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Zabed HM, Akter S, Rupani PF, Akor J, Zhang Y, Zhao M, Zhang C, Ragauskas AJ, Qi X. Biocatalytic gateway to convert glycerol into 3-hydroxypropionic acid in waste-based biorefineries: Fundamentals, limitations, and potential research strategies. Biotechnol Adv 2023; 62:108075. [PMID: 36502965 DOI: 10.1016/j.biotechadv.2022.108075] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022]
Abstract
Microbial conversion of bioenergy-derived waste glycerol into value-added chemicals has emerged as an important bioprocessing technology due to its eco-friendliness, feasible technoeconomics, and potential to provide sustainability in biodiesel and bioethanol production. Glycerol is an abundant liquid waste from bioenergy plants with a projected volume of 6 million tons by 2025, accounting for about 10% of biodiesel and 2.5% of bioethanol yields. 3-Hydroxypropionic acid (3-HP) is a major product of glycerol bioconversion, which is the third largest biobased platform compound with expected market size and value of 3.6 million tons/year and USD 10 billion/year, respectively. Despite these biorefinery values, 3-HP biosynthesis from glycerol is still at an immature stage of commercial exploitation. The main challenges behind this immaturity are the toxic effects of 3-HPA on cells, the distribution of carbon flux to undesirable pathways, low tolerance of cells to glycerol and 3-HP, co-factor dependence of enzymes, low enzyme activity and stability, and the problems of substrate inhibition and specificity of enzymes. To address these challenges, it is necessary to understand the fundamentals of glycerol bioconversion and 3-HP production in terms of metabolic pathways, related enzymes, cell factories, midstream process configurations, and downstream 3-HP recovery, as discussed in this review critically and comprehensively. It is equally important to know the current challenges and limitations in 3-HP production, which are discussed in detail along with recent research efforts and remaining gaps. Finally, possible research strategies are outlined considering the recent technological advances in microbial biosynthesis, aiming to attract further research efforts to achieve a sustainable and industrially exploitable 3-HP production technology. By discussing the use of advanced tools and strategies to overcome the existing challenges in 3-HP biosynthesis, this review will attract researchers from many other similar biosynthesis technologies and provide a common gateway for their further development.
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Affiliation(s)
- Hossain M Zabed
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Suely Akter
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Parveen Fatemah Rupani
- Department of Chemical Engineering, Ku Luven, Jan De Nayerlaan 5, 2860 Sint-Katelijne-Waver, Belgium
| | - Joseph Akor
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Yufei Zhang
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Mei Zhao
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Cunsheng Zhang
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Arthur J Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee Knoxville, Knoxville, TN 37996, USA; Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, The University of Tennessee Institute of Agriculture, Knoxville, TN 37996, USA; UTK-ORNL Joint Institute for Biological Science, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| | - Xianghui Qi
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China; School of Life Sciences, Guangzhou University, Guangzhou 510,006, Guangdong Province, China.
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2
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Gardner SH, Reinhardt CJ, Chan J. Advances in Activity-Based Sensing Probes for Isoform-Selective Imaging of Enzymatic Activity. Angew Chem Int Ed Engl 2021; 60:5000-5009. [PMID: 32274846 PMCID: PMC7544620 DOI: 10.1002/anie.202003687] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Indexed: 12/12/2022]
Abstract
Until recently, there were no generalizable methods for assessing the effects of post-translational regulation on enzymatic activity. Activity-based sensing (ABS) has emerged as a powerful approach for monitoring small-molecule and enzyme activities within living systems. Initial examples of ABS were applied for measuring general enzymatic activity; however, a recent focus has been placed on increasing the selectivity to monitor a single enzyme or isoform. The highest degree of selectivity is required for differentiating between isoforms, where the targets display significant structural similarities as a result of a gene duplication or alternative splicing. This Minireview highlights key examples of small-molecule isoform-selective probes with a focus on the relevance of isoform differentiation, design strategies to achieve selectivity, and applications in basic biology or in the clinic.
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Affiliation(s)
- Sarah H Gardner
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Christopher J Reinhardt
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jefferson Chan
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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3
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Zimmerling J, Oelschlägel M, Großmann C, Voitel M, Schlömann M, Tischler D. Biochemical Characterization of Phenylacetaldehyde Dehydrogenases from Styrene-degrading Soil Bacteria. Appl Biochem Biotechnol 2021; 193:650-667. [PMID: 33106986 PMCID: PMC7910268 DOI: 10.1007/s12010-020-03421-8] [Citation(s) in RCA: 1] [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: 04/04/2020] [Accepted: 09/11/2020] [Indexed: 10/24/2022]
Abstract
Four phenylacetaldehyde dehydrogenases (designated as FeaB or StyD) originating from styrene-degrading soil bacteria were biochemically investigated. In this study, we focused on the Michaelis-Menten kinetics towards the presumed native substrate phenylacetaldehyde and the obviously preferred co-substrate NAD+. Furthermore, the substrate specificity on four substituted phenylacetaldehydes and the co-substrate preference were studied. Moreover, these enzymes were characterized with respect to their temperature as well as long-term stability. Since aldehyde dehydrogenases are known to show often dehydrogenase as well as esterase activity, we tested this capacity, too. Almost all results showed clearly different characteristics between the FeaB and StyD enzymes. Furthermore, FeaB from Sphingopyxis fribergensis Kp5.2 turned out to be the most active enzyme with an apparent specific activity of 17.8 ± 2.1 U mg-1. Compared with that, both StyDs showed only activities less than 0.2 U mg-1 except the overwhelming esterase activity of StyD-CWB2 (1.4 ± 0.1 U mg-1). The clustering of both FeaB and StyD enzymes with respect to their characteristics could also be mirrored in the phylogenetic analysis of twelve dehydrogenases originating from different soil bacteria.
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Affiliation(s)
- Juliane Zimmerling
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany.
| | - Michel Oelschlägel
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Carolin Großmann
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Matthias Voitel
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Michael Schlömann
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Dirk Tischler
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany.
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany.
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4
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Widjaja-Adhi MAK, Golczak M. The molecular aspects of absorption and metabolism of carotenoids and retinoids in vertebrates. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158571. [PMID: 31770587 PMCID: PMC7244374 DOI: 10.1016/j.bbalip.2019.158571] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 02/08/2023]
Abstract
Vitamin A is an essential nutrient necessary for numerous basic physiological functions, including reproduction and development, immune cell differentiation and communication, as well as the perception of light. To evade the dire consequences of vitamin A deficiency, vertebrates have evolved specialized metabolic pathways that enable the absorption, transport, and storage of vitamin A acquired from dietary sources as preformed retinoids or provitamin A carotenoids. This evolutionary advantage requires a complex interplay between numerous specialized retinoid-transport proteins, receptors, and enzymes. Recent advances in molecular and structural biology resulted in a rapid expansion of our understanding of these processes at the molecular level. This progress opened new avenues for the therapeutic manipulation of retinoid homeostasis. In this review, we summarize current research related to the biochemistry of carotenoid and retinoid-processing proteins with special emphasis on the structural aspects of their physiological actions. This article is part of a Special Issue entitled Carotenoids recent advances in cell and molecular biology edited by Johannes von Lintig and Loredana Quadro.
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Affiliation(s)
- Made Airanthi K Widjaja-Adhi
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States of America
| | - Marcin Golczak
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States of America; Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States of America.
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5
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Gardner SH, Reinhardt CJ, Chan J. Fortschritte bei aktivitätsbasierten Sonden für die isoformselektive Bildgebung enzymatischer Aktivität. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003687] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sarah H. Gardner
- Department of Biochemistry University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Christopher J. Reinhardt
- Department of Chemistry Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Jefferson Chan
- Department of Chemistry Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign Urbana IL 61801 USA
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6
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Wang Y, Li PY, Zhang Y, Cao HY, Wang YJ, Li CY, Wang P, Su HN, Chen Y, Chen XL, Zhang YZ. 3,6-Anhydro-L-Galactose Dehydrogenase VvAHGD is a Member of a New Aldehyde Dehydrogenase Family and Catalyzes by a Novel Mechanism with Conformational Switch of Two Catalytic Residues Cysteine 282 and Glutamate 248. J Mol Biol 2020; 432:2186-2203. [PMID: 32087198 DOI: 10.1016/j.jmb.2020.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 12/26/2022]
Abstract
3,6-anhydro-α-L-galactose (L-AHG) is one of the main monosaccharide constituents of red macroalgae. In the recently discovered bacterial L-AHG catabolic pathway, L-AHG is first oxidized by a NAD(P)+-dependent dehydrogenase (AHGD), which is a key step of this pathway. However, the catalytic mechanism(s) of AHGDs is still unclear. Here, we identified and characterized an AHGD from marine bacterium Vibrio variabilis JCM 19239 (VvAHGD). The NADP+-dependent VvAHGD could efficiently oxidize L-AHG. Phylogenetic analysis suggested that VvAHGD and its homologs represent a new aldehyde dehydrogenase (ALDH) family with different substrate preferences from reported ALDH families, named the L-AHGDH family. To explain the catalytic mechanism of VvAHGD, we solved the structures of VvAHGD in the apo form and complex with NADP+ and modeled its structure with L-AHG. Based on structural, mutational, and biochemical analyses, the cofactor channel and the substrate channel of VvAHGD are identified, and the key residues involved in the binding of NADP+ and L-AHG and the catalysis are revealed. VvAHGD performs catalysis by controlling the consecutive connection and interruption of the cofactor channel and the substrate channel via the conformational changes of its two catalytic residues Cys282 and Glu248. Comparative analyses of structures and enzyme kinetics revealed that differences in the substrate channels (in shape, size, electrostatic surface, and residue composition) lead to the different substrate preferences of VvAHGD from other ALDHs. This study on VvAHGD sheds light on the diversified catalytic mechanisms and evolution of NAD(P)+-dependent ALDHs.
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Affiliation(s)
- Yue Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Yi Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Hai-Yan Cao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Yan-Jun Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Chun-Yang Li
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Peng Wang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Yin Chen
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China; School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China; College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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7
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Hasse D, Hülsemann J, Carlsson GH, Valegård K, Andersson I. Structure and mechanism of piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:1107-1118. [PMID: 31793904 DOI: 10.1107/s2059798319014852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 11/04/2019] [Indexed: 11/11/2022]
Abstract
The core of β-lactam antibiotics originates from amino acids of primary metabolism in certain microorganisms. β-Lactam-producing bacteria, including Streptomyces clavuligerus, synthesize the precursor of the amino acid α-aminoadipic acid by the catabolism of lysine in two steps. The second reaction, the oxidation of piperideine-6-carboxylate (or its open-chain form α-aminoadipate semialdehyde) to α-aminoadipic acid, is catalysed by the NAD+-dependent enzyme piperideine-6-carboxylate dehydrogenase (P6CDH). This structural study, focused on ligand binding and catalysis, presents structures of P6CDH from S. clavuligerus in its apo form and in complexes with the cofactor NAD+, the product α-aminoadipic acid and a substrate analogue, picolinic acid. P6CDH adopts the common aldehyde dehydrogenase fold, consisting of NAD-binding, catalytic and oligomerization domains. The product binds in the oxyanion hole, close to the catalytic residue Cys299. Clear density is observed for the entire cofactor, including the nicotinamide riboside, in the binary complex. NAD+ binds in an extended conformation with its nicotinamide ring overlapping with the binding site of the carboxylate group of the product, implying that the conformation of the cofactor may change during catalysis. The binding site of the substrate analogue overlaps with that of the product, suggesting that the cyclic form of the substrate, piperideine-6-carboxylate, may be accepted as a substrate by the enzyme. The catalytic mechanism and the roles of individual residues are discussed in light of these results.
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Affiliation(s)
- Dirk Hasse
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-751 24 Uppsala, Sweden
| | - Janne Hülsemann
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-751 24 Uppsala, Sweden
| | - Gunilla H Carlsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-751 24 Uppsala, Sweden
| | - Karin Valegård
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-751 24 Uppsala, Sweden
| | - Inger Andersson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-751 24 Uppsala, Sweden
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8
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Ahmed Laskar A, Younus H. Aldehyde toxicity and metabolism: the role of aldehyde dehydrogenases in detoxification, drug resistance and carcinogenesis. Drug Metab Rev 2019; 51:42-64. [DOI: 10.1080/03602532.2018.1555587] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Amaj Ahmed Laskar
- Enzymology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Hina Younus
- Enzymology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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9
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Hayes K, Noor M, Djeghader A, Armshaw P, Pembroke T, Tofail S, Soulimane T. The quaternary structure of Thermus thermophilus aldehyde dehydrogenase is stabilized by an evolutionary distinct C-terminal arm extension. Sci Rep 2018; 8:13327. [PMID: 30190503 PMCID: PMC6127216 DOI: 10.1038/s41598-018-31724-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/22/2018] [Indexed: 12/04/2022] Open
Abstract
Aldehyde dehydrogenases (ALDH) form a superfamily of dimeric or tetrameric enzymes that catalyze the oxidation of a broad range of aldehydes into their corresponding carboxylic acids with the concomitant reduction of the cofactor NAD(P) into NAD(P)H. Despite their varied polypeptide chain length and oligomerisation states, ALDHs possess a conserved architecture of three domains: the catalytic domain, NAD(P)+ binding domain, and the oligomerization domain. Here, we describe the structure and function of the ALDH from Thermus thermophilus (ALDHTt) which exhibits non-canonical features of both dimeric and tetrameric ALDH and a previously uncharacterized C-terminal arm extension forming novel interactions with the N-terminus in the quaternary structure. This unusual tail also interacts closely with the substrate entry tunnel in each monomer providing further mechanistic detail for the recent discovery of tail-mediated activity regulation in ALDH. However, due to the novel distal extension of the tail of ALDHTt and stabilizing termini-interactions, the current model of tail-mediated substrate access is not apparent in ALDHTt. The discovery of such a long tail in a deeply and early branching phylum such as Deinococcus-Thermus indicates that ALDHTt may be an ancestral or primordial metabolic model of study. This structure provides invaluable evidence of how metabolic regulation has evolved and provides a link to early enzyme regulatory adaptations.
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Affiliation(s)
- Kevin Hayes
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Mohamed Noor
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Ahmed Djeghader
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Patricia Armshaw
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Tony Pembroke
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Syed Tofail
- Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland.,Physics Department, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Tewfik Soulimane
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland. .,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland.
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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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11
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Crabo AG, Singh B, Nguyen T, Emami S, Gassner GT, Sazinsky MH. Structure and biochemistry of phenylacetaldehyde dehydrogenase from the Pseudomonas putida S12 styrene catabolic pathway. Arch Biochem Biophys 2017; 616:47-58. [PMID: 28153386 PMCID: PMC5318141 DOI: 10.1016/j.abb.2017.01.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 01/03/2017] [Accepted: 01/23/2017] [Indexed: 01/07/2023]
Abstract
Phenylacetaldehyde dehydrogenase catalyzes the NAD+-dependent oxidation of phenylactealdehyde to phenylacetic acid in the styrene catabolic and detoxification pathway of Pseudomonas putida (S12). Here we report the structure and mechanistic properties of the N-terminally histidine-tagged enzyme, NPADH. The 2.83 Å X-ray crystal structure is similar in fold to sheep liver cytosolic aldehyde dehydrogenase (ALDH1), but has unique set of intersubunit interactions and active site tunnel for substrate entrance. In solution, NPADH occurs as 227 kDa homotetramer. It follows a sequential reaction mechanism in which NAD+ serves as both the leading substrate and homotropic allosteric activator. In the absence of styrene monooxygenase reductase, which regenerates NAD+ from NADH in the first step of styrene catabolism, NPADH is inhibited by a ternary complex involving NADH, product, and phenylacetaldehyde, substrate. Each oligomerization domain of NPADH contains a six-residue insertion that extends this loop over the substrate entrance tunnel of a neighboring subunit, thereby obstructing the active site of the adjacent subunit. This feature could be an important factor in the homotropic activation and product inhibition mechanisms. Compared to ALDH1, the substrate channel of NPADH is narrower and lined with more aromatic residues, suggesting a means for enhancing substrate specificity.
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12
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Belmont-Díaz JA, Calleja-Castañeda LF, Yoval-Sánchez B, Rodríguez-Zavala JS. Tamoxifen, an anticancer drug, is an activator of human aldehyde dehydrogenase 1A1. Proteins 2014; 83:105-16. [PMID: 25354921 DOI: 10.1002/prot.24709] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/05/2014] [Accepted: 10/18/2014] [Indexed: 12/24/2022]
Abstract
The modulation of aldehyde dehydrogenase (ALDH) activity has been suggested as a promising option for the prevention or treatment of many diseases. To date, only few activating compounds of ALDHs have been described. In this regard, N-(1,3-benzodioxol-5-ylmethyl)-2,6-dichlorobenzamide has been used to protect the heart against ischemia/reperfusion damage. In the search for new modulating ALDH molecules, the binding capability of different compounds to the active site of human aldehyde dehydrogenase class 1A1 (ALDH1A1) was analyzed by molecular docking, and their ability to modulate the activity of the enzyme was tested. Surprisingly, tamoxifen, an estrogen receptor antagonist used for breast cancer treatment, increased the activity and decreased the Km for NAD(+) by about twofold in ALDH1A1. No drug effect on human ALDH2 or ALDH3A1 was attained, showing that tamoxifen was specific for ALDH1A1. Protection against thermal denaturation and competition with daidzin suggested that tamoxifen binds to the aldehyde site of ALDH1A1, resembling the interaction of N-(1,3-benzodioxol-5-ylmethyl)-2,6-dichlorobenzamide with ALDH2. Further kinetic analysis indicated that tamoxifen activation may be related to an increase in the Kd for NADH, favoring a more rapid release of the coenzyme, which is the rate-limiting step of the reaction for this isozyme. Therefore, tamoxifen might improve the antioxidant response, which is compromised in some diseases.
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Liu Y, Chan ZH, Li FY, Hou YP, Zeng RY. Cloning, expression and characterization of a novel aldehyde dehydrogenase gene from Flammeovirga pacifica. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683814110027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Keller MA, Zander U, Fuchs JE, Kreutz C, Watschinger K, Mueller T, Golderer G, Liedl KR, Ralser M, Kräutler B, Werner ER, Marquez JA. A gatekeeper helix determines the substrate specificity of Sjögren-Larsson Syndrome enzyme fatty aldehyde dehydrogenase. Nat Commun 2014; 5:4439. [PMID: 25047030 PMCID: PMC4109017 DOI: 10.1038/ncomms5439] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 06/17/2014] [Indexed: 11/09/2022] Open
Abstract
Mutations in the gene coding for membrane-bound fatty aldehyde dehydrogenase (FALDH) lead to toxic accumulation of lipid species and development of the Sjögren-Larsson Syndrome (SLS), a rare disorder characterized by skin defects and mental retardation. Here, we present the crystallographic structure of human FALDH, the first model of a membrane-associated aldehyde dehydrogenase. The dimeric FALDH displays a previously unrecognized element in its C-terminal region, a 'gatekeeper' helix, which extends over the adjacent subunit, controlling the access to the substrate cavity and helping orientate both substrate cavities towards the membrane surface for efficient substrate transit between membranes and catalytic site. Activity assays demonstrate that the gatekeeper helix is important for directing the substrate specificity of FALDH towards long-chain fatty aldehydes. The gatekeeper feature is conserved across membrane-associated aldehyde dehydrogenases. Finally, we provide insight into the previously elusive molecular basis of SLS-causing mutations.
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Affiliation(s)
- Markus A. Keller
- Division of Biological Chemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, 6020 Innsbruck, Austria
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis court Rd, Cambridge CB2 1GA, UK
| | - Ulrich Zander
- European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France
| | - Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Katrin Watschinger
- Division of Biological Chemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, 6020 Innsbruck, Austria
| | - Thomas Mueller
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Georg Golderer
- Division of Biological Chemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, 6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis court Rd, Cambridge CB2 1GA, UK
- MRC National Institute for Medical Research, the Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Bernhard Kräutler
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Ernst R. Werner
- Division of Biological Chemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, 6020 Innsbruck, Austria
- These authors contributed equally to this work
| | - Jose A. Marquez
- European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France
- Unit of Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France
- These authors contributed equally to this work
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15
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Koppaka V, Thompson DC, Chen Y, Ellermann M, Nicolaou KC, Juvonen RO, Petersen D, Deitrich RA, Hurley TD, Vasiliou V. Aldehyde dehydrogenase inhibitors: a comprehensive review of the pharmacology, mechanism of action, substrate specificity, and clinical application. Pharmacol Rev 2012; 64:520-39. [PMID: 22544865 PMCID: PMC3400832 DOI: 10.1124/pr.111.005538] [Citation(s) in RCA: 403] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aldehyde dehydrogenases (ALDHs) belong to a superfamily of enzymes that play a key role in the metabolism of aldehydes of both endogenous and exogenous derivation. The human ALDH superfamily comprises 19 isozymes that possess important physiological and toxicological functions. The ALDH1A subfamily plays a pivotal role in embryogenesis and development by mediating retinoic acid signaling. ALDH2, as a key enzyme that oxidizes acetaldehyde, is crucial for alcohol metabolism. ALDH1A1 and ALDH3A1 are lens and corneal crystallins, which are essential elements of the cellular defense mechanism against ultraviolet radiation-induced damage in ocular tissues. Many ALDH isozymes are important in oxidizing reactive aldehydes derived from lipid peroxidation and thereby help maintain cellular homeostasis. Increased expression and activity of ALDH isozymes have been reported in various human cancers and are associated with cancer relapse. As a direct consequence of their significant physiological and toxicological roles, inhibitors of the ALDH enzymes have been developed to treat human diseases. This review summarizes known ALDH inhibitors, their mechanisms of action, isozyme selectivity, potency, and clinical uses. The purpose of this review is to 1) establish the current status of pharmacological inhibition of the ALDHs, 2) provide a rationale for the continued development of ALDH isozyme-selective inhibitors, and 3) identify the challenges and potential therapeutic rewards associated with the creation of such agents.
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Affiliation(s)
- Vindhya Koppaka
- Department of Pharmaceutical Sciences, University of Colorado Denver, 12850 East Montview Blvd., Aurora, CO 80045, USA
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16
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Smith NE, Vrielink A, Attwood PV, Corry B. Biological channeling of a reactive intermediate in the bifunctional enzyme DmpFG. Biophys J 2012; 102:868-77. [PMID: 22385858 DOI: 10.1016/j.bpj.2012.01.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 12/26/2011] [Accepted: 01/03/2012] [Indexed: 11/15/2022] Open
Abstract
It has been hypothesized that the bifunctional enzyme DmpFG channels its intermediate, acetaldehyde, from one active site to the next using a buried intermolecular channel identified in the crystal structure. This channel appears to switch between an open and a closed conformation depending on whether the coenzyme NAD(+) is present or absent. Here, we applied molecular dynamics and metadynamics to investigate channeling within DmpFG in both the presence and absence of NAD(+). We found that substrate channeling within this enzyme is energetically feasible in the presence of NAD(+) but was less likely in its absence. Tyr-291, a proposed control point at the channel's entry, does not appear to function as a molecular gate. Instead, it is thought to orientate the substrate 4-hydroxy-2-ketovalerate in DmpG before reaction occurs, and may function as a proton shuttle for the DmpG reaction. Three hydrophobic residues at the channel's exit appear to have an important role in controlling the entry of acetaldehyde into the DmpF active site.
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Affiliation(s)
- Natalie E Smith
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, Western Australia
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17
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Lo HF, Su JY, Chen HL, Chen JC, Lin LL. Biophysical studies of an NAD(P)(+)-dependent aldehyde dehydrogenase from Bacillus licheniformis. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2011; 40:1131-1142. [PMID: 21874381 DOI: 10.1007/s00249-011-0744-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 08/09/2011] [Indexed: 05/31/2023]
Abstract
Aldehyde dehydrogenase (ALDH) catalyzes the conversion of aldehydes to the corresponding acids by means of an NAD(P)(+)-dependent virtually irreversible reaction. In this investigation, the biophysical properties of a recombinant Bacillus licheniformis ALDH (BlALDH) were characterized in detail by analytical ultracentrifuge (AUC) and various spectroscopic techniques. The oligomeric state of BlALDH in solution was determined to be tetrameric by AUC. Far-UV circular dichroism analysis revealed that the secondary structures of BlALDH were not altered in the presence of acetone and ethanol, whereas SDS had a detrimental effect on the folding of the enzyme. Thermal unfolding of this enzyme was found to be highly irreversible. The native enzyme started to unfold beyond ~0.2 M guanidine hydrochloride (GdnHCl) and reached an unfolded intermediate, [GdnHCl](05, N-U), at 0.93 M. BlALDH was active at concentrations of urea below 2 M, but it experienced an irreversible unfolding under 8 M denaturant. Taken together, this study provides a foundation for the future structural investigation of BlALDH, a typical member of ALDH superfamily enzymes.
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Affiliation(s)
- Huei-Fen Lo
- Department of Food Science and Technology, Hungkuang University, Shalu, Taichung City, Taiwan
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18
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Bains J, Leon R, Temke KG, Boulanger MJ. Elucidating the reaction mechanism of the benzoate oxidation pathway encoded aldehyde dehydrogenase from Burkholderia xenovorans LB400. Protein Sci 2011; 20:1048-59. [PMID: 21495107 DOI: 10.1002/pro.639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 04/04/2011] [Accepted: 04/07/2011] [Indexed: 11/09/2022]
Abstract
Oxidation of cis-3,4-dehydroadipyl-CoA semialdehyde to cis-3,4-dehydroadipyl-CoA by the aldehyde dehydrogenase, ALDH(C) (EC.1.2.1.77), is an essential step in the metabolism of benzoate in Burkholderia xenovorans LB400. In a previous study, we established a structural blueprint for this novel group of ALDH enzymes. Here, we build significantly on this initial work and propose a detailed reaction mechanism for ALDH(C) based on comprehensive structural and functional investigations of active site residues. Kinetic analyses reveal essential roles for C296 as the nucleophile and E257 as the associated general base. Structural analyses of E257Q and C296A variants suggest a dynamic charge repulsion relationship between E257 and C296 that contributes to the inherent flexibility of E257 in the native enzyme, which is further regulated by E496 and E167. A proton relay network anchored by E496 and supported by E167 and K168 serves to reset E257 for the second catalytic step. We also propose that E167, which is unique to ALDH(C) and its homologs, serves a critical role in presenting the catalytic water to the newly reset E257 such that the enzyme can proceed with deacylation and product release. Collectively, the reaction mechanism proposed for ALDH(C) promotes a greater understanding of these novel ALDH enzymes, the ALDH super-family in general, and benzoate degradation in B. xenovorans LB400.
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Affiliation(s)
- Jasleen Bains
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W3P6, Canada
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19
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Estey T, Chen Y, Carpenter JF, Vasiliou V. Structural and functional modifications of corneal crystallin ALDH3A1 by UVB light. PLoS One 2010; 5:e15218. [PMID: 21203538 PMCID: PMC3006428 DOI: 10.1371/journal.pone.0015218] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 10/29/2010] [Indexed: 11/18/2022] Open
Abstract
As one of the most abundantly expressed proteins in the mammalian corneal epithelium, aldehyde dehydrogenase 3A1 (ALDH3A1) plays critical and multifaceted roles in protecting the cornea from oxidative stress. Recent studies have demonstrated that one protective mechanism of ALDH3A1 is the direct absorption of UV-energy, which reduces damage to other corneal proteins such as glucose-6-phosphate dehydrogenase through a competition mechanism. UV-exposure, however, leads to the inactivation of ALDH3A1 in such cases. In the current study, we demonstrate that UV-light caused soluble, non-native aggregation of ALDH3A1 due to both covalent and non-covalent interactions, and that the formation of the aggregates was responsible for the loss of ALDH3A1 enzymatic activity. Spectroscopic studies revealed that as a result of aggregation, the secondary and tertiary structure of ALDH3A1 were perturbed. LysC peptide mapping using MALDI-TOF mass spectrometry shows that UV-induced damage to ALDH3A1 also includes chemical modifications to Trp, Met, and Cys residues. Surprisingly, the conserved active site Cys of ALDH3A1 does not appear to be affected by UV-exposure; this residue remained intact after exposure to UV-light that rendered the enzyme completely inactive. Collectively, our data suggest that the UV-induced inactivation of ALDH3A1 is a result of non-native aggregation and associated structural changes rather than specific damage to the active site Cys.
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Affiliation(s)
- Tia Estey
- Center for Pharmaceutical Biotechnology, Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Ying Chen
- Molecular Toxicology & Environmental Health Sciences Program, Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colorado, United States of America
| | - John F. Carpenter
- Center for Pharmaceutical Biotechnology, Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Vasilis Vasiliou
- Center for Pharmaceutical Biotechnology, Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colorado, United States of America
- Molecular Toxicology & Environmental Health Sciences Program, Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colorado, United States of America
- * E-mail:
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20
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Kollock R, Rost K, Batke M, Glatt H. Effect of pentachlorophenol and 2,6-dichloro-4-nitrophenol on the activity of cDNA-expressed human alcohol and aldehyde dehydrogenases. Toxicol Lett 2009; 191:360-4. [DOI: 10.1016/j.toxlet.2009.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 09/16/2009] [Accepted: 10/06/2009] [Indexed: 10/20/2022]
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21
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Muñoz-Clares RA, Díaz-Sánchez AG, González-Segura L, Montiel C. Kinetic and structural features of betaine aldehyde dehydrogenases: mechanistic and regulatory implications. Arch Biochem Biophys 2009; 493:71-81. [PMID: 19766587 DOI: 10.1016/j.abb.2009.09.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2009] [Revised: 09/05/2009] [Accepted: 09/14/2009] [Indexed: 11/19/2022]
Abstract
The betaine aldehyde dehydrogenases (BADH; EC 1.2.1.8) are so-called because they catalyze the irreversible NAD(P)(+)-dependent oxidation of betaine aldehyde to glycine betaine, which may function as (i) a very efficient osmoprotectant accumulated by both prokaryotic and eukaryotic organisms to cope with osmotic stress, (ii) a metabolic intermediate in the catabolism of choline in some bacteria such as the pathogen Pseudomonas aeruginosa, or (iii) a methyl donor for methionine synthesis. BADH enzymes can also use as substrates aminoaldehydes and other quaternary ammonium and tertiary sulfonium compounds, thereby participating in polyamine catabolism and in the synthesis of gamma-aminobutyrate, carnitine, and 3-dimethylsulfoniopropionate. This review deals with what is known about the kinetics and structural properties of these enzymes, stressing those properties that have only been found in them and not in other aldehyde dehydrogenases, and discussing their mechanistic and regulatory implications.
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Affiliation(s)
- Rosario A Muñoz-Clares
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, México DF 04510, México.
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22
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The crystal structure of a ternary complex of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa Provides new insight into the reaction mechanism and shows a novel binding mode of the 2'-phosphate of NADP+ and a novel cation binding site. J Mol Biol 2008; 385:542-57. [PMID: 19013472 DOI: 10.1016/j.jmb.2008.10.082] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Revised: 10/10/2008] [Accepted: 10/22/2008] [Indexed: 11/23/2022]
Abstract
In the human pathogen Pseudomonas aeruginosa, the NAD(P)(+)-dependent betaine aldehyde dehydrogenase (PaBADH) may play the dual role of assimilating carbon and nitrogen from choline or choline precursors--abundant at infection sites--and producing glycine betaine and NADPH, potentially protective against the high-osmolarity and oxidative stresses prevalent in the infected tissues. Disruption of the PaBADH gene negatively affects the growth of bacteria, suggesting that this enzyme could be a target for antibiotic design. PaBADH is one of the few ALDHs that efficiently use NADP(+) and one of the even fewer that require K(+) ions for stability. Crystals of PaBADH were obtained under aerobic conditions in the presence of 2-mercaptoethanol, glycerol, NADP(+) and K(+) ions. The three-dimensional structure was determined at 2.1-A resolution. The catalytic cysteine (C286, corresponding to C302 of ALDH2) is oxidized to sulfenic acid or forms a mixed disulfide with 2-mercaptoethanol. The glutamyl residue involved in the deacylation step (E252, corresponding to E268 of ALDH2) is in two conformations, suggesting a proton relay system formed by two well-conserved residues (E464 and K162, corresponding to E476 and K178, respectively, of ALDH2) that connects E252 with the bulk water. In some active sites, a bound glycerol molecule mimics the thiohemiacetal intermediate; its hydroxyl oxygen is hydrogen bonded to the nitrogen of the amide groups of the side chain of the conserved N153 (N169 of ALDH2) and those of the main chain of C286, which form the "oxyanion hole." The nicotinamide moiety of the nucleotide is not observed in the crystal, and the adenine moiety binds in the usual way. A salt bridge between E179 (E195 of ALDH2) and R40 (E53 of ALDH2) moves the carboxylate group of the former away from the 2'-phosphate of the NADP(+), thus avoiding steric clashes and/or electrostatic repulsion between the two groups. Finally, the crystal shows two K(+) binding sites per subunit. One is in an intrasubunit cavity that we found to be present in all known ALDH structures. The other--not described before for any ALDH but most likely present in most of them--is located in between the dimeric unit, helping structure a region involved in coenzyme binding and catalysis. This may explain the effects of K(+) ions on the activity and stability of PaBADH.
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Wymore T, Deerfield DW, Hempel J. Mechanistic implications of the cysteine-nicotinamide adduct in aldehyde dehydrogenase based on quantum mechanical/molecular mechanical simulations. Biochemistry 2007; 46:9495-506. [PMID: 17655326 PMCID: PMC2529467 DOI: 10.1021/bi700555g] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent computer simulations of the cysteine nucleophilic attack on propanal in human mitochondrial aldehyde dehydrogenase (ALDH2) yielded an unexpected result: the chemically reasonable formation of a dead-end cysteine-cofactor adduct when NAD+ was in the "hydride transfer" position. More recently, this adduct found independent crystallographic support in work on formyltetrahydrofolate dehydrogenase, work which further found evidence of the same adduct on re-examination of deposited electron densities of ALDH2. Although the experimental data showed that this adduct was reversible, several mechanistic questions arise from the fact that it forms at all. Here, we present results from further quantum mechanical/molecular mechanical (QM/MM) simulations toward understanding the mechanistic implications of adduct formation. These simulations revealed formation of the oxyanion thiohemiacetal intermediate only when the nicotinamide ring of NAD+ is oriented away from the active site, contrary to prior arguments. In contrast, and in seeming paradox, when NAD is oriented to receive the hydride, disassociation of the oxyanion intermediate to form the dead-end adduct is more thermodynamically favored than maintaining the oxyanion intermediate necessary for catalysis to proceed. However, this disassociation to the adduct could be avoided through proton transfer from the enzyme to the intermediate. Our results continue to indicate that the unlikely source of this proton is the Cys302 main chain amide.
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Affiliation(s)
- Troy Wymore
- National Resource for Biomedical Supercomputing, Pittsburgh, Pennsylvania 15213, USA.
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Wymore T, Hempel J, Cho SS, Mackerell AD, Nicholas HB, Deerfield DW. Molecular recognition of aldehydes by aldehyde dehydrogenase and mechanism of nucleophile activation. Proteins 2006; 57:758-71. [PMID: 15390260 DOI: 10.1002/prot.20256] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Experimental structural data on the state of substrates bound to class 3 Aldehyde Dehydrogenases (ALDH3A1) is currently unknown. We have utilized molecular mechanics (MM) simulations, in conjunction with new force field parameters for aldehydes, to study the atomic details of benzaldehyde binding to ALDH3A1. Our results indicate that while the nucleophilic Cys243 must be in the neutral state to form what are commonly called near-attack conformers (NACs), these structures do not correlate with increased complexation energy calculated with the MM-Generalized Born Molecular Volume (GBMV) method. The negatively charged Cys243 (thiolate form) of ALDH3A1 also binds benzaldehyde in a stable conformation but in this complex the sulfur of Cys243 is oriented away from benzaldehyde yet yields the most favorable MM-GBMV complexation energy. The identity of the general base, Glu209 or Glu333, in ALDHs remains uncertain. The MM simulations reveal structural and possible functional roles for both Glu209 and Glu333. Structures from the MM simulations that would support either glutamate residue as the general base were further examined with Hybrid Quantum Mechanical (QM)/MM simulations. These simulations show that, with the PM3/OPLS potential, Glu209 must go through a step-wise mechanism to activate Cys243 through an intervening water molecule while Glu333 can go through a more favorable concerted mechanism for the same activation process.
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Affiliation(s)
- Troy Wymore
- Pittsburgh Supercomputing Center, Biomedical Initiative Group, Pittsburgh, Pennsylvania 15213, USA.
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25
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Gescher J, Ismail W, Olgeschläger E, Eisenreich W, Wörth J, Fuchs G. Aerobic benzoyl-coenzyme A (CoA) catabolic pathway in Azoarcus evansii: conversion of ring cleavage product by 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase. J Bacteriol 2006; 188:2919-27. [PMID: 16585753 PMCID: PMC1446997 DOI: 10.1128/jb.188.8.2919-2927.2006] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Accepted: 01/27/2006] [Indexed: 11/20/2022] Open
Abstract
Benzoate, a strategic intermediate in aerobic aromatic metabolism, is metabolized in various bacteria via an unorthodox pathway. The intermediates of this pathway are coenzyme A (CoA) thioesters throughout, and ring cleavage is nonoxygenolytic. The fate of the ring cleavage product 3,4-dehydroadipyl-CoA semialdehyde was studied in the beta-proteobacterium Azoarcus evansii. Cell extracts contained a benzoate-induced, NADP(+)-specific aldehyde dehydrogenase, which oxidized this intermediate. A postulated putative long-chain aldehyde dehydrogenase gene, which might encode this new enzyme, is located on a cluster of genes encoding enzymes and a transport system required for aerobic benzoate oxidation. The gene was expressed in Escherichia coli, and the maltose-binding protein-tagged enzyme was purified and studied. It is a homodimer composed of 54 kDa (without tag) subunits and was confirmed to be the desired 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase. The reaction product was identified by nuclear magnetic resonance spectroscopy as the corresponding acid 3,4-dehydroadipyl-CoA. Hence, the intermediates of aerobic benzoyl-CoA catabolic pathway recognized so far are benzoyl-CoA; 2,3-dihydro-2,3-dihydroxybenzoyl-CoA; 3,4-dehydroadipyl-CoA semialdehyde plus formate; and 3,4-dehydroadipyl-CoA. The further metabolism is thought to lead to 3-oxoadipyl-CoA, the intermediate at which the conventional and the unorthodox pathways merge.
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Affiliation(s)
- Johannes Gescher
- Mikrobiologie, Institut für Biologie II, Universität Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
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26
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Gruez A, Roig-Zamboni V, Grisel S, Salomoni A, Valencia C, Campanacci V, Tegoni M, Cambillau C. Crystal structure and kinetics identify Escherichia coli YdcW gene product as a medium-chain aldehyde dehydrogenase. J Mol Biol 2004; 343:29-41. [PMID: 15381418 DOI: 10.1016/j.jmb.2004.08.030] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2004] [Revised: 07/30/2004] [Accepted: 08/10/2004] [Indexed: 11/17/2022]
Abstract
In the context of a medium-scaled structural genomics program aiming at solving the structures of as many as possible bacterial unknown open reading frame products from Escherichia coli (Y prefix), we have solved the structure of YdcW at 2.1A resolution, using molecular replacement. According to its sequence identity, YdcW has been classified into the betaine aldehyde dehydrogenases family (EC 1.2.1.8), catalysing the oxidation of betaine aldehyde into glycine betaine. The structure of YdcW resembles that of other aldehyde dehydrogenases: it is tetrameric and binds a NADH molecule in each monomer. The NADH molecules, bound in the active site by soaking, are revealed to be in the "hydrolysis position". Activities experiments demonstrate that YdcW is more active on medium-chains aldehyde than on betaine aldehyde. However, soaking of betaine into YdcW crystals revealed its presence in one of the subunits, in two positions, a putative resting position and a hydride transfer ready position. Analysis of kinetics data and of the active site shape suggest an optimum binding of n-alkyl aldehydes up to seven to eight carbon atoms, possibly followed by a bulky cyclic or aromatic group.
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Affiliation(s)
- Arnaud Gruez
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, 31 chemin J. Aiguier, F-13402 Marseille Cedex 20, France
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Manjasetty BA, Powlowski J, Vrielink A. Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate. Proc Natl Acad Sci U S A 2003; 100:6992-7. [PMID: 12764229 PMCID: PMC165818 DOI: 10.1073/pnas.1236794100] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The crystal structure of the bifunctional enzyme 4-hydroxy-2-ketovalerate aldolase (DmpG)/acylating acetaldehyde dehydrogenase (DmpF), which is involved in the bacterial degradation of toxic aromatic compounds, has been determined by multiwavelength anomalous dispersion (MAD) techniques and refined to 1.7-A resolution. Structures of the two polypeptides represent a previously unrecognized subclass of metal-dependent aldolases, and of a CoA-dependent dehydrogenase. The structure reveals a mixed state of NAD+ binding to the DmpF protomer. Domain movements associated with cofactor binding in the DmpF protomer may be correlated with channeling and activity at the DmpG protomer. In the presence of NAD+ a 29-A-long sequestered tunnel links the two active sites. Two barriers are visible along the tunnel and suggest control points for the movement of the reactive and volatile acetaldehyde intermediate between the two active sites.
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Affiliation(s)
- Babu A Manjasetty
- Department of Molecular, Cellular and Developmental Biology Sinsheimer Laboratory, 1156 High Street, University of California, Santa Cruz, CA 95064, USA
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28
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Hempel J, Perozich J, Wymore T, Nicholas HB. An algorithm for identification and ranking of family-specific residues, applied to the ALDH3 family. Chem Biol Interact 2003; 143-144:23-8. [PMID: 12604185 DOI: 10.1016/s0009-2797(02)00165-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An algorithm for detecting amino acid residues characteristic of individual protein families from within aligned collections of paralogous sequences, and its application to the ALDH3 family versus the rest of the ALDH extended family is described. Residues illuminated by this analysis include a key intramolecular tether, a lysine that makes an intersubunit contact at the dimer interface, three residues in close association with the substrate-binding funnel, and a pair of residues suggested to participate in proton relay during the catalytic cycle.
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Affiliation(s)
- John Hempel
- Department of Biological Sciences, University of Pittsburgh, Clapp Hall 301, Pittsburgh, PA 15260, USA.
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29
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Adam GC, Sorensen EJ, Cravatt BF. Proteomic profiling of mechanistically distinct enzyme classes using a common chemotype. Nat Biotechnol 2002; 20:805-9. [PMID: 12091914 DOI: 10.1038/nbt714] [Citation(s) in RCA: 171] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Proteomics research requires methods to characterize the expression and function of proteins in complex mixtures. Toward this end, chemical probes that incorporate known affinity labeling agents have facilitated the activity-based profiling of certain enzyme families. To accelerate the discovery of proteomics probes for enzyme classes lacking cognate affinity labels, we describe here a combinatorial strategy. Members of a probe library bearing a sulfonate ester chemotype were screened against complex proteomes for activity-dependent protein reactivity, resulting in the labeling of at least six mechanistically distinct enzyme classes. Surprisingly, none of these enzymes represented targets of previously described proteomics probes. The sulfonate library was used to identify an omega-class glutathione S-transferase whose activity was upregulated in invasive human breast cancer lines. These results indicate that activity-based probes compatible with whole-proteome analysis can be developed for numerous enzyme classes and applied to identify enzymes associated with discrete pathological states.
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Affiliation(s)
- Gregory C Adam
- The Skaggs Institute for Chemical Biology and Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
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30
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Izaguirre G, Pietruszko R, Cho S, MacKerell A. Human aldehyde dehydrogenase catalytic activity and structural interactions with coenzyme analogs. J Biomol Struct Dyn 2001; 19:429-47. [PMID: 11790142 DOI: 10.1080/07391102.2001.10506752] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
K(m) and V(max) values for 10 coenzyme analogs never previously studied with any aldehyde dehydrogenase and NADP(+) were compared with those for NAD(+) for three human aldehyde dehydrogenases (EC 1.2.1.3); the cytoplasmic E1 (the product of the aldh1 gene), the mitochondrial E2 (the product of the aldh2 gene) and the cytoplasmic E3 (the product of the aldh9 gene) isozymes. Structural information on changes in coenzyme-protein interactions were obtained via molecular dynamics (MD) studies with the E2 isozyme and quantum mechanical (QM) calculations were used to study changes in charge distribution of the pyridine ring and relative free energies of solvation of the purine ring in the analogs. E1 showed the broadest substrate specificity and was the only isozyme subject to substrate inhibition, both of which are suggested to be due to the two coenzyme conformations observed previously in the sheep crystal structure. NADP(+) selectivity is indicated to be influenced by Glu195 in E1 and E2. Substitutions in the purine ring affected K(m) but not V(max), with the changes in K(m) being dominated by the hydrophobicity of the purine ring as indicted by the QM calculations. Substitutions in the pyridine ring sometimes rendered the coenzymes inactive, with no consistent pattern observed for the three coenzymes. Structural analysis of the coenzyme analog-E2 MD simulations revealed different structural perturbations of the surrounding active site, though interactions with Asn169 and Glu399 were preserved in all cases.
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Affiliation(s)
- G Izaguirre
- Center for Alcohol Studies and Department of Molecular Biology and Biochemistry, Rutgers The State University of New Jersey, Piscataway, NJ 08854- 8001, USA
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31
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Hempel J, Kuo I, Perozich J, Wang BC, Lindahl R, Nicholas H. Aldehyde dehydrogenase. Maintaining critical active site geometry at motif 8 in the class 3 enzyme. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:722-6. [PMID: 11168411 DOI: 10.1046/j.1432-1327.2001.01926.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Alignment of all known, diverse members of the aldehyde dehydrogenase (ALDH) extended family revealed only two strictly conserved, nonglycine residues, a glutamate and a phenylalanine residue. Both occur in one of the highly conserved 'motif' segments and both occupy strategic locations in the tertiary structure at the bottom of the catalytic funnel. In class 3 ALDH, these are Glu333 and Phe335. In addition, Asp247, which is not highly conserved but is characteristic of class 3 ALDHs, hydrogen bonds the main chain between Glu333 and Phe335. These three residues were mutated conservatively. Michaelis constants determined for both NAD/propanal and NADP/benzaldehyde substrate pairs show all three residues to be crucial to effective catalysis, and suggest that the hydrogen bond to Asp247 is a key element in maintaining precise geometry of key elements at the active site.
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Affiliation(s)
- J Hempel
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh 15620, USA.
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32
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Hempel J, Lindahl R, Perozich J, Wang B, Kuo I, Nicholas H. Beyond the catalytic core of ALDH: a web of important residues begins to emerge. Chem Biol Interact 2001; 130-132:39-46. [PMID: 11306029 DOI: 10.1016/s0009-2797(00)00220-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Site-directed mutagenesis was performed in class 3 aldehyde dehydrogenase (ALDH) on both strictly conserved, non-glycine residues, Glu-333 and Phe-335. Both lie in Motif 8 and are indicated to be of central catalytic importance from their positions in the tertiary structure. In addition, a highly conserved residue at the end of Motif 8, Pro-337, and Asp-247, which interacts with the main chain of Motif 8, were also mutated. All substitutions were conservative. Kinetic values clearly show that Glu-333 and Phe-335 are crucial to efficient catalysis, along with Asp-247. Pro-337 appears to have a different role, most likely relating to folding.
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Affiliation(s)
- J Hempel
- Department of Biological Sciences, University of Pittsburgh, 301 Clapp Hall, 15260, Pittsburgh, PA, USA.
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33
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Abstract
Influences on coenzyme preference are explored. Lysine 137 (192 in class 1/2 ALDH) lies close to the adenine ribose, directly interacting with the adenine ribose in NAD-specific ALDHs and the 2'-phosphate of NADP in NADP-specific ALDHs. Lys-137 in class 3 ALDH interacts with the adenine ribose indirectly through an intervening water molecule. However, this residue is present in all ALDHs and, as a result, is unlikely to directly influence coenzyme specificity. Glutamate 140 (195) coordinates the 2'- and 3'-hydroxyls of the adenine ribose of NAD in the class 3 tertiary structure. Thus, it appeared that this residue would influence coenzyme specificity. Mutation to aspartate, asparagine, glutamine or threonine shifts the coenzyme specificity towards NADP, but did not completely change the specificity. Still, the mutants show the 2'-phosphate of NADP is repelled by Glu-140 (195). Although Glu-140 (195) has a major influence on coenzyme specificity, it is not the only influence since class 3 ALDHs, can use both coenzymes, and class 2 ALDHs, which are NAD-specific, have a glutamate at this position. One explanation may be that the larger space between Lys-137 (192) and the adenine ribose hydroxyls in the class 3 ALDH:NAD binary structure may provide space to accommodate the 2'-phosphate of NADP. Also, a structural shift upon binding NADP may also occur in class 3 ALDHs to help accommodate the 2'-phosphate of NADP.
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Affiliation(s)
- J Perozich
- Department of Biological Sciences, University of Pittsburgh, 15260, Pittsburgh, PA, USA.
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34
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Zhang L, Ahvazi B, Szittner R, Vrielink A, Meighen E. Differences in nucleotide specificity and catalytic mechanism between Vibrio harveyi aldehyde dehydrogenase and other members of the aldehyde dehydrogenase superfamily. Chem Biol Interact 2001; 130-132:29-38. [PMID: 11306028 DOI: 10.1016/s0009-2797(00)00219-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The fatty aldehyde dehydrogenase (Vh-ALDH) isolated from the luminescent bacterium, Vibrio harveyi, differs from other aldehyde dehydrogenases in its high affinity for NADP(+). The binding of NADP(+) appears to arise from the interaction of the 2'-phosphate of the adenosine moiety of NADP(+) with a threonine (T175) in the nucleotide recognition site just after the beta(B) strand as well as with an arginine (R210) that pi stacks over the adenosine moiety. The active site of Vh-ALDH contains the usual suspects of a cysteine (C289), two glutamates (E253 and E377) and an asparagine (N147) involved in the aldehyde dehydrogenase mechanism. However, Vh-ALDH has one polar residue in the active site that distinguishes it from other ALDHs; a histidine (H450) is in close contact with the cysteine nucleophile. As a glutamate has been implicated in promoting the nucleophilicity of the active site cysteine residue in ALDHs, the close contact of a histidine with the cysteine nucleophile in Vh-ALDH raises the possibility of alternate routes to increase the reactivity of the cysteine nucleophile. The effects of mutation of these residues on the different functions catalyzed by Vh-ALDH including acylation, (thio)esterase, reductase and dehydrogenase activities should help define the specific roles of the residues in the active site of ALDHs.
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Affiliation(s)
- L Zhang
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Quebec, H3G1Y6, Montreal, Canada
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35
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Adam GC, Cravatt BF, Sorensen EJ. Profiling the specific reactivity of the proteome with non-directed activity-based probes. CHEMISTRY & BIOLOGY 2001; 8:81-95. [PMID: 11182321 DOI: 10.1016/s1074-5521(00)90060-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
BACKGROUND The field of proteomics aims to characterize dynamics in protein function on a global level. However, several classes of proteins, in particular low abundance proteins, remain difficult to characterize using standard proteomics technologies. Recently, chemical strategies have emerged that profile classes of proteins based on activity rather than quantity, thereby greatly facilitating the analysis of low abundance constituents of the proteome. RESULTS In order to expand the classes of proteins susceptible to analysis by activity-based methods, we have synthesized a library of biotinylated sulfonate esters and applied its members to complex proteomes under conditions that distinguish patterns of specific protein reactivity. Individual sulfonates exhibited unique profiles of proteome reactivity that in extreme cases appeared nearly orthogonal to one another. A robustly labeled protein was identified as a class I aldehyde dehydrogenase and shown to be irreversibly inhibited by members of the sulfonate library. CONCLUSIONS Through screening the proteome with a non-directed library of chemical probes, diverse patterns of protein reactivity were uncovered. These probes labeled protein targets based on properties other than abundance, circumventing one of the major challenges facing contemporary proteomics research. Considering further that the probes were found to inhibit a target enzyme's catalytic activity, the methods described herein should facilitate the identification of compounds possessing both selective proteome reactivities and novel bioactivities.
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Affiliation(s)
- G C Adam
- The Skaggs Institute for Chemical Biology, La Jolla, CA 92037, USA
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36
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Giorgianni F, Bridson PK, Sorrentino BP, Pohl J, Blakley RL. Inactivation of aldophosphamide by human aldehyde dehydrogenase isozyme 3. Biochem Pharmacol 2000; 60:325-38. [PMID: 10856427 DOI: 10.1016/s0006-2952(00)00344-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tumors resistant to chemotherapeutic oxazaphosphorines such as cyclophosphamide often overexpress aldehyde dehydrogenase (ALDH), some isozymes of which catalyze the oxidization of aldophosphamide, an intermediate of cyclophosphamide activation, with formation of inert carboxyphosphamide. Since resistance to oxazaphosphorines can be produced in mammalian cells by transfecting them with the gene for human ALDH isozyme 3 (hALDH3), it seems possible that patients receiving therapy for solid tumors with cyclophosphamide might be protected from myelosuppression by their prior transplantation with autologous bone marrow that has been transduced with a retroviral vector causing overexpression of hALDH3. We investigated whether retroviral introduction of hALDH3 into a human leukemia cell line confers resistance to oxazaphosphorines. This was examined in the polyclonal transduced population, that is, without selecting out high expression clones. hALDH3 activity was 0.016 IU/mg protein in the transduced cells (compared with 2x10(-5) IU/mg in untransduced cells), but there was no detectable resistance to aldophosphamide-generating compounds (mafosfamide or 4-hydroperoxycyclophosphamide). The lack of protection was due, in part, to low catalytic activity of hALDH3 towards aldophosphamide, since, with NAD as cofactor, the catalytic efficiency of homogeneous, recombinant hALDH3 for aldophosphamide oxidation was shown to be about seven times lower than that of recombinant hALDH1. The two polymorphic forms of hALDH3 had identical kinetics with either benzaldehyde or aldophosphamide as substrate. Results of initial velocity measurements were consistent with an ordered sequential mechanism for ALDH1 but not for hALDH3; a kinetic mechanism for the latter is proposed, and the corresponding rate equation is presented.
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Affiliation(s)
- F Giorgianni
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, 38105, Memphis, TN, USA
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37
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Oppermann UC, Maser E. Molecular and structural aspects of xenobiotic carbonyl metabolizing enzymes. Role of reductases and dehydrogenases in xenobiotic phase I reactions. Toxicology 2000; 144:71-81. [PMID: 10781873 DOI: 10.1016/s0300-483x(99)00192-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The major metabolic pathways involved in synthesis and disposition of carbonyl and hydroxyl group containing compounds are presented, and structural and functional characteristics of the enzyme families involved are discussed. Alcohol and aldehyde dehydrogenases (ADH, ALDH) participate in oxidative pathways, whereas reductive routes are accomplished by members of the aldo-keto reductase (AKR), short-chain dehydrogenases/reductases (SDR) and quinone reductase (QR) superfamilies. A wealth of biochemical, genetic and structural data now establishes these families to constitute important phase I enzymes.
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Affiliation(s)
- U C Oppermann
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77, Stockholm, Sweden.
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38
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Mann CJ, Weiner H. Differences in the roles of conserved glutamic acid residues in the active site of human class 3 and class 2 aldehyde dehydrogenases. Protein Sci 1999; 8:1922-9. [PMID: 10548037 PMCID: PMC2144141 DOI: 10.1110/ps.8.10.1922] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Although the three-dimensional structure of the dimeric class 3 rat aldehyde dehydrogenase has recently been published (Liu ZJ et al., 1997, Nature Struct Biol 4:317-326), few mechanistic studies have been conducted on this isoenzyme. We have characterized the enzymatic properties of recombinant class 3 human stomach aldehyde dehydrogenase, which is very similar in amino acid sequence to the class 3 rat aldehyde dehydrogenase. We have determined that the rate-limiting step for the human class 3 isozyme is hydride transfer rather than deacylation as observed for the human liver class 2 mitochondrial enzyme. No enhancement of NADH fluorescence was observed upon binding to the class 3 enzyme, while fluorescence enhancement of NADH has been previously observed upon binding to the class 2 isoenzyme. It was also observed that binding of the NAD cofactor inhibited the esterase activity of the class 3 enzyme while activating the esterase activity of the class 2 enzyme. Site-directed mutagenesis of two conserved glutamic acid residues (209 and 333) to glutamine residues indicated that, unlike in the class 2 enzyme, Glu333 served as the general base in the catalytic reaction and E209Q had only marginal effects on enzyme activity, thus confirming the proposed mechanism (Hempel J et al., 1999, Adv Exp Med Biol 436:53-59). Together, these data suggest that even though the subunit structures and active site residues of the isozymes are similar, the enzymes have very distinct properties besides their oligomeric state (dimer vs. tetramer) and substrate specificity.
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Affiliation(s)
- C J Mann
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907-1153, USA
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39
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Perozich J, Nicholas H, Lindahl R, Hempel J. The big book of aldehyde dehydrogenase sequences. An overview of the extended family. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1999; 463:1-7. [PMID: 10352663 DOI: 10.1007/978-1-4615-4735-8_1] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- J Perozich
- Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pennsylvania 15261, USA
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40
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Hurley TD, Steinmetz CG, Weiner H. Three-dimensional structure of mitochondrial aldehyde dehydrogenase. Mechanistic implications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1999; 463:15-25. [PMID: 10352665 DOI: 10.1007/978-1-4615-4735-8_3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- T D Hurley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis 46202, USA
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41
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Hurley TD, Weiner H. Evaluation of the roles of the conserved residues of aldehyde dehydrogenase. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1999; 463:45-52. [PMID: 10352668 DOI: 10.1007/978-1-4615-4735-8_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Affiliation(s)
- T D Hurley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis 46202, USA
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42
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Perozich J, Nicholas H, Wang BC, Lindahl R, Hempel J. Relationships within the aldehyde dehydrogenase extended family. Protein Sci 1999; 8:137-46. [PMID: 10210192 PMCID: PMC2144113 DOI: 10.1110/ps.8.1.137] [Citation(s) in RCA: 231] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
One hundred-forty-five full-length aldehyde dehydrogenase-related sequences were aligned to determine relationships within the aldehyde dehydrogenase (ALDH) extended family. The alignment reveals only four invariant residues: two glycines, a phenylalanine involved in NAD binding, and a glutamic acid that coordinates the nicotinamide ribose in certain E-NAD binary complex crystal structures, but which may also serve as a general base for the catalytic reaction. The cysteine that provides the catalytic thiol and its closest neighbor in space, an asparagine residue, are conserved in all ALDHs with demonstrated dehydrogenase activity. Sixteen residues are conserved in at least 95% of the sequences; 12 of these cluster into seven sequence motifs conserved in almost all ALDHs. These motifs cluster around the active site of the enzyme. Phylogenetic analysis of these ALDHs indicates at least 13 ALDH families, most of which have previously been identified but not grouped separately by alignment. ALDHs cluster into two main trunks of the phylogenetic tree. The largest, the "Class 3" trunk, contains mostly substrate-specific ALDH families, as well as the class 3 ALDH family itself. The other trunk, the "Class 1/2" trunk, contains mostly variable substrate ALDH families, including the class 1 and 2 ALDH families. Divergence of the substrate-specific ALDHs occurred earlier than the division between ALDHs with broad substrate specificities. A site on the World Wide Web has also been devoted to this alignment project.
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Affiliation(s)
- J Perozich
- Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pennsylvania 15261, USA
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