dara AA, Skelly PJ. Multifunctional Fructose 1,6-Bisphosphate Aldolase as a Therapeutic Target. Front Mol Biosci 2021; 8:719678. [PMID: 34458323 PMCID: PMC8385298 DOI: 10.3389/fmolb.2021.719678] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/31/2021] [Indexed: 01/01/2023] Open
Abstract
Fructose 1,6-bisphosphate aldolase is a ubiquitous cytosolic enzyme that catalyzes the fourth step of glycolysis. Aldolases are classified into three groups: Class-I, Class-IA, and Class-II; all classes share similar structural features but low amino acid identity. Apart from their conserved role in carbohydrate metabolism, aldolases have been reported to perform numerous non-enzymatic functions. Here we review the myriad "moonlighting" functions of this classical enzyme, many of which are centered on its ability to bind to an array of partner proteins that impact cellular scaffolding, signaling, transcription, and motility. In addition to the cytosolic location, aldolase has been found the extracellular surface of several pathogenic bacteria, fungi, protozoans, and metazoans. In the extracellular space, the enzyme has been reported to perform virulence-enhancing moonlighting functions e.g., plasminogen binding, host cell adhesion, and immunomodulation. Aldolase's importance has made it both a drug target and vaccine candidate. In this review, we note the several inhibitors that have been synthesized with high specificity for the aldolases of pathogens and cancer cells and have been shown to inhibit classical enzyme activity and moonlighting functions. We also review the many trials in which recombinant aldolases have been used as vaccine targets against a wide variety of pathogenic organisms including bacteria, fungi, and metazoan parasites. Most of such trials generated significant protection from challenge infection, correlated with antigen-specific cellular and humoral immune responses. We argue that refinement of aldolase antigen preparations and expansion of immunization trials should be encouraged to promote the advancement of promising, protective aldolase vaccines.
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Affiliation(s)
- David B. Pirovich
- Molecular Helminthology Laboratory, Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States
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Schultenkämper K, Gütle DD, López MG, Keller LB, Zhang L, Einsle O, Jacquot JP, Wendisch VF. Interrogating the Role of the Two Distinct Fructose-Bisphosphate Aldolases of Bacillus methanolicus by Site-Directed Mutagenesis of Key Amino Acids and Gene Repression by CRISPR Interference. Front Microbiol 2021; 12:669220. [PMID: 33995334 PMCID: PMC8119897 DOI: 10.3389/fmicb.2021.669220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/30/2021] [Indexed: 12/13/2022] Open
Abstract
The Gram-positive Bacillus methanolicus shows plasmid-dependent methylotrophy. This facultative ribulose monophosphate (RuMP) cycle methylotroph possesses two fructose bisphosphate aldolases (FBA) with distinct kinetic properties. The chromosomally encoded FBAC is the major glycolytic aldolase. The gene for the major gluconeogenic aldolase FBAP is found on the natural plasmid pBM19 and is induced during methylotrophic growth. The crystal structures of both enzymes were solved at 2.2 Å and 2.0 Å, respectively, and they suggested amino acid residue 51 to be crucial for binding fructose-1,6-bisphosphate (FBP) as substrate and amino acid residue 140 for active site zinc atom coordination. As FBAC and FBAP differed at these positions, site-directed mutagenesis (SDM) was performed to exchange one or both amino acid residues of the respective proteins. The aldol cleavage reaction was negatively affected by the amino acid exchanges that led to a complete loss of glycolytic activity of FBAP. However, both FBAC and FBAP maintained gluconeogenic aldol condensation activity, and the amino acid exchanges improved the catalytic efficiency of the major glycolytic aldolase FBAC in gluconeogenic direction at least 3-fold. These results confirmed the importance of the structural differences between FBAC and FBAP concerning their distinct enzymatic properties. In order to investigate the physiological roles of both aldolases, the expression of their genes was repressed individually by CRISPR interference (CRISPRi). The fba C RNA levels were reduced by CRISPRi, but concomitantly the fba P RNA levels were increased. Vice versa, a similar compensatory increase of the fba C RNA levels was observed when fba P was repressed by CRISPRi. In addition, targeting fba P decreased tkt P RNA levels since both genes are cotranscribed in a bicistronic operon. However, reduced tkt P RNA levels were not compensated for by increased RNA levels of the chromosomal transketolase gene tkt C.
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Affiliation(s)
- Kerstin Schultenkämper
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany
| | | | - Marina Gil López
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Laura B Keller
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Lin Zhang
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Oliver Einsle
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | | | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany
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Choi MY, Shin KC, Ho TH, Park H, Nguyen DQ, Park YS, Kim DW, Oh DK, Kang LW. Fructuronate-tagaturonate epimerase UxaE from Cohnella laeviribosi has a versatile TIM-barrel scaffold suitable for a sugar metabolizing biocatalyst. Int J Biol Macromol 2020; 163:1369-1374. [PMID: 32758598 DOI: 10.1016/j.ijbiomac.2020.07.285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 10/23/2022]
Abstract
Xylan and pectin are major structural components of plant cell walls. There are two independent catabolic pathways for xylan and pectin. UxaE bridges these two pathways by reversibly epimerizing D-fructuronate and D-tagaturonate. The crystal structure of UxaE from Cohnella laeviribosi (ClUxaE) shows a core scaffold of TIM-barrel with a position-changing divalent metal cofactor. ClUxaE has the flexible metal-coordination loop to allow the metal shift and the extra domains to bind a phosphate ion in the active site, which are important for catalysis and substrate specificity. Elucidation of the structure and mechanism of ClUxaE will assist in understanding the catalytic mechanism of UxaE family members, which are useful for processing both xylan and pectin-derived carbohydrates for practical and industrial purposes, including the transformation of agricultural wastes into numerous valuable products.
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Affiliation(s)
- Moon Young Choi
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Kyung-Chul Shin
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Thien-Hoang Ho
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Hyunjae Park
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Diem Quynh Nguyen
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Yoon Sik Park
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Dae Wook Kim
- Forest Plant Industry Department, Baekdudaegan National Arboretum, Bonghwa 36209, Republic of Korea
| | - Deok-Kun Oh
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea.
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea.
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7
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Méndez ST, Castillo-Villanueva A, Martínez-Mayorga K, Reyes-Vivas H, Oria-Hernández J. Structure-based identification of a potential non-catalytic binding site for rational drug design in the fructose 1,6-biphosphate aldolase from Giardia lamblia. Sci Rep 2019; 9:11779. [PMID: 31409864 PMCID: PMC6692403 DOI: 10.1038/s41598-019-48192-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/30/2019] [Indexed: 12/15/2022] Open
Abstract
Giardia lamblia is the causal agent of giardiasis, one of the most prevalent parasitosis in the world. Even though effective pharmacotherapies against this parasite are available, the disadvantages associated with its use call for the development of new antigiardial compounds. Based on the Giardia dependence on glycolysis as a main energy source, glycolytic enzymes appear to be attractive targets with antiparasitic potential. Among these, fructose 1,6-biphosphate aldolase (GlFBPA) has been highlighted as a promising target for drug design. Current efforts are based on the design of competitive inhibitors of GlFBPA; however, in the kinetic context of metabolic pathways, competitive inhibitors seem to have low potential as therapeutic agents. In this work, we performed an experimental and in silico structure-based approach to propose a non-catalytic binding site which could be used as a hot spot for antigardial drug design. The druggability of the selected binding site was experimentally tested; the alteration of the selected region by site directed mutagenesis disturbs the catalytic properties and the stability of the enzyme. A computational automated search of binding sites supported the potential of this region as functionally relevant. A preliminary docking study was performed, in order to explore the feasibility and type of molecules to be able to accommodate in the proposed binding region. Altogether, the results validate the proposed region as a specific molecular binding site with pharmacological potential.
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Affiliation(s)
- Sara-Teresa Méndez
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Insurgentes Sur 3700-C, Col. Insurgentes Cuicuilco, Alcaldía Coyoacán, CP 04530, Ciudad de México, Mexico
| | - Adriana Castillo-Villanueva
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Insurgentes Sur 3700-C, Col. Insurgentes Cuicuilco, Alcaldía Coyoacán, CP 04530, Ciudad de México, Mexico
| | - Karina Martínez-Mayorga
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Alcaldía Coyoacán, C.P. 04510, Ciudad de México, Mexico
| | - Horacio Reyes-Vivas
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Insurgentes Sur 3700-C, Col. Insurgentes Cuicuilco, Alcaldía Coyoacán, CP 04530, Ciudad de México, Mexico.
| | - Jesús Oria-Hernández
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Insurgentes Sur 3700-C, Col. Insurgentes Cuicuilco, Alcaldía Coyoacán, CP 04530, Ciudad de México, Mexico.
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Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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Howard TS, Cohen RD, Nwajiobi O, Muneeswaran ZP, Sim YE, Lahankar NN, Yeh JTH, Raj M. Amino-Acid-Catalyzed Direct Aldol Bioconjugation. Org Lett 2018; 20:5344-5347. [PMID: 30125118 PMCID: PMC7751349 DOI: 10.1021/acs.orglett.8b02265] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A site-specific bioconjugation was developed based on direct aldol coupling using amino-acid-derived organocatalysts. The functionalization exhibits fast kinetics and occurs under mild, biocompatible conditions (viz., aqueous media, moderate temperature, and neutral pH). The resulting bioconjugates were found to be stable toward abundant aldolase enzymes, as well as acidic and basic pH. The methodology was demonstrated through conjugation of a variety of small molecules, dyes, and peptides to proteins, including a single-domain antibody, which was then used for cellular imaging.
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Affiliation(s)
- Tiauna S Howard
- Department of Chemistry and Biochemistry , Seton Hall University , South Orange , New Jersey 07079 , United States
| | - Ryan D Cohen
- Department of Chemistry and Biochemistry , Seton Hall University , South Orange , New Jersey 07079 , United States
- Department of Process Research and Development , Merck & Co., Inc. , Rahway , New Jersey 07065 , United States
| | - Ogonna Nwajiobi
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
| | - Zilma P Muneeswaran
- Department of Chemistry and Biochemistry , Seton Hall University , South Orange , New Jersey 07079 , United States
| | - Yonnette E Sim
- Department of Chemistry and Biochemistry , Seton Hall University , South Orange , New Jersey 07079 , United States
| | - Neelam N Lahankar
- Department of Chemistry and Biochemistry , Seton Hall University , South Orange , New Jersey 07079 , United States
| | - Johannes T-H Yeh
- Cold Spring Harbor Laboratory , Cold Spring Harbor , New York 11724 , United States
| | - Monika Raj
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
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10
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Jacques B, Coinçon M, Sygusch J. Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases. J Biol Chem 2018; 293:7737-7753. [PMID: 29593097 PMCID: PMC5961046 DOI: 10.1074/jbc.ra117.001098] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/21/2018] [Indexed: 01/07/2023] Open
Abstract
Crystal structures of two bacterial metal (Zn2+)-dependent d-fructose-1,6-bisphosphate (FBP) aldolases in complex with substrate, analogues, and triose-P reaction products were determined to 1.5-2.0 Å resolution. The ligand complexes cryotrapped in native or mutant Helicobacter pylori aldolase crystals enabled a novel mechanistic description of FBP C3-C4 bond cleavage. The reaction mechanism uses active site remodeling during the catalytic cycle, implicating relocation of the Zn2+ cofactor that is mediated by conformational changes of active site loops. Substrate binding initiates conformational changes triggered upon P1 phosphate binding, which liberates the Zn2+-chelating His-180, allowing it to act as a general base for the proton abstraction at the FBP C4 hydroxyl group. A second zinc-chelating His-83 hydrogen bonds the substrate C4 hydroxyl group and assists cleavage by stabilizing the developing negative charge during proton abstraction. Cleavage is concerted with relocation of the metal cofactor from an interior to a surface-exposed site, thereby stabilizing the nascent enediolate form. Conserved residue Glu-142 is essential for protonation of the enediolate form prior to product release. A d-tagatose 1,6-bisphosphate enzymatic complex reveals how His-180-mediated proton abstraction controls stereospecificity of the cleavage reaction. Recognition and discrimination of the reaction products, dihydroxyacetone-P and d-glyceraldehyde 3-P, occurs via charged hydrogen bonds between hydroxyl groups of the triose-Ps and conserved residues, Asp-82 and Asp-255, respectively, and are crucial aspects of the enzyme's role in gluconeogenesis. Conformational changes in mobile loops β5-α7 and β6-α8 (containing catalytic residues Glu-142 and His-180, respectively) drive active site remodeling, enabling the relocation of the metal cofactor.
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Affiliation(s)
- Benoit Jacques
- From the Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Mathieu Coinçon
- From the Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Jurgen Sygusch
- From the Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada, To whom correspondence should be addressed:
Biochimie et Médecine moléculaire, Université de Montréal, CP 6128, Station Centre Ville, Montréal, Quebec H3C 3J7, Canada. Tel.:
514-343-2389; Fax:
514-343-6463; E-mail:
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11
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Galvao Ferrarini M, Mucha SG, Parrot D, Meiffrein G, Ruggiero Bachega JF, Comte G, Zaha A, Sagot MF. Hydrogen peroxide production and myo-inositol metabolism as important traits for virulence of Mycoplasma hyopneumoniae. Mol Microbiol 2018; 108:683-696. [PMID: 29624763 DOI: 10.1111/mmi.13957] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2018] [Indexed: 01/18/2023]
Abstract
Mycoplasma hyopneumoniae is the causative agent of enzootic pneumonia. In our previous work, we reconstructed the metabolic models of this species along with two other mycoplasmas from the respiratory tract of swine: Mycoplasma hyorhinis, considered less pathogenic but which nonetheless causes disease and Mycoplasma flocculare, a commensal bacterium. We identified metabolic differences that partially explained their different levels of pathogenicity. One important trait was the production of hydrogen peroxide from the glycerol metabolism only in the pathogenic species. Another important feature was a pathway for the metabolism of myo-inositol in M. hyopneumoniae. Here, we tested these traits to understand their relation to the different levels of pathogenicity, comparing not only the species but also pathogenic and attenuated strains of M. hyopneumoniae. Regarding the myo-inositol metabolism, we show that only M. hyopneumoniae assimilated this carbohydrate and remained viable when myo-inositol was the primary energy source. Strikingly, only the two pathogenic strains of M. hyopneumoniae produced hydrogen peroxide in complex medium. We also show that this production was dependent on the presence of glycerol. Although further functional tests are needed, we present in this work two interesting metabolic traits of M. hyopneumoniae that might be directly related to its enhanced virulence.
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Affiliation(s)
- Mariana Galvao Ferrarini
- ERABLE Team, Institut Nationale de Recherche en Informatique et Automation, Villeurbanne, France.,Laboratoire de Biometrie et Biologie Evolutive, Universite Claude Bernard Lyon 1, Villeurbanne, France.,Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Scheila Gabriele Mucha
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Delphine Parrot
- ERABLE Team, Institut Nationale de Recherche en Informatique et Automation, Villeurbanne, France.,Laboratoire de Biometrie et Biologie Evolutive, Universite Claude Bernard Lyon 1, Villeurbanne, France
| | - Guillaume Meiffrein
- Centre d'Etude des Substances Naturelles, Universite Claude Bernard Lyon 1, Villeurbanne, France
| | - Jose Fernando Ruggiero Bachega
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Departamento de Farmacociencias, Universidade Federal de Ciencias da Saude de Porto Alegre, Porto Alegre, Brazil
| | - Gilles Comte
- Centre d'Etude des Substances Naturelles, Universite Claude Bernard Lyon 1, Villeurbanne, France
| | - Arnaldo Zaha
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Marie-France Sagot
- ERABLE Team, Institut Nationale de Recherche en Informatique et Automation, Villeurbanne, France.,Laboratoire de Biometrie et Biologie Evolutive, Universite Claude Bernard Lyon 1, Villeurbanne, France
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12
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Tran HT, Lee SH, Ho TH, Hong SH, Huynh KH, Ahn YJ, Oh DK, Kang LW. Crystallographic snapshots of active site metal shift in E. coli fructose 1,6-bisphosphate aldolase. BMB Rep 2016; 49:681-686. [PMID: 27733232 PMCID: PMC5346313 DOI: 10.5483/bmbrep.2016.49.12.132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 08/30/2016] [Accepted: 10/10/2016] [Indexed: 11/30/2022] Open
Abstract
Fructose 1,6-bisphosphate aldolase (FBA) is important for both glycolysis and gluconeogenesis in life. Class II (zinc dependent) FBA is an attractive target for the development of antibiotics against protozoa, bacteria, and fungi, and is also widely used to produce various high-value stereoisomers in the chemical and pharmaceutical industry. In this study, the crystal structures of class II Escherichia coli FBA (EcFBA) were determined from four different crystals, with resolutions between 1.8 Å and 2.0 Å. Native EcFBA structures showed two separate sites of Zn1 (interior position) and Zn2 (active site surface position) for Zn2+ ion. Citrate and TRIS bound EcFBA structures showed Zn2+ position exclusively at Zn2. Crystallographic snapshots of EcFBA structures with and without ligand binding proposed the rationale of metal shift at the active site, which might be a hidden mechanism to keep the trace metal cofactor Zn2+ within EcFBA without losing it. [BMB Reports 2016; 49(12): 681-686].
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Affiliation(s)
- Huyen-Thi Tran
- Department of Biological Sciences, Konkuk University, Seoul 05029,
Korea
- Department of Biotechnology and Food Technology, Industrial University of Ho Chi Minh City, 12 Nguyen Van Bao Street, Ward 4, Go Vap District, Ho Chi Minh City,
Vietnam
| | - Seon-Hwa Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029,
Korea
| | - Thien-Hoang Ho
- Department of Biological Sciences, Konkuk University, Seoul 05029,
Korea
| | - Seung-Hye Hong
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029,
Korea
| | - Kim-Hung Huynh
- Department of Biological Sciences, Konkuk University, Seoul 05029,
Korea
| | - Yeh-Jin Ahn
- Department of Life Science, Sangmyung University, Seoul 03016,
Korea
| | - Deok-Kun Oh
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029,
Korea
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Seoul 05029,
Korea
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13
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Katebi AR, Jernigan RL. Aldolases Utilize Different Oligomeric States To Preserve Their Functional Dynamics. Biochemistry 2015; 54:3543-54. [PMID: 25982518 DOI: 10.1021/acs.biochem.5b00042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aldolases are essential enzymes in the glycolysis pathway and catalyze the reaction cleaving fructose/tagatose 1,6-bisphosphate into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. To determine how the aldolase motions relate to its catalytic process, we studied the dynamics of three different class II aldolase structures through simulations. We employed coarse-grained elastic network normal-mode analyses to investigate the dynamics of Escherichia coli fructose 1,6-bisphosphate aldolase, E. coli tagatose 1,6-bisphosphate aldolase, and Thermus aquaticus fructose 1,6-bisphosphate aldolase and compared their motions in different oligomeric states. The first one is a dimer, and the second and third are tetramers. Our analyses suggest that oligomerization not only stabilizes the aldolase structures, showing fewer fluctuations at the subunit interfaces, but also allows the enzyme to achieve the required dynamics for its functional loops. The essential mobility of these loops in the functional oligomeric states can facilitate the enzymatic mechanism, substrate recruitment in the open state, bringing the catalytic residues into their required configuration in the closed bound state, and moving back to the open state to release the catalytic products and repositioning the enzyme for its next catalytic cycle. These findings suggest that the aldolase global motions are conserved among aldolases having different oligomeric states to preserve its catalytic mechanism. The coarse-grained approaches taken permit an unprecedented view of the changes in the structural dynamics and how these relate to the critical structural stabilities essential for catalysis. The results are supported by experimental findings from many previous studies.
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Affiliation(s)
- Ataur R Katebi
- L. H. Baker Center for Bioinformatics and Biological Statistics, Department of Biochemistry, Biophysics and Molecular Biology, and Interdepartmental Program for Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa 50011-3020, United States
| | - Robert L Jernigan
- L. H. Baker Center for Bioinformatics and Biological Statistics, Department of Biochemistry, Biophysics and Molecular Biology, and Interdepartmental Program for Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa 50011-3020, United States
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14
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Navarrete-Vázquez G, Chávez-Silva F, Colín-Lozano B, Estrada-Soto S, Hidalgo-Figueroa S, Guerrero-Álvarez J, Méndez ST, Reyes-Vivas H, Oria-Hernández J, Canul-Canché J, Ortiz-Andrade R, Moo-Puc R. Synthesis of nitro(benzo)thiazole acetamides and in vitro antiprotozoal effect against amitochondriate parasites Giardia intestinalis and Trichomonas vaginalis. Bioorg Med Chem 2015; 23:2204-10. [PMID: 25801157 DOI: 10.1016/j.bmc.2015.02.059] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 02/17/2015] [Accepted: 02/26/2015] [Indexed: 01/03/2023]
Abstract
We synthesized four 5-nitrothiazole (1-4) and four 6-nitrobenzothiazole acetamides (5-8) using an easy two step synthetic route. All compounds were tested in vitro against amitochondriate parasites Giardia intestinalis and Trichomonas vaginalis, showing excellent antiprotozoal effects. IC₅₀'s of the most potent compounds range from nanomolar to low micromolar order, being more active than their drugs of choice. Compound 1 (IC₅₀=122 nM), was 44-times more active than Metronidazole, and 10-fold more effective than Nitazoxanide against G. intestinalis and showed good trichomonicidal activity (IC₅₀=2.24 μM). This compound did not display in vitro cytotoxicity against VERO cells. The in vitro inhibitory effect of compounds 1-8 and Nitazoxanide against G. intestinalis fructose-1,6-biphosphate aldolase (GiFBPA) was evaluated as potential drug target, showing a clear inhibitory effect over the enzyme activity. Molecular docking of compounds 1, 4 and Nitazoxanide into the ligand binding pocket of GiFBPA, revealed contacts with the active site residues of the enzyme. Ligand efficiency metrics of 1 revealed optimal combinations of physicochemical and antiprotozoal properties, better than Nitazoxanide.
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Affiliation(s)
- Gabriel Navarrete-Vázquez
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico.
| | - Fabiola Chávez-Silva
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico
| | - Blanca Colín-Lozano
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico
| | - Samuel Estrada-Soto
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico
| | - Sergio Hidalgo-Figueroa
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; Laboratorio de Farmacología, Depto. Ciencias de la Salud, Universidad Autónoma Metropolitana-Iztapalapa, 09340 México, D.F., Mexico
| | - Jorge Guerrero-Álvarez
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico
| | - Sara T Méndez
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 México, D.F., Mexico
| | - Horacio Reyes-Vivas
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 México, D.F., Mexico
| | - Jesús Oria-Hernández
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 México, D.F., Mexico
| | | | - Rolffy Ortiz-Andrade
- Facultad de Química, Universidad Autónoma de Yucatán, Mérida, Yucatán 97150, Mexico
| | - Rosa Moo-Puc
- Unidad de Investigación Médica Yucatán, IMSS Mérida, Yucatán 97000, Mexico
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15
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Capodagli GC, Lee SA, Boehm KJ, Brady KM, Pegan SD. Structural and functional characterization of methicillin-resistant Staphylococcus aureus's class IIb fructose 1,6-bisphosphate aldolase. Biochemistry 2014; 53:7604-14. [PMID: 25390935 PMCID: PMC4263427 DOI: 10.1021/bi501141t] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
Staphylococcus aureus is one of the most common
nosocomial sources of soft-tissue and skin infections and has more
recently become prevalent in the community setting as well. Since
the use of penicillins to combat S. aureus infections
in the 1940s, the bacterium has been notorious for developing resistances
to antibiotics, such as methicillin-resistant Staphylococcus
aureus (MRSA). With the persistence of MRSA as well as many
other drug resistant bacteria and parasites, there is a growing need
to focus on new pharmacological targets. Recently, class II fructose
1,6-bisphosphate aldolases (FBAs) have garnered attention to fill
this role. Regrettably, scarce biochemical data and no structural
data are currently available for the class II FBA found in MRSA (SaFBA).
With the recent finding of a flexible active site zinc-binding loop
(Z-Loop) in class IIa FBAs and its potential for broad spectrum class
II FBA inhibition, the lack of information regarding this feature
of class IIb FBAs, such as SaFBA, has been limiting for further Z-loop
inhibitor development. Therefore, we elucidated the crystal structure
of SaFBA to 2.1 Å allowing for a more direct structural analysis
of SaFBA. Furthermore, we determined the KM for one of SaFBA’s substrates, fructose 1,6-bisphosphate,
as well as performed mode of inhibition studies for an inhibitor that
takes advantage of the Z-loop’s flexibility. Together the data
offers insight into a class IIb FBA from a pervasively drug resistant
bacterium and a comparison of Z-loops and other features between the
different subtypes of class II FBAs.
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Affiliation(s)
- Glenn C Capodagli
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
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16
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Zhang L, Guo Z, Huang J, Liu M, Wang Y, Ji C. Expression, purification, crystallization and preliminary X-ray crystallographic analysis of fructose-1,6-bisphosphate aldolase from Escherichia coli. Acta Crystallogr F Struct Biol Commun 2014; 70:1376-9. [PMID: 25286943 PMCID: PMC4188083 DOI: 10.1107/s2053230x14018408] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 08/12/2014] [Indexed: 11/11/2022] Open
Abstract
Fructose-1,6-bisphosphate aldolase is one of the most important enzymes in the glycolytic pathway and catalyzes the reversible cleavage of fructose-1,6-bisphosphate to dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. The full-length fbaB gene encoding fructose-1,6-bisphosphate aldolase class I (FBPA I) was cloned from Escherichia coli strain BL21. FBPA I was overexpressed in E. coli and purified. Biochemical analysis found that the optimum reaction temperature of FBPA I is 330.5 K and that the enzyme has a high temperature tolerance. Crystals of recombinant FBPA I were obtained by the sitting-drop vapour-diffusion technique in a condition consisting of 19 mg ml(-1) FBPA I in 0.1 M Tris pH 9.0, 10%(w/v) polyethylene glycol 8000 and diffracted to 2.0 Å resolution. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 217.7, b = 114.9, c = 183.9 Å, β = 124.6°. The asymmetric unit of these crystals may contain ten molecules, giving a Matthews coefficient of 2.48 Å(3) Da(-1) and a solvent content of 50.5%.
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Affiliation(s)
- Li Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, People’s Republic of China
| | - Zheng Guo
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, People’s Republic of China
| | - Jing Huang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, People’s Republic of China
| | - Meiruo Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, People’s Republic of China
| | - Yuandong Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, People’s Republic of China
| | - Chaoneng Ji
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, People’s Republic of China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200433, People’s Republic of China
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17
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Capodagli GC, Sedhom WG, Jackson M, Ahrendt KA, Pegan SD. A noncompetitive inhibitor for Mycobacterium tuberculosis's class IIa fructose 1,6-bisphosphate aldolase. Biochemistry 2014; 53:202-13. [PMID: 24325645 PMCID: PMC4167715 DOI: 10.1021/bi401022b] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Class II fructose 1,6-bisphosphate aldolase (FBA) is an enzyme critical for bacterial, fungal, and protozoan glycolysis/gluconeogenesis. Importantly, humans lack this type of aldolase, having instead a class I FBA that is structurally and mechanistically distinct from class II FBAs. As such, class II FBA is considered a putative pharmacological target for the development of novel antibiotics against pathogenic bacteria such as Mycobacterium tuberculosis, the causative agent for tuberculosis (TB). To date, several competitive class II FBA substrate mimic-styled inhibitors have been developed; however, they lack either specificity, potency, or properties that limit their potential as possible therapeutics. Recently, through the use of enzymatic and structure-based assisted screening, we identified 8-hydroxyquinoline carboxylic acid (HCA) that has an IC50 of 10 ± 1 μM for the class II FBA present in M. tuberculosis (MtFBA). As opposed to previous inhibitors, HCA behaves in a noncompetitive manner, shows no inhibitory properties toward human and rabbit class I FBAs, and possesses anti-TB properties. Furthermore, we were able to determine the crystal structure of HCA bound to MtFBA to 2.1 Å. HCA also demonstrates inhibitory effects for other class II FBAs, including pathogenic bacteria such as methicillin-resistant Staphylococcus aureus. With its broad-spectrum potential, unique inhibitory characteristics, and flexibility of functionalization, the HCA scaffold likely represents an important advancement in the development of class II FBA inhibitors that can serve as viable preclinical candidates.
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Affiliation(s)
- Glenn C. Capodagli
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Wafik G. Sedhom
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Kateri A. Ahrendt
- Department of Chemistry, Regis University, Denver, Colorado 80221, United States,Corresponding Authors Department of Chemistry, Regis University, 3333 Regis Blvd., Denver, CO 80221. . Telephone: (303) 964-5088. Eleanor Roosevelt Institute and Department of Chemistry and Biochemistry, University of Denver, 2190 E. Iliff Ave., Olin 202, Denver, CO 80208. . Telephone: (303) 871-2533
| | - Scott D. Pegan
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States,Eleanor Roosevelt Institute, University of Denver, Denver, Colorado 80208, United States,Corresponding Authors Department of Chemistry, Regis University, 3333 Regis Blvd., Denver, CO 80221. . Telephone: (303) 964-5088. Eleanor Roosevelt Institute and Department of Chemistry and Biochemistry, University of Denver, 2190 E. Iliff Ave., Olin 202, Denver, CO 80208. . Telephone: (303) 871-2533
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18
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Barnett JP, Scanlan DJ, Blindauer CA. Identification of major zinc-binding proteins from a marine cyanobacterium: insight into metal uptake in oligotrophic environments. Metallomics 2014; 6:1254-68. [DOI: 10.1039/c4mt00048j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The open ocean cyanobacteriumSynechococcussp. WH8102 thrives at extremely low zinc concentrations. Metalloproteomics experiments have identified an outer-membrane bound porin with zinc-binding ability that is upregulated at low zinc levels, suggesting a role for porins in highly efficient zinc uptake.
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19
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Yamaguchi M, Shigeno M, Saito N, Yamamoto K. Synthesis, Double-Helix Formation, and Higher-Assembly Formation of Chiral Polycyclic Aromatic Compounds: Conceptual Development of Polyketide Aldol Synthesis. CHEM REC 2013; 14:15-27. [DOI: 10.1002/tcr.201300014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Indexed: 01/23/2023]
Affiliation(s)
- Masahiko Yamaguchi
- Department of Organic Chemistry, Graduate School of Pharmaceutical Sciences; Tohoku University; Aoba Sendai 980-8578 Japan
| | - Masanori Shigeno
- Department of Organic Chemistry, Graduate School of Pharmaceutical Sciences; Tohoku University; Aoba Sendai 980-8578 Japan
| | - Nozomi Saito
- International Advanced Research and Education Organization; Tohoku University; Sendai 980-8578 Japan
| | - Koji Yamamoto
- Department of Organic Chemistry, Graduate School of Pharmaceutical Sciences; Tohoku University; Aoba Sendai 980-8578 Japan
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20
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DHAP-dependent aldolases from (hyper)thermophiles: biochemistry and applications. Extremophiles 2013; 18:1-13. [DOI: 10.1007/s00792-013-0593-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 10/10/2013] [Indexed: 12/20/2022]
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21
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Itoh S, Tokunaga T, Sonoike S, Kitamura M, Yamano A, Aoki S. Asymmetric Aldol Reactions between Acetone and Benzaldehydes Catalyzed by Chiral Zn2+Complexes of Aminoacyl 1,4,7,10-Tetraazacyclododecane: Fine-Tuning of the Amino-Acid Side Chains and a Revised Reaction Mechanism. Chem Asian J 2013; 8:2125-35. [DOI: 10.1002/asia.201300308] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 04/29/2013] [Indexed: 10/26/2022]
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22
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Pegan SD, Rukseree K, Capodagli GC, Baker EA, Krasnykh O, Franzblau SG, Mesecar AD. Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis. Biochemistry 2013; 52:912-25. [PMID: 23298222 PMCID: PMC4170518 DOI: 10.1021/bi300928u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Class II fructose 1,6-bisphosphate aldolases (FBAs, EC 4.1.2.13) comprise one of two families of aldolases. Instead of forming a Schiff base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate, forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs have been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies of class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria, and protozoa have been reported, the structure of the active site loop responsible for catalyzing the protonation-deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI- and DHAP-bound form of the enzyme and determined the X-ray structure of the MtFBA-PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information and site-directed mutagenesis and kinetic studies conducted on a series of residues within the active site loop revealed that E169 facilitates a water-mediated deprotonation-protonation step of the MtFBA reaction mechanism. Also, solvent isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form.
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Affiliation(s)
- Scott D. Pegan
- Eleanor Roosevelt Institute and Department of Chemistry and Biochemistry, the University of Denver, 80208,Correspondence addressed to Department of Biological Sciences and the Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907 (ADM) or Eleanor Roosevelt Institute and Department of Chemistry and Biochemistry, University of Denver, 2190 E. Iliff Ave, Olin 202, Denver, CO 80208 (SDP). Tel: (312) 996-1877 (ADM) or (303) 871 2533 (SDP); (ADM) or (SDP)
| | - Kamolchanok Rukseree
- National Center for Genetic Engineering and Biotechnology (BIOTEC), NSTDA, Thailand Science Park, 12120,Institute for Tuberculosis Research, the University of Illinois at Chicago, 60612
| | - Glenn C. Capodagli
- Eleanor Roosevelt Institute and Department of Chemistry and Biochemistry, the University of Denver, 80208
| | - Erica A Baker
- Eleanor Roosevelt Institute and Department of Chemistry and Biochemistry, the University of Denver, 80208
| | - Olga Krasnykh
- Institute for Tuberculosis Research, the University of Illinois at Chicago, 60612,Department of Medicinal Chemistry, the University of Illinois at Chicago, 60607
| | - Scott G Franzblau
- Institute for Tuberculosis Research, the University of Illinois at Chicago, 60612,Department of Medicinal Chemistry, the University of Illinois at Chicago, 60607
| | - Andrew D Mesecar
- Department of Biological Sciences and Chemistry and the Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA,Correspondence addressed to Department of Biological Sciences and the Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907 (ADM) or Eleanor Roosevelt Institute and Department of Chemistry and Biochemistry, University of Denver, 2190 E. Iliff Ave, Olin 202, Denver, CO 80208 (SDP). Tel: (312) 996-1877 (ADM) or (303) 871 2533 (SDP); (ADM) or (SDP)
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23
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Steinborn M, Suhanji M, Klüfers P. Mixed sugar-core–phosphate chelation of d-fructose 1,6-bisphosphate with the ReVO(tmen) metal fragment. Dalton Trans 2013; 42:5749-54. [DOI: 10.1039/c3dt32901a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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24
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Li Y, Chooi YH, Sheng Y, Valentine JS, Tang Y. Comparative characterization of fungal anthracenone and naphthacenedione biosynthetic pathways reveals an α-hydroxylation-dependent Claisen-like cyclization catalyzed by a dimanganese thioesterase. J Am Chem Soc 2011; 133:15773-85. [PMID: 21866960 DOI: 10.1021/ja206906d] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The linear tetracyclic TAN-1612 (1) and BMS-192548 (2) were isolated from different filamentous fungal strains and have been examined as potential neuropeptide Y and neurokinin-1 receptor antagonists, respectively. Although the biosynthesis of fungal aromatic polyketides has attracted much interest in recent years, the biosynthetic mechanism for such naphthacenedione-containing products has not been established. Using a targeted genome mining approach, we first located the ada gene cluster responsible for the biosynthesis of 1 in Aspergillus niger ATCC 1015. The connection between 1 and the ada pathway was verified through overexpression of the Zn(2)Cys(6)-type pathway-specific transcriptional regulator AdaR and subsequent gene expression analysis. The enzymes encoded in the ada gene cluster share high sequence similarities to the known apt pathway linked to the biosynthesis of anthraquinone asperthecin 3. Subsequent comparative investigation of these two highly homologous gene clusters by heterologous pathway reconstitution in Saccharomyces cerevisiae revealed a novel α-hydroxylation-dependent Claisen cyclization cascade, which involves a flavin-dependent monooxygenase that hydroxylates the α-carbon of an acyl carrier protein-bound polyketide and a bifunctional metallo-β-lactamase-type thioesterase (MβL-TE). The bifunctional MβL-TE catalyzes the fourth ring cyclization to afford the naphthacenedione scaffold upon α-hydroxylation, whereas it performs hydrolytic release of an anthracenone product in the absence of α-hydroxylation. Through in vitro biochemical characterizations and metal analyses, we verified that the apt MβL-TE is a dimanganese enzyme and requires both Mn(2+) cations for the observed activities. The MβL-TE is the first example of a thioesterase in polyketide biosynthesis that catalyzes the Claisen-like condensation without an α/β hydrolase fold and forms no covalent bond with the substrate. These mechanistic features should be general to the biosynthesis of tetracyclic naphthacenedione compounds in fungi.
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Affiliation(s)
- Yanran Li
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
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25
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Gardberg A, Sankaran B, Davies D, Bhandari J, Staker B, Stewart L. Structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1055-9. [PMID: 21904050 PMCID: PMC3169402 DOI: 10.1107/s1744309111021841] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 06/06/2011] [Indexed: 11/11/2022]
Abstract
Fructose bisphosphate aldolose (FBPA) enzymes have been found in a broad range of eukaryotic and prokaryotic organisms. FBPA catalyses the cleavage of fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. The SSGCID has reported several FBPA structures from pathogenic sources. Bioinformatic analysis of the genome of the eukaryotic microsporidian parasite Encephalitozoon cuniculi revealed an FBPA homolog. The structures of this enzyme in the presence of the native substrate FBP and also with the partial substrate analog phosphate are reported. The purified enzyme crystallized in 90 mM Bis-Tris propane pH 6.5, 18% PEG 3350, 18 mM NaKHPO(4), 10 mM urea for the phosphate-bound form and 100 mM Bis-Tris propane pH 6.5, 20% PEG 3350, 20 mM fructose 1,6-bisphosphate for the FBP-bound form. In both cases protein was present at 25 mg ml(-1) and the sitting-drop vapour-diffusion method was used. For the FBP-bound form, a data set to 2.37 Å resolution was collected from a single crystal at 100 K. The crystal belonged to the orthorhombic space group C222(1), with unit-cell parameters a=121.46, b=135.82, c=61.54 Å. The structure was refined to a final free R factor of 20.8%. For the phosphate-bound form, a data set was collected to 2.00 Å resolution. The space group was also C222(1) and the unit-cell parameters were a=121.96, b=137.61, c=62.23 Å. The structure shares the typical barrel tertiary structure reported for previous FBPA structures and exhibits the same Schiff base in the active site. The quaternary structure is dimeric. This work provides a direct experimental result for the substrate-binding conformation of the product state of E. cuniculi FBPA.
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Affiliation(s)
- Anna Gardberg
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA.
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Li Z, Liu Z, Cho DW, Zou J, Gong M, Breece RM, Galkin A, Li L, Zhao H, Maestas GD, Tierney DL, Herzberg O, Dunaway-Mariano D, Mariano PS. Rational design, synthesis and evaluation of first generation inhibitors of the Giardia lamblia fructose-1,6-biphosphate aldolase. J Inorg Biochem 2011; 105:509-17. [PMID: 21333622 PMCID: PMC3071891 DOI: 10.1016/j.jinorgbio.2010.12.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2010] [Revised: 12/22/2010] [Accepted: 12/23/2010] [Indexed: 11/16/2022]
Abstract
Inhibitors of the Giardia lamblia fructose 1,6-bisphosphate aldolase (GlFBPA), which transforms fructose 1,6-bisphosphate (FBP) to dihydroxyacetone phosphate and glyceraldehyde 3-phosphate, were designed based on 3-hydroxy-2-pyridone and 1,2-dihydroxypyridine scaffolds that position two negatively charged tetrahedral groups for interaction with substrate phosphate binding residues, a hydrogen bond donor to the catalytic Asp83, and a Zn(2+) binding group. The inhibition activities for the GlFBPA catalyzed reaction of FBP of the prepared alkyl phosphonate/phosphate substituted 3-hydroxy-2-pyridinones and a dihydroxypyridine were determined. The 3-hydroxy-2-pyridone inhibitor 8 was found to bind to GlFBPA with an affinity (K(i)=14μM) that is comparable to that of FBP (K(m)=2μM) or its inert analog TBP (K(i)=1μM). The X-ray structure of the GlFBPA-inhibitor 8 complex (2.3Å) shows that 8 binds to the active site in the manner predicted by in silico docking with the exception of coordination with Zn(2+). The observed distances and orientation of the pyridone ring O=C-C-OH relative to Zn(2+) are not consistent with a strong interaction. To determine if Zn(2+)coordination occurs in the GlFBPA-inhibitor 8 complex in solution, EXAFS spectra were measured. A four coordinate geometry comprised of the three enzyme histidine ligands and an oxygen atom from the pyridone ring O=C-C-OH was indicated. Analysis of the Zn(2+) coordination geometries in recently reported structures of class II FBPAs suggests that strong Zn(2+) coordination is reserved for the enediolate-like transition state, accounting for minimal contribution of Zn(2+) coordination to binding of 8 to GlFBPA.
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Affiliation(s)
- Zhimin Li
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | | | - Dae Won Cho
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Jiwen Zou
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Maozhen Gong
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Robert M. Breece
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - Andrey Galkin
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850
| | - Ling Li
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Hong Zhao
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Gabriel D. Maestas
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - David L. Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - Osnat Herzberg
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850
| | - Debra Dunaway-Mariano
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Patrick S. Mariano
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
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Brovetto M, Gamenara D, Méndez PS, Seoane GA. C-C bond-forming lyases in organic synthesis. Chem Rev 2011; 111:4346-403. [PMID: 21417217 DOI: 10.1021/cr100299p] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Margarita Brovetto
- Grupo de Fisicoquímica Orgánica y Bioprocesos, Departamento de Química Orgánica, DETEMA, Facultad de Química, Universidad de la República (UdelaR), Gral. Flores 2124, 11800 Montevideo, Uruguay
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Gilg K, Mayer T, Ghaschghaie N, Klüfers P. The metal-binding sites of glycose phosphates. Dalton Trans 2009:7934-45. [PMID: 19771356 DOI: 10.1039/b909431h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In aqueous solution, the reducing sugar phosphates D-arabinose 5-phosphate, D-ribose 5-phosphate, D-fructose 1,6-bisphosphate, D-fructose 6-phosphate, D-glucose 6-phosphate and D-mannose 6-phosphate provide metal-binding sites at their glycose core on reaction with Pd(II)(en) or M(III)(tacn) residues (M = Ga, Co; en = ethylenediamine, tacn = 1,4,7-triazacyclononane). The individual species were detected by one- and two-dimensional NMR spectroscopy. The coordination patterns are related to the metal-binding modes of the respective parent glycoses. In detail, ribo- and arabinofuranose phosphate favour kappaO(1,3) coordination, whereas the ketofuranose core of fructose phosphate and fructose bisphosphate provides the kappaO(2,3) chelator thus maintaining the configuration of the respective major solution anomer. On palladium excess, D-fructose 6-phosphate is metallated twice in a unique kappaO(1,3):kappaO(2,4) metallation pattern. Dimetallation is also found for the aldohexose phosphates. A mixed glycose-core-phosphate chelation was detected for Pd(II)(en) and M(III)(tacn) residues with M = Al, Ga in the pH range just above the physiological pH for the D-fructose 1,6-bisphosphate ligand. The results are discussed in relation to D-fructose-1,6-bisphosphate-metabolism in class-II aldolases.
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Affiliation(s)
- Kathrin Gilg
- Department of Chemistry and Biochemistry of the Ludwig Maximilian University Munich, Butenandtstr. 5-13, D-81377 Munich, Germany
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