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Östberg LJ, Höög JO, Persson B. Computational analysis of human medium-chain dehydrogenases/reductases revealing substrate- and coenzyme-binding characteristics. Chem Biol Interact 2024; 390:110876. [PMID: 38266864 DOI: 10.1016/j.cbi.2024.110876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/29/2023] [Accepted: 01/15/2024] [Indexed: 01/26/2024]
Abstract
The medium-chain dehydrogenase/reductase (MDR) superfamily has more than 600,000 members in UniProt as of March 2023. As the family has been growing, the proportion of functionally characterized proteins has been falling behind. The aim of this project was to investigate the binding pockets of nine different MDR protein families based on sequence conservation patterns and three-dimensional structures of members within the respective families. A search and analysis methodology was developed. Using this, a total of 2000 eukaryotic MDR sequences belonging to nine different families were identified. The pairwise sequence identities within each of the families were 80-90 % for the mammalian sequences, like the levels observed for alcohol dehydrogenase, another MDR family. Twenty conserved residues were identified in the coenzyme part of the binding site by matching structural and conservation data of all nine protein families. The conserved residues in the substrate part of the binding pocket varied between the nine MDR families, implying divergent functions for the different families. Studying each family separately made it possible to identify multiple conserved residues that are expected to be important for substrate binding or catalysis of the enzymatic reaction. By combining structural data with the conservation of the amino acid residues in each protein, important residues in the binding pocket were identified for each of the nine MDRs. The obtained results add new positions of interest for the binding and activity of the enzyme family as well as fit well to earlier published data. Three distinct types of binding pockets were identified, containing no, one, or two tyrosine residues.
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Affiliation(s)
- Linus J Östberg
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
| | - Jan-Olov Höög
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
| | - Bengt Persson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-751 05 Uppsala, Sweden.
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2
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Vishwakarma C, Ansari A, Pratap JV. Distinct oligomerization and NADPH binding modes observed between L. donovani and human quinone oxidoreductases. Biochem Biophys Res Commun 2024; 690:149096. [PMID: 37988924 DOI: 10.1016/j.bbrc.2023.10.028] [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: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 11/23/2023]
Abstract
Electron-driven process helps the living organism in the generations of energy, biomass production and detoxification of synthetic compounds. Soluble quinone oxidoreductases (QORs) mediate the transfer of an electron from NADPH to various quinone and other compounds, helping in the detoxification of quinones. QORs play a crucial role in cellular metabolism and are thus potential targets for drug development. Here we report the crystal structure of the NADPH-dependent QOR from Leishmania donovani (LdQOR) at 2.05 Å. The enzyme exists as a homo-dimer, with each protomer consisting of two domains, responsible for binding NADPH cofactor and the substrate. Interestingly, the human QOR exists as a tetramer. Comparative analysis of the oligomeric interfaces of LdQOR with HsQOR shows no significant differences in the protomer/dimer assembly. The tetrameric interface of HsQOR is stabilized by salt bridges formed between Arg 169 and Glu 271 which is non-existent in LdQOR, with an Alanine replacing the glutamate. This distinct feature is conserved across other dimeric QORs, indicating the importance of this interaction for tetramer association. Among the homologs, the sequences of the loop region involved in the stabilization and binding of the adenine ring of the NADPH shows significant differences except for an Arginine & glycine residues. In dimer QORs, this Arginine acts as a gate to the co-factor, while the NADPH binding mode in the human homolog is distinct, stabilized by His 200 and Asn 229, which are not conserved in LdQOR. These distinct features have the potential to be utilized for therapeutic interventions.
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Affiliation(s)
- Chandan Vishwakarma
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Ahmadullah Ansari
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - J Venkatesh Pratap
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India.
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3
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Yang C, Huang Z, Zhang X, Zhu C. Structural Insights into the NAD(P)H:Quinone Oxidoreductase from Phytophthora capsici. ACS OMEGA 2022; 7:25705-25714. [PMID: 35910145 PMCID: PMC9330140 DOI: 10.1021/acsomega.2c02954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Soluble quinone oxidoreductases catalyze transfer of electrons from NADPH to quinones. Transfer of electrons is essential for detoxification of synthetic compounds. Here, we present the crystal structure of a NADPH-dependent QOR from Phytophthora capsici (Pc) complexed with NADPH at 2.4 Å resolution. The enzyme exhibits a bi-modular architecture, containing a NADPH-binding groove and a substrate-binding pocket in each subunit. In the crystal, each asymmetric unit of PcQOR contains two molecules stabilized by intermolecular interactions. Gel filtration and ultracentrifugation analyses reveal that it functions as a tetramer in solution. Alignment of homologous structures exhibits a conserved topology. However, the active sites vary among the homologues, indicating differences in substrate specificities. Enzymatic assays indicate that PcQOR tends to catalyze the large substrates, like 9,10-phenanthrenequinone. Computational simulation associated with site-directed mutagenesis and enzymatic activity analysis declares a potential quinone-binding channel. The ability to reduce quinones probably helps P. capsici to detoxify some harmful chemicals encountered during invasion.
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Affiliation(s)
- Cancan Yang
- Shandong
Provincial Key Laboratory for Biology of Vegetable Diseases and Insect
Pests, College of Plant Protection, Shandong
Agricultural University, Taian 271018, China
| | - Zhenling Huang
- Shandong
Provincial Key Laboratory for Biology of Vegetable Diseases and Insect
Pests, College of Plant Protection, Shandong
Agricultural University, Taian 271018, China
| | - Xiuguo Zhang
- Shandong
Provincial Key Laboratory for Biology of Vegetable Diseases and Insect
Pests, College of Plant Protection, Shandong
Agricultural University, Taian 271018, China
| | - Chunyuan Zhu
- College
of Life Sciences, Shandong Agricultural
University, Taian 271018, China
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4
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Senabouth A, Daniszewski M, Lidgerwood GE, Liang HH, Hernández D, Mirzaei M, Keenan SN, Zhang R, Han X, Neavin D, Rooney L, Lopez Sanchez MIG, Gulluyan L, Paulo JA, Clarke L, Kearns LS, Gnanasambandapillai V, Chan CL, Nguyen U, Steinmann AM, McCloy RA, Farbehi N, Gupta VK, Mackey DA, Bylsma G, Verma N, MacGregor S, Watt MJ, Guymer RH, Powell JE, Hewitt AW, Pébay A. Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration. Nat Commun 2022; 13:4233. [PMID: 35882847 PMCID: PMC9325891 DOI: 10.1038/s41467-022-31707-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 06/29/2022] [Indexed: 11/08/2022] Open
Abstract
There are currently no treatments for geographic atrophy, the advanced form of age-related macular degeneration. Hence, innovative studies are needed to model this condition and prevent or delay its progression. Induced pluripotent stem cells generated from patients with geographic atrophy and healthy individuals were differentiated to retinal pigment epithelium. Integrating transcriptional profiles of 127,659 retinal pigment epithelium cells generated from 43 individuals with geographic atrophy and 36 controls with genotype data, we identify 445 expression quantitative trait loci in cis that are asssociated with disease status and specific to retinal pigment epithelium subpopulations. Transcriptomics and proteomics approaches identify molecular pathways significantly upregulated in geographic atrophy, including in mitochondrial functions, metabolic pathways and extracellular cellular matrix reorganization. Five significant protein quantitative trait loci that regulate protein expression in the retinal pigment epithelium and in geographic atrophy are identified - two of which share variants with cis- expression quantitative trait loci, including proteins involved in mitochondrial biology and neurodegeneration. Investigation of mitochondrial metabolism confirms mitochondrial dysfunction as a core constitutive difference of the retinal pigment epithelium from patients with geographic atrophy. This study uncovers important differences in retinal pigment epithelium homeostasis associated with geographic atrophy.
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Affiliation(s)
- Anne Senabouth
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Maciej Daniszewski
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | - Grace E Lidgerwood
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | - Helena H Liang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | - Damián Hernández
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | - Mehdi Mirzaei
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Stacey N Keenan
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ran Zhang
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Xikun Han
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Drew Neavin
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Louise Rooney
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Lerna Gulluyan
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Linda Clarke
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | - Lisa S Kearns
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | | | - Chia-Ling Chan
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Uyen Nguyen
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Angela M Steinmann
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Rachael A McCloy
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Nona Farbehi
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Vivek K Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - David A Mackey
- Lions Eye Institute, Centre for Vision Sciences, University of Western Australia, Perth, WA, 6009, Australia
- School of Medicine, University of Tasmania, Hobart, TAS, 7005, Australia
| | - Guy Bylsma
- Lions Eye Institute, Centre for Vision Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Nitin Verma
- School of Medicine, University of Tasmania, Hobart, TAS, 7005, Australia
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Matthew J Watt
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Robyn H Guymer
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
- Department of Surgery, Ophthalmology, Royal Victorian Eye and Ear Hospital, The University of Melbourne, East Melbourne, VIC, 3002, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW, 2052, Australia.
| | - Alex W Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia.
- School of Medicine, University of Tasmania, Hobart, TAS, 7005, Australia.
- Department of Surgery, Ophthalmology, Royal Victorian Eye and Ear Hospital, The University of Melbourne, East Melbourne, VIC, 3002, Australia.
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, 7000, Australia.
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia.
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, 3010, Australia.
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5
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Abstract
Drug metabolizing enzymes catalyze the biotransformation of many of drugs and chemicals. The drug metabolizing enzymes are distributed among several evolutionary families and catalyze a range of detoxication reactions, including oxidation/reduction, conjugative, and hydrolytic reactions that serve to detoxify potentially toxic compounds. This detoxication function requires that drug metabolizing enzymes exhibit substrate promiscuity. In addition to their catalytic functions, many drug metabolizing enzymes possess functions unrelated to or in addition to catalysis. Such proteins are termed 'moonlighting proteins' and are defined as proteins with multiple biochemical or biophysical functions that reside in a single protein. This review discusses the diverse moonlighting functions of drug metabolizing enzymes and the roles they play in physiological functions relating to reproduction, vision, cell signaling, cancer, and transport. Further research will likely reveal new examples of moonlighting functions of drug metabolizing enzymes.
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Affiliation(s)
- Philip G Board
- John Curtin School of Medical Research, ANU College of Health and Medicine, The Australian National University, Canberra, ACT, Australia
| | - M W Anders
- Department of Pharmacology and Physiology, University of Rochester Medical Center, New York, NY, USA
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6
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Activation of farnesoid X receptor (FXR) induces crystallin zeta expression in mouse medullary collecting duct cells. Pflugers Arch 2020; 472:1631-1641. [PMID: 32914211 DOI: 10.1007/s00424-020-02456-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/24/2020] [Accepted: 08/28/2020] [Indexed: 02/05/2023]
Abstract
Crystallin zeta (CRYZ) is a phylogenetically restricted water-soluble protein and provides cytoprotection against oxidative stress via multiple mechanisms. Increasing evidence suggests that CRYZ is high abundantly expressed in the kidney where it acts as a transacting factor in increasing glutaminolysis and the Na+/K+/2Cl- cotransporter (BSC1/NKCC2) expression to help maintain acid-base balance and medullary hyperosmotic gradient. However, the mechanism by which CRYZ is regulated in the kidney remains largely uncharacterized. Here, we show that CRYZ is a direct target of farnesoid X receptor (FXR), a nuclear receptor important for renal physiology. We found that CRYZ was ubiquitously expressed in mouse kidney and constitutively expressed in the cytoplasm of medullary collecting duct cells (MCDs). In primary cultured mouse MCDs, CRYZ expression was significantly upregulated by the activation and overexpression of FXR. FXR-induced CRYZ expression was almost completely abolished in the MCD cells with siRNA-mediated FXR knockdown. Consistently, treatment with FXR agonists failed to induce CRYZ expression in the MCDs isolated from mice with global and collecting duct-specific FXR deficiency. We identified a putative FXR response element (FXRE) on the CRYZ gene promoter. The luciferase reporter and ChIP assays revealed that FXR can bind directly to the FXRE site, which was further markedly enhanced by FXR activation. Furthermore, we found CRYZ overexpression in MCDs significantly attenuated hypertonicity-induced cell death possibly via increasing Bcl-2 expression. Collectively, our findings demonstrate that CRYZ is constitutively expressed in renal medullary collecting duct cells, where it is transcriptionally controlled by FXR. Given a critical role of FXR in MCDs, CRYZ may be responsible for protective effect of FXR on the survival of MCDs under hypertonic condition during dehydration.
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7
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Lulli M, Nencioni D, Papucci L, Schiavone N. Zeta-crystallin: a moonlighting player in cancer. Cell Mol Life Sci 2020; 77:965-976. [PMID: 31563996 PMCID: PMC11104887 DOI: 10.1007/s00018-019-03301-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 09/10/2019] [Accepted: 09/16/2019] [Indexed: 12/13/2022]
Abstract
Crystallins were firstly found as structural proteins of the eye lens. To this family belong proteins, such as ζ-crystallin, expressed ubiquitously, and endowed with enzyme activity. ζ-crystallin is a moonlighting protein endowed with two main different functions: (1) mRNA binding with stabilizing activity; (2) NADPH:quinone oxidoreductase. ζ-crystallin has been clearly demonstrated to stabilize mRNAs encoding proteins involved in renal glutamine catabolism during metabolic acidosis resulting in ammoniagenesis and bicarbonate ion production that concur to compensate such condition. ζ-crystallin binds also mRNAs encoding for antiapoptotic proteins, such as Bcl-2 in leukemia cells. On the other hand, the physiological role of its enzymatic activity is still elusive. Gathering research evidences and data mined from public databases, we provide a framework where all the known ζ-crystallin properties are called into question, making it a hypothetical pivotal player in cancer, allowing cells to hijack or subjugate the acidity response mechanism to increase their ability to resist oxidative stress and apoptosis, while fueling their glutamine addicted metabolism.
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Affiliation(s)
- Matteo Lulli
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Università Degli Studi di Firenze, Viale G.B. Morgagni, 50, Firenze, 50134, Italy.
| | - Daniele Nencioni
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Università Degli Studi di Firenze, Viale G.B. Morgagni, 50, Firenze, 50134, Italy
| | - Laura Papucci
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Università Degli Studi di Firenze, Viale G.B. Morgagni, 50, Firenze, 50134, Italy
| | - Nicola Schiavone
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Università Degli Studi di Firenze, Viale G.B. Morgagni, 50, Firenze, 50134, Italy.
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8
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Mas y mas S, Curien G, Giustini C, Rolland N, Ferrer JL, Cobessi D. Crystal Structure of the Chloroplastic Oxoene Reductase ceQORH from Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:329. [PMID: 28337214 PMCID: PMC5343027 DOI: 10.3389/fpls.2017.00329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 02/24/2017] [Indexed: 05/17/2023]
Abstract
Enzymatic and non-enzymatic peroxidation of polyunsaturated fatty acids give rise to accumulation of aldehydes, ketones, and α,β-unsaturated carbonyls of various lengths, known as oxylipins. Oxylipins with α,β-unsaturated carbonyls are reactive electrophile species and are toxic. Cells have evolved several mechanisms to scavenge reactive electrophile oxylipins and decrease their reactivity such as by coupling with glutathione, or by reduction using NAD(P)H-dependent reductases and dehydrogenases of various substrate specificities. Plant cell chloroplasts produce reactive electrophile oxylipins named γ-ketols downstream of enzymatic lipid peroxidation. The chloroplast envelope quinone oxidoreductase homolog (ceQORH) from Arabidopsis thaliana was previously shown to reduce the reactive double bond of γ-ketols. In marked difference with its cytosolic homolog alkenal reductase (AtAER) that displays a high activity toward the ketodiene 13-oxo-9(Z),11(E)-octadecadienoic acid (13-KODE) and the ketotriene 13-oxo-9(Z), 11(E), 15(Z)-octadecatrienoic acid (13-KOTE), ceQORH binds, but does not reduce, 13-KODE and 13-KOTE. Crystal structures of apo-ceQORH and ceQORH bound to 13-KOTE or to NADP+ and 13-KOTE have been solved showing a large ligand binding site, also observed in the structure of the cytosolic alkenal/one reductase. Positioning of the α,β-unsaturated carbonyl of 13-KOTE in ceQORH-NADP+-13-KOTE, far away from the NADP+ nicotinamide ring, provides a rational for the absence of activity with the ketodienes and ketotrienes. ceQORH is a monomeric enzyme in solution whereas other enzymes from the quinone oxidoreductase family are stable dimers and a structural explanation of this difference is proposed. A possible in vivo role of ketodienes and ketotrienes binding to ceQORH is also discussed.
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Affiliation(s)
- Sarah Mas y mas
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, Centre National de la Recherche Scientifique (CNRS)Grenoble, France
| | - Gilles Curien
- Laboratoire de Physiologie Cellulaire & Végétale, BIG, Univ. Grenoble Alpes, CEA, Centre National de la Recherche Scientifique (CNRS), INRAGrenoble, France
| | - Cécile Giustini
- Laboratoire de Physiologie Cellulaire & Végétale, BIG, Univ. Grenoble Alpes, CEA, Centre National de la Recherche Scientifique (CNRS), INRAGrenoble, France
| | - Norbert Rolland
- Laboratoire de Physiologie Cellulaire & Végétale, BIG, Univ. Grenoble Alpes, CEA, Centre National de la Recherche Scientifique (CNRS), INRAGrenoble, France
| | - Jean-Luc Ferrer
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, Centre National de la Recherche Scientifique (CNRS)Grenoble, France
| | - David Cobessi
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, Centre National de la Recherche Scientifique (CNRS)Grenoble, France
- *Correspondence: David Cobessi
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9
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Curien G, Giustini C, Montillet JL, Mas-Y-Mas S, Cobessi D, Ferrer JL, Matringe M, Grechkin A, Rolland N. The chloroplast membrane associated ceQORH putative quinone oxidoreductase reduces long-chain, stress-related oxidized lipids. PHYTOCHEMISTRY 2016; 122:45-55. [PMID: 26678323 DOI: 10.1016/j.phytochem.2015.11.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 11/16/2015] [Accepted: 11/30/2015] [Indexed: 05/11/2023]
Abstract
Under oxidative stress conditions the lipid constituents of cells can undergo oxidation whose frequent consequence is the production of highly reactive α,β-unsaturated carbonyls. These molecules are toxic because they can add to biomolecules (such as proteins and nucleic acids) and several enzyme activities cooperate to eliminate these reactive electrophile species. CeQORH (chloroplast envelope Quinone Oxidoreductase Homolog, At4g13010) is associated with the inner membrane of the chloroplast envelope and imported into the organelle by an alternative import pathway. In the present study, we show that the recombinant ceQORH exhibits the activity of a NADPH-dependent α,β-unsaturated oxoene reductase reducing the double bond of medium-chain (C⩾9) to long-chain (18 carbon atoms) reactive electrophile species deriving from poly-unsaturated fatty acid peroxides. The best substrates of ceQORH are 13-lipoxygenase-derived γ-ketols. γ-Ketols are spontaneously produced in the chloroplast from the unstable allene oxide formed in the biochemical pathway leading to 12-oxo-phytodienoic acid, a precursor of the defense hormone jasmonate. In chloroplasts, ceQORH could detoxify 13-lipoxygenase-derived γ-ketols at their production sites in the membranes. This finding opens new routes toward the understanding of γ-ketols role and detoxification.
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Affiliation(s)
- Gilles Curien
- Univ. Grenoble Alpes, F-38054 Grenoble, France; Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, F-38054 Grenoble, France; INRA, USC1359, 17 rue des Martyrs, F-38054 Grenoble, France; CNRS, Laboratoire de Physiologie Cellulaire & Végétale, UMR 5168, 17 rue des Martyrs, F-38054 Grenoble, France.
| | - Cécile Giustini
- Univ. Grenoble Alpes, F-38054 Grenoble, France; Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, F-38054 Grenoble, France; INRA, USC1359, 17 rue des Martyrs, F-38054 Grenoble, France; CNRS, Laboratoire de Physiologie Cellulaire & Végétale, UMR 5168, 17 rue des Martyrs, F-38054 Grenoble, France
| | - Jean-Luc Montillet
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre de Cadarache, Direction des Sciences du Vivant (DSV), Institut de Biologie Environnementale et Biotechnologie (IBEB), Service de Biologie Végétale et de Microbiologie Environnementale (SBVME), Laboratoire d'Ecophysiologie Moléculaire des Plantes, UMR 7265, Centre National de la Recherche Scientifique (CNRS)/CEA/Aix-Marseille Université, F-13108 Saint-Paul-lez-Durance, France
| | - Sarah Mas-Y-Mas
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38044 Grenoble, France
| | - David Cobessi
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38044 Grenoble, France
| | - Jean-Luc Ferrer
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38044 Grenoble, France
| | - Michel Matringe
- Univ. Grenoble Alpes, F-38054 Grenoble, France; Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, F-38054 Grenoble, France; INRA, USC1359, 17 rue des Martyrs, F-38054 Grenoble, France; CNRS, Laboratoire de Physiologie Cellulaire & Végétale, UMR 5168, 17 rue des Martyrs, F-38054 Grenoble, France
| | - Alexander Grechkin
- Kazan Institute of Biochemistry and Biophysics, Russian Academy of Sciences, P.O. Box 30, 420111 Kazan, Russia
| | - Norbert Rolland
- Univ. Grenoble Alpes, F-38054 Grenoble, France; Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, F-38054 Grenoble, France; INRA, USC1359, 17 rue des Martyrs, F-38054 Grenoble, France; CNRS, Laboratoire de Physiologie Cellulaire & Végétale, UMR 5168, 17 rue des Martyrs, F-38054 Grenoble, France
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10
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Franklin MC, Cheung J, Rudolph MJ, Burshteyn F, Cassidy M, Gary E, Hillerich B, Yao ZK, Carlier PR, Totrov M, Love JD. Structural genomics for drug design against the pathogen Coxiella burnetii. Proteins 2015; 83:2124-36. [PMID: 26033498 DOI: 10.1002/prot.24841] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 05/01/2015] [Accepted: 05/19/2015] [Indexed: 11/11/2022]
Abstract
Coxiella burnetii is a highly infectious bacterium and potential agent of bioterrorism. However, it has not been studied as extensively as other biological agents, and very few of its proteins have been structurally characterized. To address this situation, we undertook a study of critical metabolic enzymes in C. burnetii that have great potential as drug targets. We used high-throughput techniques to produce novel crystal structures of 48 of these proteins. We selected one protein, C. burnetii dihydrofolate reductase (CbDHFR), for additional work to demonstrate the value of these structures for structure-based drug design. This enzyme's structure reveals a feature in the substrate binding groove that is different between CbDHFR and human dihydrofolate reductase (hDHFR). We then identified a compound by in silico screening that exploits this binding groove difference, and demonstrated that this compound inhibits CbDHFR with at least 25-fold greater potency than hDHFR. Since this binding groove feature is shared by many other prokaryotes, the compound identified could form the basis of a novel antibacterial agent effective against a broad spectrum of pathogenic bacteria.
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Affiliation(s)
| | - Jonah Cheung
- Special Projects Division, New York Structural Biology Center, New York
| | - Michael J Rudolph
- Special Projects Division, New York Structural Biology Center, New York
| | - Fiana Burshteyn
- Special Projects Division, New York Structural Biology Center, New York
| | - Michael Cassidy
- Special Projects Division, New York Structural Biology Center, New York
| | - Ebony Gary
- Special Projects Division, New York Structural Biology Center, New York
| | - Brandan Hillerich
- Special Projects Division, New York Structural Biology Center, New York
| | - Zhong-Ke Yao
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia
| | - Paul R Carlier
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia
| | | | - James D Love
- Special Projects Division, New York Structural Biology Center, New York
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Zheng Q, Song Y, Zhang W, Shaw N, Zhou W, Rao Z. Structural views of quinone oxidoreductase from Mycobacterium tuberculosis reveal large conformational changes induced by the co-factor. FEBS J 2015; 282:2697-707. [PMID: 25924579 DOI: 10.1111/febs.13312] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/21/2015] [Accepted: 04/27/2015] [Indexed: 11/28/2022]
Abstract
UNLABELLED Energy generation, synthesis of biomass and detoxification of synthetic compounds are driven by electron transfer in all living organisms. Soluble quinone oxidoreductases (QORs) catalyze transfer of electrons from NADPH to substrates. The open reading frame Rv1454c of Mycobacterium tuberculosis (Mtb) encodes a NADPH-dependent QOR that is known to catalyze one-electron reduction of quinones to produce semiquinones. Here, we report the crystal structures of the apo-enzyme of MtbQOR and its binary complex with NADPH determined at 1.80 and 1.85 Å resolutions, respectively. The enzyme is bi-modular. Domain I binds the substrate, while domain II folds into a typical Rossmann fold for tethering NADPH. Binding of NADPH induces conformational changes. Among the known structures of QORs, MtbQOR exhibits the largest conformational change. Movement of Phe41 to stack against Ala244 results in partial closure of the active site. Comparison of the structure with homologs suggests a conserved topology. However, differences are observed in the region around the site of hydride transfer, highlighting differences in substrate specificities amongst the homologs. Unliganded as well as NADPH-bound MtbQOR crystallized as a dimer. Dimerization is mediated by homotypic intermolecular interactions involving main chain Cα as well as side-chain atoms of residues. The results of analytical ultracentrifugation analysis revealed that MtbQOR exists as a dimer in solution. Enzymatic assays indicate that MtbQOR prefers 9,10-phenanthrenequinone over 1,4-benzoquinone as a substrate. The ability to reduce quinones probably assists Mtb in detoxification of a range of harmful chemicals encountered in the host during invasion. DATABASE The coordinates and structure factors for apo- and NADPH-bound MtbQOR have been deposited in the Protein Data Bank under accession codes 4RVS and 4RVU, respectively.
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Affiliation(s)
- Qianqian Zheng
- College of Life Sciences, Nankai University, Tianjin, China
| | - Yunlong Song
- College of Life Sciences, Nankai University, Tianjin, China
| | - Wei Zhang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Neil Shaw
- College of Life Sciences, Nankai University, Tianjin, China.,National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Weihong Zhou
- College of Life Sciences, Nankai University, Tianjin, China
| | - Zihe Rao
- College of Life Sciences, Nankai University, Tianjin, China.,National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China.,Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing, China
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12
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Crosas E, Sumoy L, González E, Díaz M, Bartolomé S, Farrés J, Parés X, Biosca JA, Fernández MR. The yeast ζ-crystallin/NADPH:quinone oxidoreductase (Zta1p) is under nutritional control by the target of rapamycin pathway and is involved in the regulation of argininosuccinate lyase mRNA half-life. FEBS J 2015; 282:1953-64. [PMID: 25715111 DOI: 10.1111/febs.13246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 01/28/2015] [Accepted: 02/19/2015] [Indexed: 12/30/2022]
Abstract
The yeast ζ-crystallin (Zta1p) is a quinone oxidoreductase belonging to the ζ-crystallin family, with activity in the reduction of alkenal/alkenone compounds. Various biological functions have been ascribed to the members of this protein family, such as their ability to interact specifically with AU-rich sequences in mRNA, and thus they have been proposed to act as AU-rich element-binding proteins (AREBPs). In this study, we evaluated the specificity of Zta1p for RNA versus DNA by means of a novel nonisotopic method for the in vitro quantitative detection of protein · RNA complexes. Through comparative transcriptomic analysis, we found that the lack of Zta1p negatively affects the expression of a group of genes involved in amino acid biosynthesis, the argininosuccinate lyase (ARG4) gene being one of them. Here, we propose that Zta1p participates in the post-transcriptional regulation of ARG4 expression by increasing the ARG4 mRNA half-life. In addition, expression of the ζ-crystallin gene (ZTA1) is itself regulated by nutrient availability through the general amino acid control and target of rapamycin pathways. Our results shed new light on the ζ-crystallin family members from yeast to humans as stress response proteins with a bifunctional role in the detoxification of alkenal and alkenone compounds, and the regulation of gene expression.
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Affiliation(s)
- Eva Crosas
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Spain.,ALBA Synchrotron Light Source, NCD Beamline - Experiments Division, Barcelona, Spain
| | - Lauro Sumoy
- Microarray Unit, Genomics Core Facility, Center for Genomic Regulation (CRG) - Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institut de Medicina Predictiva i Personalitzada del Càncer, IGTP, Campus Can Ruti, Badalona, Barcelona, Spain
| | - Eva González
- Microarray Unit, Genomics Core Facility, Center for Genomic Regulation (CRG) - Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Maykelis Díaz
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Spain
| | - Salvador Bartolomé
- Laboratory of Luminescence and Spectroscopy of Biomolecules (LLEB), Universitat Autònoma de Barcelona, Spain
| | - Jaume Farrés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Spain
| | - Xavier Parés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Spain
| | - Josep Antoni Biosca
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Spain
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13
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Direct evidence for a covalent ene adduct intermediate in NAD(P)H-dependent enzymes. Nat Chem Biol 2013; 10:50-5. [PMID: 24240506 DOI: 10.1038/nchembio.1385] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 10/01/2013] [Indexed: 11/08/2022]
Abstract
The pyridine nucleotides NADH and NADPH (NAD(P)H) are ubiquitous redox coenzymes that are present in all living cells. Although about 16% of all characterized enzymes use pyridine nucleotides as hydride donors or acceptors during catalysis, a detailed understanding of how the hydride is transferred between NAD(P)H and the corresponding substrate is lacking for many enzymes. Here we present evidence for a new mechanism that operates during enzymatic hydride transfers using crotonyl-CoA carboxylase/reductase (Ccr) as a case study. We observed a covalent ene intermediate between NADPH and the substrate, crotonyl-CoA, using NMR, high-resolution MS and stopped-flow spectroscopy. Preparation of the ene intermediate further allowed direct access to the catalytic cycle of other NADPH-dependent enzymes-including those from type II fatty acid biosynthesis-in an unprecedented way, suggesting that formation of NAD(P)H ene intermediates is a more general principle in catalysis.
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15
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Guo PC, Ma XX, Bao ZZ, Ma JD, Chen Y, Zhou CZ. Structural insights into the cofactor-assisted substrate recognition of yeast quinone oxidoreductase Zta1. J Struct Biol 2011; 176:112-8. [PMID: 21820057 DOI: 10.1016/j.jsb.2011.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 07/14/2011] [Accepted: 07/19/2011] [Indexed: 10/17/2022]
Abstract
Quinone oxidoreductase (QOR EC1.6.5.5) catalyzes the reduction of quinone to hydroxyquinone using NADPH as a cofactor. Here we present the crystal structure of the ζ-crystallin-like QOR Zta1 from Saccharomycescerevisiae in apo-form at 2.00 Å and complexed with NADPH at 1.59 Å resolution. Zta1 forms a homodimer, with each subunit containing a catalytic and a cofactor-binding domain. Upon NADPH binding to the interdomain cleft, the two domains shift towards each other, producing a better fit for NADPH, and tightening substrate binding. Computational simulation combined with site-directed mutagenesis and enzymatic activity analysis defined a potential quinone-binding site that determines the stringent substrate specificity. Moreover, multiple-sequence alignment and kinetics assays implied that a single-residue change from Arg in lower organisms to Gly in vertebrates possibly resulted in elevation of enzymatic activity of ζ-crystallin-like QORs throughout evolution.
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Affiliation(s)
- Peng-Chao Guo
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui 230027, People's Republic of China
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