1
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Peng X, Liao W, Lin X, Lilley DMJ, Huang L. Crystal structures of the NAD+-II riboswitch reveal two distinct ligand-binding pockets. Nucleic Acids Res 2023; 51:2904-2914. [PMID: 36840714 PMCID: PMC10085692 DOI: 10.1093/nar/gkad102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/01/2023] [Accepted: 02/16/2023] [Indexed: 02/26/2023] Open
Abstract
We present crystal structures of a new NAD+-binding riboswitch termed NAD+-II, bound to nicotinamide mononucleotide (NMN), nicotinamide adenine dinucleotide (NAD+) and nicotinamide riboside (NR). The RNA structure comprises a number of structural features including three helices, one of which forms a triple helix by interacting with an A5 strand in its minor-groove, and another formed from a long-range pseudoknot. The core of the structure (centrally located and coaxial with the triplex and the pseudoknot) includes two consecutive quadruple base interactions. Unusually the riboswitch binds two molecules of ligand, bound at distinct, non-overlapping sites in the RNA. Binding occurs primarily through the nicotinamide moiety of each ligand, held by specific hydrogen bonding and stacking interactions with the pyridyl ring. The mode of binding is the same for NMN, NR and the nicotinamide moiety of NAD+. In addition, when NAD+ is bound into one site it adopts an elongated conformation such that its diphosphate linker occupies a groove on the surface of the RNA, following which the adenine portion inserts into a pocket and makes specific hydrogen bonding interactions. Thus the NAD+-II riboswitch is distinct from the NAD+-I riboswitch in that it binds two molecules of ligand at separate sites, and that binding occurs principally through the nicotinamide moiety.
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Affiliation(s)
- Xuemei Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Wenjian Liao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xiaowei Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
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2
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Dinh T, Rahn KT, Phillips RS. Crystallographic snapshots of ternary complexes of thermophilic secondary alcohol dehydrogenase from
Thermoanaerobacter pseudoethanolicus
reveal the dynamics of ligand exchange and the proton relay network. Proteins 2022; 90:1570-1583. [DOI: 10.1002/prot.26339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/16/2022] [Accepted: 03/27/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Tung Dinh
- Department of Chemistry University of Georgia Athens Georgia USA
| | - K. Troy Rahn
- Department of Chemistry University of Georgia Athens Georgia USA
| | - Robert S. Phillips
- Department of Chemistry University of Georgia Athens Georgia USA
- Department of Biochemistry and Molecular Biology University of Georgia Athens Georgia USA
- Center for Metalloenzyme Studies University of Georgia Athens Georgia USA
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3
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Wang T, Yang K, Tian Q, Han R, Zhang X, Li A, Zhang L. Acetoacetyl-CoA reductase PhaB as an excellent anti-Prelog biocatalyst for the synthesis of chiral β-hydroxyl ester and the molecular basis of its catalytic performance. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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4
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Plapp BV, Subramanian R. Alternative binding modes in abortive NADH-alcohol complexes of horse liver alcohol dehydrogenase. Arch Biochem Biophys 2021; 701:108825. [PMID: 33675814 PMCID: PMC7980771 DOI: 10.1016/j.abb.2021.108825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 10/22/2022]
Abstract
Enzymes typically have high specificity for their substrates, but the structures of substrates and products differ, and multiple modes of binding are observed. In this study, high resolution X-ray crystallography of complexes with NADH and alcohols show alternative modes of binding in the active site. Enzyme crystallized with the good substrates NAD+ and 4-methylbenzyl alcohol was found to be an abortive complex of NADH with 4-methylbenzyl alcohol rotated to a "non-productive" mode as compared to the structures that resemble reactive Michaelis complexes with NAD+ and 2,2,2-trifluoroethanol or 2,3,4,5,6-pentafluorobenzyl alcohol. The NADH is formed by reduction of the NAD+ with the alcohol during the crystallization. The same structure was also formed by directly crystallizing the enzyme with NADH and 4-methylbenzyl alcohol. Crystals prepared with NAD+ and 4-bromobenzyl alcohol also form the abortive complex with NADH. Surprisingly, crystals prepared with NAD+ and the strong inhibitor 1H,1H-heptafluorobutanol also had NADH, and the alcohol was bound in two different conformations that illustrate binding flexibility. Oxidation of 2-methyl-2,4-pentanediol during the crystallization apparently led to reduction of the NAD+. Kinetic studies show that high concentrations of alcohols can bind to the enzyme-NADH complex and activate or inhibit the enzyme. Together with previous studies on complexes with NADH and formamide analogues of the carbonyl substrates, models for the Michaelis complexes with NAD+-alcohol and NADH-aldehyde are proposed.
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Affiliation(s)
- Bryce V Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242, USA.
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5
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Guntupalli SR, Li Z, Chang L, Plapp BV, Subramanian R. Cryo-Electron Microscopy Structures of Yeast Alcohol Dehydrogenase. Biochemistry 2021; 60:663-677. [PMID: 33620215 DOI: 10.1021/acs.biochem.0c00921] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structures of yeast alcohol dehydrogenase determined by X-ray crystallography show that the subunits have two different conformational states in each of the two dimers that form the tetramer. Apoenzyme and holoenzyme complexes relevant to the catalytic mechanism were described, but the asymmetry led to questions about the cooperativity of the subunits in catalysis. This study used cryo-electron microscopy (cryo-EM) to provide structures for the apoenzyme, two different binary complexes with NADH, and a ternary complex with NAD+ and 2,2,2-trifluoroethanol. All four subunits in each of these complexes are identical, as the tetramers have D2 symmetry, suggesting that there is no preexisting asymmetry and that the subunits can be independently active. The apoenzyme and one enzyme-NADH complex have "open" conformations and the inverted coordination of the catalytic zinc with Cys-43, His-66, Glu-67, and Cys-153, whereas another enzyme-NADH complex and the ternary complex have closed conformations with the classical coordination of the zinc with Cys-43, His-66, Cys-153, and a water or the oxygen of trifluoroethanol. The conformational change involves interactions of Arg-340 with the pyrophosphate group of the coenzyme and Glu-67. The cryo-EM and X-ray crystallography studies provide structures relevant for the catalytic mechanism.
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Affiliation(s)
- Sai Rohit Guntupalli
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.,Manipal University, Manipal, India.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhuang Li
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Leifu Chang
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Bryce V Plapp
- Department of Biochemistry, Bowen Science Building, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Ramaswamy Subramanian
- Department of Biological Sciences and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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6
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Petratos K, Gessmann R, Daskalakis V, Papadovasilaki M, Papanikolau Y, Tsigos I, Bouriotis V. Structure and Dynamics of a Thermostable Alcohol Dehydrogenase from the Antarctic Psychrophile Moraxella sp. TAE123. ACS OMEGA 2020; 5:14523-14534. [PMID: 32596590 PMCID: PMC7315583 DOI: 10.1021/acsomega.0c01210] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/26/2020] [Indexed: 06/11/2023]
Abstract
The structure of a recombinant (His-tagged at C-terminus) alcohol dehydrogenase (MoADH) from the cold-adapted bacterium Moraxella sp. TAE123 has been refined with X-ray diffraction data extending to 1.9 Å resolution. The enzyme assumes a homo-tetrameric structure. Each subunit comprises two distinct structural domains: the catalytic domain (residues 1-150 and 288-340/345) and the nucleotide-binding domain (residues 151-287). There are two Zn2+ ions in each protein subunit. Two additional zinc ions have been found in the crystal structure between symmetry-related subunits. The structure has been compared with those of homologous enzymes from Geobacillus stearothermophilus (GsADH), Escherichia coli (EcADH), and Thermus sp. ATN1 (ThADH) that thrive in environments of diverse temperatures. Unexpectedly, MoADH has been found active from 10 to at least 53 °C and unfolds at 89 °C according to circular dichroism spectropolarimetry data. MoADH with substrate ethanol exhibits a small value of activation enthalpy ΔH ‡ of 30 kJ mol-1. Molecular dynamics simulations for single subunits of the closely homologous enzymes MoADH and GsADH performed at 280, 310, and 340 K showed enhanced wide-ranging mobility of MoADH at high temperatures and generally lower but more distinct and localized mobility for GsADH. Principal component analysis of the fluctuations of both ADHs resulted in a prominent open-close transition of the structural domains mainly at 280 K for MoADH and 340 K for GsADH. In conclusion, MoADH is a very thermostable, cold-adapted enzyme and the small value of activation enthalpy allows the enzyme to function adequately at low temperatures.
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Affiliation(s)
- Kyriacos Petratos
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, 70013 Heraklion, Greece
| | - Renate Gessmann
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, 70013 Heraklion, Greece
| | - Vangelis Daskalakis
- Department
of Chemical Engineering, Cyprus University
of Technology, 3603 Limassol, Cyprus
| | - Maria Papadovasilaki
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, 70013 Heraklion, Greece
| | - Yannis Papanikolau
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, 70013 Heraklion, Greece
| | - Iason Tsigos
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, 70013 Heraklion, Greece
| | - Vassilis Bouriotis
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, 70013 Heraklion, Greece
- Department
of Biology, University of Crete, 70013 Heraklion, Greece
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7
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Endo S, Wako H. Normal mode analysis calculation for a full-atom model with a smaller number of degrees of freedom for huge protein molecules. Biophys Physicobiol 2020; 16:205-212. [PMID: 31984173 PMCID: PMC6975923 DOI: 10.2142/biophysico.16.0_205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 06/27/2019] [Indexed: 12/01/2022] Open
Abstract
The number of degrees of freedom (DOF), N, in normal mode analysis (NMA) calculations of proteins is a crucial problem in huge systems because the eigenvalue problem of an N-by-N matrix must be solved. If it were possible to perform the analysis with a smaller number of DOF for the same system with minimal deterioration in accuracy, this would make a significant impact on the computational study of protein dynamics. We examined two models in which the number of DOF was reduced. Both of them adopted a full-atom model with dihedral angles as independent variables. In one model, side-chain dihedral angles, χ's, and a main-chain dihedral angle, ω, were fixed and only the main-chain dihedral angles, ϕ and ψ, were variable. In another model, the dihedral angles around virtual bonds that connect neighboring Cα atoms were tested. The number of DOFs for the two models was two and one per residue, respectively. The residue-by-residue fluctuation profiles for atoms and dihedral angles were well reproduced in both models. The motion of atoms in the individual lowest-frequency normal modes of the two models was also very similar to those of the original model in which all rotatable dihedral angles were variable. Consequently, these models could predict large-amplitude concerted motion. These results also imply that proteins in a full-atom model can undergo only limited large-scale conformational changes around the native conformation, and consequently, NMA results do not strongly depend on the independent variables adopted.
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Affiliation(s)
- Shigeru Endo
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Hiroshi Wako
- School of Social Sciences, Waseda University, Shinjuku-ku, Tokyo 169-8050, Japan
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8
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Herzik MA, Wu M, Lander GC. High-resolution structure determination of sub-100 kDa complexes using conventional cryo-EM. Nat Commun 2019; 10:1032. [PMID: 30833564 PMCID: PMC6399227 DOI: 10.1038/s41467-019-08991-8] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 02/11/2019] [Indexed: 12/31/2022] Open
Abstract
Determining high-resolution structures of biological macromolecules amassing less than 100 kilodaltons (kDa) has been a longstanding goal of the cryo-electron microscopy (cryo-EM) community. While the Volta phase plate has enabled visualization of specimens in this size range, this instrumentation is not yet fully automated and can present technical challenges. Here, we show that conventional defocus-based cryo-EM methodologies can be used to determine high-resolution structures of specimens amassing less than 100 kDa using a transmission electron microscope operating at 200 keV coupled with a direct electron detector. Our ~2.7 Å structure of alcohol dehydrogenase (82 kDa) proves that bound ligands can be resolved with high fidelity to enable investigation of drug-target interactions. Our ~2.8 Å and ~3.2 Å structures of methemoglobin demonstrate that distinct conformational states can be identified within a dataset for proteins as small as 64 kDa. Furthermore, we provide the sub-nanometer cryo-EM structure of a sub-50 kDa protein.
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Affiliation(s)
- Mark A Herzik
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Mengyu Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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9
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Yamada M, Matsuhira T, Yamamoto K, Sakai H. Antioxidative Pseudoenzymatic Mechanism of NAD(P)H Coexisting with Oxyhemoglobin for Suppressed Methemoglobin Formation. Biochemistry 2019; 58:1400-1410. [PMID: 30789715 DOI: 10.1021/acs.biochem.8b01314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Oxyhemoglobin (HbO2) coexisting with equimolar NADH retards autoxidation and oxidant-induced metHb formation based on the pseudocatalase (CAT) and pseudosuperoxide dismutase (SOD) activities. In this work, we compared the effects of NADH with those of NADPH and estimated the binding site of NAD(P)H to HbO2 to elucidate the antioxidative mechanisms. The results clarified that pseudo-CAT and pseudo-SOD activities of HbO2 coexisting with NADPH were similar to activities obtained with NADH. Prompt MetHb formation (<40 min) facilitated by oxidants (H2O2, NO, and NaNO2) was hindered by NADPH. These effects were similar to those of NADH. However, we found that NADPH is thermally unstable compared to NADH and that NADPH cannot sustain antioxidative effects for a long period of autoxidation to metHb such as 24 h. Lineweaver-Burk plots clarified that the Michaelis constants of these pseudoenzymatic activities are in the millimolar range. Addition of inositol hexaphosphate (IHP) and 2,3-diphosphoglycerate (DPG), which are known to bind not only with deoxyHb but also weakly with HbO2, showed competitive inhibition of pseudoenzymatic activities. These results suggest that the binding site of NADH and NADPH on HbO2 is the same as those of IHP and DPG. 31P nuclear magnetic resonance definitively showed 1:1 stoichiometric binding of NADH to HbO2. High-performance liquid chromatography analysis showed that NADH preferentially inhibited autoxidation of α-subunit heme. Docking simulations also predicted that the binding site of relaxed-state HbO2 with NAD(P)H is the same as those with IHP and DPG. Collectively, the pseudoenzymatic activities of HbO2 coexisting with NAD(P)H are induced by the 1:1 stoichiometric binding of NAD(P)H to HbO2.
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Affiliation(s)
- Magohei Yamada
- Department of Chemistry , Nara Medical University , 840 Shijo-cho , Kashihara , Nara 634-8521 , Japan
| | - Takashi Matsuhira
- Department of Chemistry , Nara Medical University , 840 Shijo-cho , Kashihara , Nara 634-8521 , Japan
| | - Keizo Yamamoto
- Department of Chemistry , Nara Medical University , 840 Shijo-cho , Kashihara , Nara 634-8521 , Japan
| | - Hiromi Sakai
- Department of Chemistry , Nara Medical University , 840 Shijo-cho , Kashihara , Nara 634-8521 , Japan
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10
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Aggarwal N, Ananthathamula R, Karanam VK, Doble M, Chadha A. Understanding substrate specificity and enantioselectivity of carbonyl reductase from Candida parapsilosis ATCC 7330 (CpCR): Experimental and modeling studies. MOLECULAR CATALYSIS 2018. [DOI: 10.1016/j.mcat.2018.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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van Haren MJ, Thomas MG, Sartini D, Barlow DJ, Ramsden DB, Emanuelli M, Klamt F, Martin NI, Parsons RB. The kinetic analysis of the N-methylation of 4-phenylpyridine by nicotinamide N-methyltransferase: Evidence for a novel mechanism of substrate inhibition. Int J Biochem Cell Biol 2018; 98:127-136. [PMID: 29549048 DOI: 10.1016/j.biocel.2018.03.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 02/23/2018] [Accepted: 03/12/2018] [Indexed: 12/17/2022]
Abstract
The N-methylation of 4-phenylpyridine produces the neurotoxin 1-methyl-4-phenylpyridinium ion (MPP+). We investigated the kinetics of 4-phenylpyridine N-methylation by nicotinamide N-methyltransferase (NNMT) and its effect upon 4-phenylpyridine toxicity in vitro. Human recombinant NNMT possessed 4-phenylpyridine N-methyltransferase activity, with a specific activity of 1.7 ± 0.03 nmol MPP+ produced/h/mg NNMT. Although the Km for 4-phenylpyridine was similar to that reported for nicotinamide, its kcat of 9.3 × 10-5 ± 2 × 10-5 s-1 and specificity constant, kcat/Km, of 0.8 ± 0.8 s-1 M-1 were less than 0.15% of the respective values for nicotinamide, demonstrating that 4-phenylpyridine is a poor substrate for NNMT. At low (<2.5 mM) substrate concentration, 4-phenylpyridine N-methylation was competitively inhibited by dimethylsulphoxide, with a Ki of 34 ± 8 mM. At high (>2.5 mM) substrate concentration, enzyme activity followed substrate inhibition kinetics, with a Ki of 4 ± 1 mM. In silico molecular docking suggested that 4-phenylpyridine binds to the active site of NNMT in two non-redundant poses, one a substrate binding mode and the other an inhibitory mode. Finally, the expression of NNMT in the SH-SY5Y cell-line had no effect cell death, viability, ATP content or mitochondrial membrane potential. These data demonstrate that 4-phenylpyridine N-methylation by NNMT is unlikely to serve as a source of MPP+. The possibility for competitive inhibition by dimethylsulphoxide should be considered in NNMT-based drug discovery studies. The potential for 4-phenylpyridine to bind to the active site in two binding orientations using the same active site residues is a novel mechanism of substrate inhibition.
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Affiliation(s)
- Matthijs J van Haren
- Utrecht University, Utrecht Institute for Pharmaceutical Science, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Martin G Thomas
- King's College London, Institute of Pharmaceutical Science, 150 Stamford Street, London SE1 9NH, UK
| | - Davide Sartini
- Universitá Politecnica delle Marche, Department of Clinical Sciences, School of Medicine, Ancona, Italy
| | - David J Barlow
- King's College London, Institute of Pharmaceutical Science, 150 Stamford Street, London SE1 9NH, UK
| | - David B Ramsden
- University of Birmingham, Institute of Metabolism and Systems Research, Edgbaston, Birmingham B15 2TH, UK
| | - Monica Emanuelli
- Universitá Politecnica delle Marche, Department of Clinical Sciences, School of Medicine, Ancona, Italy
| | - Fábio Klamt
- Universidade Federal do Rio Grande do Sul, Departmento de Bioquímica, Instituto de Ciêncas Básicas de Saúde, Rua Ramiro Barcelos, Porto Alegre, RS 90035 003, Brazil
| | - Nathaniel I Martin
- Utrecht University, Utrecht Institute for Pharmaceutical Science, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands.
| | - Richard B Parsons
- King's College London, Institute of Pharmaceutical Science, 150 Stamford Street, London SE1 9NH, UK.
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12
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Julius K, Al-Ayoubi SR, Paulus M, Tolan M, Winter R. The effects of osmolytes and crowding on the pressure-induced dissociation and inactivation of dimeric LADH. Phys Chem Chem Phys 2018; 20:7093-7104. [DOI: 10.1039/c7cp08242h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Compatible osmolytes are able to efficiently modulate the oligomeric state, stability and activity of enzymes at high pressures.
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Affiliation(s)
- Karin Julius
- Fakultät Physik/DELTA
- TU Dortmund University
- 44221 Dortmund
- Germany
| | - Samy R. Al-Ayoubi
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - Michael Paulus
- Fakultät Physik/DELTA
- TU Dortmund University
- 44221 Dortmund
- Germany
| | - Metin Tolan
- Fakultät Physik/DELTA
- TU Dortmund University
- 44221 Dortmund
- Germany
| | - Roland Winter
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
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13
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Peng HL, Callender R. Mechanistic Analysis of Fluorescence Quenching of Reduced Nicotinamide Adenine Dinucleotide by Oxamate in Lactate Dehydrogenase Ternary Complexes. Photochem Photobiol 2017; 93:1193-1203. [PMID: 28391608 PMCID: PMC5603363 DOI: 10.1111/php.12775] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/11/2017] [Indexed: 11/27/2022]
Abstract
Fluorescence of Reduced Nicotinamide Adenine Dinucleotide (NADH) is extensively employed in studies of oxidoreductases. A substantial amount of static and kinetic work has focused on the binding of pyruvate or substrate mimic oxamate to the binary complex of lactate dehydrogenase (LDH)-NADH where substantial fluorescence quenching is typically observed. However, the quenching mechanism is not well understood limiting structural interpretation. Based on time-dependent density functional theory (TDDFT) computations with cam-B3LYP functional in conjunction with the analysis of previous experimental results, we propose that bound oxamate acts as an electron acceptor in the quenching of fluorescence of NADH in the ternary complex, where a charge transfer (CT) state characterized by excitation from the highest occupied molecular orbital (HOMO) of the nicotinamide moiety of NADH to the lowest unoccupied molecular orbital (LUMO) of oxamate exists close to the locally excited (LE) state involving only the nicotinamide moiety. Efficient quenching in the encounter complex like in pig heart LDH requires that oxamate forms a salt bridge with Arg-171 and hydrogen bonds with His-195, Thr-246 and Asn-140. Further structural rearrangement and loop closure, which also brings about another hydrogen bond between oxamate and Arg-109, will increase the rate of fluorescence quenching as well.
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Affiliation(s)
- Huo-Lei Peng
- Department of Biochemistry, Albert Einstein College of Medicine, New
York, NY 10461, USA
| | - Robert Callender
- Department of Biochemistry, Albert Einstein College of Medicine, New
York, NY 10461, USA
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14
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Plapp BV, Savarimuthu BR, Ferraro DJ, Rubach JK, Brown EN, Ramaswamy S. Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis. Biochemistry 2017. [PMID: 28640600 PMCID: PMC5518280 DOI: 10.1021/acs.biochem.7b00446] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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During catalysis
by liver alcohol dehydrogenase (ADH), a water
bound to the catalytic zinc is replaced by the oxygen of the substrates.
The mechanism might involve a pentacoordinated zinc or a double-displacement
reaction with participation by a nearby glutamate residue, as suggested
by studies of human ADH3, yeast ADH1, and some other tetrameric ADHs.
Zinc coordination and participation of water in the enzyme mechanism
were investigated by X-ray crystallography. The apoenzyme and its
complex with adenosine 5′-diphosphoribose have an open protein
conformation with the catalytic zinc in one position, tetracoordinated
by Cys-46, His-67, Cys-174, and a water molecule. The bidentate chelators
2,2′-bipyridine and 1,10-phenanthroline displace the water
and form a pentacoordinated zinc. The enzyme–NADH complex has
a closed conformation similar to that of ternary complexes with coenzyme
and substrate analogues; the coordination of the catalytic zinc is
similar to that found in the apoenzyme, except that a minor, alternative
position for the catalytic zinc is ∼1.3 Å from the major
position and closer to Glu-68, which could form the alternative coordination
to the catalytic zinc. Complexes with NADH and N-1-methylhexylformamide
or N-benzylformamide (or with NAD+ and
fluoro alcohols) have the classical tetracoordinated zinc, and no
water is bound to the zinc or the nicotinamide rings. The major forms
of the enzyme in the mechanism have a tetracoordinated zinc, where
the carboxylate group of Glu-68 could participate in the exchange
of water and substrates on the zinc. Hydride transfer in the Michaelis
complexes does not involve a nearby water.
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Affiliation(s)
- Bryce V Plapp
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Baskar Raj Savarimuthu
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Daniel J Ferraro
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Jon K Rubach
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Eric N Brown
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - S Ramaswamy
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
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15
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Mielcarek A, Daszkiewicz M, Kazimierczuk K, Ciborska A, Dołęga A. Variable-temperature X-ray diffraction study of structural parameters of NH---S hydrogen bonds in triethylammonium and pyridinium silanethiolates. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:763-770. [PMID: 27698318 DOI: 10.1107/s2052520616011562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/15/2016] [Indexed: 06/06/2023]
Abstract
Two hydrogen-bonded, well defined compounds were synthesized from tris(2,6-diisopropyl)phenoxysilanethiol (TDST) and triethylamine (TDST-TEA) or pyridine (TDST-py). The crystalline compounds were characterized in the solid state by variable-temperature X-ray diffraction measurements and ATR FT-IR spectroscopy. The toluene solutions of TDST-TEA and TDST-py were studied by NMR spectroscopy. The total hydrogen-bond energies and FT-IR spectra were calculated with the use of BLYP-D/TZP and B3LYP/6-31G(d,p)/GD3BJ methods. Thermochemical parameters and potential energy scans were calculated at the B3LYP/6-31G(d,p)/GD3BJ level. All results point to the higher energy of bonding in TDST-TEA both in the solid state and in solution. At the same time the potential energy scan reveals a very broad double-well hydrogen bond in TDST-py, indicating good stabilization of the system for a wide range of D-H...A distances.
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Affiliation(s)
- Agnieszka Mielcarek
- Department of Inorganic Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk 80-233, Poland
| | - Marek Daszkiewicz
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Okólna 2, PO Box 1410, Wrocław 50-950, Poland
| | - Katarzyna Kazimierczuk
- Department of Inorganic Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk 80-233, Poland
| | - Anna Ciborska
- Department of Inorganic Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk 80-233, Poland
| | - Anna Dołęga
- Department of Inorganic Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk 80-233, Poland
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16
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Krotzky T, Klebe G. Acceleration of Binding Site Comparisons by Graph Partitioning. Mol Inform 2015; 34:550-8. [PMID: 27490500 DOI: 10.1002/minf.201500028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/04/2015] [Indexed: 11/05/2022]
Abstract
The comparison of protein binding sites is a prominent task in computational chemistry and has been studied in many different ways. For the automatic detection and comparison of putative binding cavities the Cavbase system has been developed which uses a coarse-grained set of pseudocenters to represent the physicochemical properties of a binding site and employs a graph-based procedure to calculate similarities between two binding sites. However, the comparison of two graphs is computationally quite demanding which makes large-scale studies such as the rapid screening of entire databases hardly feasible. In a recent work, we proposed the method Local Cliques (LC) for the efficient comparison of Cavbase binding sites. It employs a clique heuristic to detect the maximum common subgraph of two binding sites and an extended graph model to additionally compare the shape of individual surface patches. In this study, we present an alternative to further accelerate the LC method by partitioning the binding-site graphs into disjoint components prior to their comparisons. The pseudocenter sets are split with regard to their assigned phyiscochemical type, which leads to seven much smaller graphs than the original one. Applying this approach on the same test scenarios as in the former comprehensive way results in a significant speed-up without sacrificing accuracy.
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Affiliation(s)
- Timo Krotzky
- Department of Pharmaceutical Chemistry, Philipps-Universität, 35032 Marburg, Germany
| | - Gerhard Klebe
- Department of Pharmaceutical Chemistry, Philipps-Universität, 35032 Marburg, Germany.
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17
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Bonjack-Shterengartz M, Avnir D. The near-symmetry of proteins. Proteins 2015; 83:722-34. [PMID: 25354765 DOI: 10.1002/prot.24706] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/06/2014] [Accepted: 10/18/2014] [Indexed: 11/07/2022]
Abstract
The majority of protein oligomers form clusters which are nearly symmetric. Understanding of that imperfection, its origins, and perhaps also its advantages requires the conversion of the currently used vague qualitative descriptive language of the near-symmetry into an accurate quantitative measure that will allow to answer questions such as: "What is the degree of symmetry deviation of the protein?," "how do these deviations compare within a family of proteins?," and so on. We developed quantitative methods to answer this type of questions, which are capable of analyzing the whole protein, its backbone or selected portions of it, down to comparison of symmetry-related specific amino-acids, and which are capable of visualizing the various levels of symmetry deviations in the form of symmetry maps. We have applied these methods on an extensive list of homomers and heteromers and found that apparently all proteins never reach perfect symmetry. Strikingly, even homomeric protein clusters are never ideally symmetric. We also found that the main burden of symmetry distortion is on the amino-acids near the symmetry axis; that it is mainly the more hydrophilic amino-acids that take place in symmetry-distortive interactions; and more. The remarkable ability of heteromers to preserve near-symmetry, despite the different sequences, was also shown and analyzed. The comprehensive literature on the suggested advantages symmetric oligomerizations raises a yet-unsolved key question: If symmetry is so advantageous, why do proteins stop shy of perfect symmetry? Some tentative answers to be tested in further studies are suggested in a concluding outlook.
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Affiliation(s)
- Maayan Bonjack-Shterengartz
- Institute of Chemistry and the Lise Meitner Minerva Center for Computational Quantum Chemistry, the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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18
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Raj S, Ramaswamy S, Plapp BV. Yeast alcohol dehydrogenase structure and catalysis. Biochemistry 2014; 53:5791-803. [PMID: 25157460 PMCID: PMC4165444 DOI: 10.1021/bi5006442] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 08/22/2014] [Indexed: 11/30/2022]
Abstract
Yeast (Saccharomyces cerevisiae) alcohol dehydrogenase I (ADH1) is the constitutive enzyme that reduces acetaldehyde to ethanol during the fermentation of glucose. ADH1 is a homotetramer of subunits with 347 amino acid residues. A structure for ADH1 was determined by X-ray crystallography at 2.4 Å resolution. The asymmetric unit contains four different subunits, arranged as similar dimers named AB and CD. The unit cell contains two different tetramers made up of "back-to-back" dimers, AB:AB and CD:CD. The A and C subunits in each dimer are structurally similar, with a closed conformation, bound coenzyme, and the oxygen of 2,2,2-trifluoroethanol ligated to the catalytic zinc in the classical tetrahedral coordination with Cys-43, Cys-153, and His-66. In contrast, the B and D subunits have an open conformation with no bound coenzyme, and the catalytic zinc has an alternative, inverted coordination with Cys-43, Cys-153, His-66, and the carboxylate of Glu-67. The asymmetry in the dimeric subunits of the tetramer provides two structures that appear to be relevant for the catalytic mechanism. The alternative coordination of the zinc may represent an intermediate in the mechanism of displacement of the zinc-bound water with alcohol or aldehyde substrates. Substitution of Glu-67 with Gln-67 decreases the catalytic efficiency by 100-fold. Previous studies of structural modeling, evolutionary relationships, substrate specificity, chemical modification, and site-directed mutagenesis are interpreted more fully with the three-dimensional structure.
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Affiliation(s)
| | | | - Bryce V. Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, Iowa 52242, United States
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19
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Friedman R. Structural and computational insights into the versatility of cadmium binding to proteins. Dalton Trans 2014; 43:2878-87. [PMID: 24346117 DOI: 10.1039/c3dt52810c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cadmium is a highly toxic group XII metal, similar to zinc and mercury. Unlike zinc, which is one of the most common metal cofactors in biology, cadmium is highly toxic. Many Zn(2+)-binding proteins can bind Cd(2+)-ions without significantly affecting their structures. Here, the protein data bank is analysed with regard to protein-cadmium interactions, which shows that cadmium can bind to a variety of ion binding sites in proteins. Statistical analysis of Cd(2+)-side chain interactions is compared with a similar analysis of other ions. This analysis reveals that with regard to amino acid side-chain preference, Cd(2+) is more similar to Mn(2+) than to Zn(2+) or Hg(2+). Finally, the interaction energies of three native metal binding proteins are calculated where Cd(2+) binds instead of Zn(2+), Ca(2+) or Cu(2+). The interaction energies are decomposed into individual components whose contributions are discussed.
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Affiliation(s)
- Ran Friedman
- Computational Chemistry and Biochemistry Research Group, Department of Chemistry and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden
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20
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García-Sevillano MA, García-Barrera T, Navarro F, Gómez-Ariza JL. Cadmium toxicity in Mus musculus mice based on a metallomic study. Antagonistic interaction between Se and Cd in the bloodstream. Metallomics 2014; 6:672-81. [PMID: 24553457 DOI: 10.1039/c3mt00350g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cadmium (Cd) is an important inorganic toxicant in the environment which impacts on human health. A metallomic approach based on size-exclusion chromatography (SEC) coupled to inductively coupled plasma-mass spectrometry (ICP-MS) and multidimensional chromatography separation based on SEC coupled to affinity chromatography 2D-SEC-AF-ICP-MS have been applied to achieve a better understanding of the function, detoxification processes and regulation of metals in mice (Mus musculus) under controlled exposure to both Cd and Cd plus (77)Se. Isotopic dilution analysis (IDA) was performed to quantify selenium containing proteins in mice plasma with ICP-qMS as a multielemental detector. Additionally, isotope pattern deconvolution (IPD) was applied to study the fate of enriched (77)selenite in mice subjected to cadmium exposure and the effect of selenoprotein production in plasma. Moreover, the affinity of Cd for SeP in plasma of mice was corroborated using anion exchange chromatography (AEC) after AF separation and identified by organic mass spectrometry. This work illustrates the high reliability of the integrated use of inorganic and organic mass spectrometry to get a metallomic approximation, which provides a good alternative to gain deep insight into the fate of elements in exposed organisms, providing information about metal trafficking, interactions and homeostasis.
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Affiliation(s)
- M A García-Sevillano
- Department of Chemistry and Materials Science, Faculty of Experimental Sciences, University of Huelva, Campus de El Carmen, 21007-Huelva, Spain.
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21
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Tang L, Qiu R, Tang Y, Wang S. Cadmium–zinc exchange and their binary relationship in the structure of Zn-related proteins: a mini review. Metallomics 2014; 6:1313-23. [DOI: 10.1039/c4mt00080c] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we give an overview of ongoing work on discovering the structural mechanisms of Cd–Zn exchange and the potentially diverse roles of Cd at Zn functional sites in proteins.
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Affiliation(s)
- Lu Tang
- School of Environmental Science and Engineering
- Sun Yat-Sen University
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology
- Guangzhou 510275, China
| | - Rongliang Qiu
- School of Environmental Science and Engineering
- Sun Yat-Sen University
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology
- Guangzhou 510275, China
| | - Yetao Tang
- School of Environmental Science and Engineering
- Sun Yat-Sen University
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology
- Guangzhou 510275, China
| | - Shizhong Wang
- School of Environmental Science and Engineering
- Sun Yat-Sen University
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology
- Guangzhou 510275, China
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22
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Sacquin-Mora S. Motions and mechanics: investigating conformational transitions in multi-domain proteins with coarse-grain simulations. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.843176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS UPR9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005, Paris, France
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23
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Kubienová L, Kopečný D, Tylichová M, Briozzo P, Skopalová J, Šebela M, Navrátil M, Tâche R, Luhová L, Barroso JB, Petřivalský M. Structural and functional characterization of a plant S-nitrosoglutathione reductase from Solanum lycopersicum. Biochimie 2012; 95:889-902. [PMID: 23274177 DOI: 10.1016/j.biochi.2012.12.009] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 12/10/2012] [Indexed: 12/25/2022]
Abstract
S-nitrosoglutathione reductase (GSNOR), also known as S-(hydroxymethyl)glutathione (HMGSH) dehydrogenase, belongs to the large alcohol dehydrogenase superfamily, namely to the class III ADHs. GSNOR catalyses the oxidation of HMGSH to S-formylglutathione using a catalytic zinc and NAD(+) as a coenzyme. The enzyme also catalyses the NADH-dependent reduction of S-nitrosoglutathione (GSNO). In plants, GSNO has been suggested to serve as a nitric oxide (NO) reservoir locally or possibly as NO donor in distant cells and tissues. NO and NO-related molecules such as S-nitrosothiols (S-NOs) play a central role in the regulation of normal plant physiological processes and host defence. The enzyme thus participates in the cellular homeostasis of S-NOs and in the metabolism of reactive nitrogen species. Although GSNOR has recently been characterized from several organisms, this study represents the first detailed biochemical and structural characterization of a plant GSNOR, that from tomato (Solanum lycopersicum). SlGSNOR gene expression is higher in roots and stems compared to leaves of young plants. It is highly expressed in the pistil and stamens and in fruits during ripening. The enzyme is a dimer and preferentially catalyses reduction of GSNO while glutathione and S-methylglutathione behave as non-competitive inhibitors. Using NAD(+), the enzyme oxidizes HMGSH and other alcohols such as cinnamylalcohol, geraniol and ω-hydroxyfatty acids. The crystal structures of the apoenzyme, of the enzyme in complex with NAD(+) and in complex with NADH, solved up to 1.9 Å resolution, represent the first structures of a plant GSNOR. They confirm that the binding of the coenzyme is associated with the active site zinc movement and changes in its coordination. In comparison to the well characterized human GSNOR, plant GSNORs exhibit a difference in the composition of the anion-binding pocket, which negatively influences the affinity for the carboxyl group of ω-hydroxyfatty acids.
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Affiliation(s)
- Lucie Kubienová
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
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24
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Plapp BV, Ramaswamy S. Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes. Biochemistry 2012; 51:4035-48. [PMID: 22531044 DOI: 10.1021/bi300378n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structures of horse liver alcohol dehydrogenase complexed with NAD(+) and unreactive substrate analogues, 2,2,2-trifluoroethanol or 2,3,4,5,6-pentafluorobenzyl alcohol, were determined at 100 K at 1.12 or 1.14 Å resolution, providing estimates of atomic positions with overall errors of ~0.02 Å, the geometry of ligand binding, descriptions of alternative conformations of amino acid residues and waters, and evidence of a strained nicotinamide ring. The four independent subunits from the two homodimeric structures differ only slightly in the peptide backbone conformation. Alternative conformations for amino acid side chains were identified for 50 of the 748 residues in each complex, and Leu-57 and Leu-116 adopt different conformations to accommodate the different alcohols at the active site. Each fluoroalcohol occupies one position, and the fluorines of the alcohols are well-resolved. These structures closely resemble the expected Michaelis complexes with the pro-R hydrogens of the methylene carbons of the alcohols directed toward the re face of C4N of the nicotinamide rings with a C-C distance of 3.40 Å. The oxygens of the alcohols are ligated to the catalytic zinc at a distance expected for a zinc alkoxide (1.96 Å) and participate in a low-barrier hydrogen bond (2.52 Å) with the hydroxyl group of Ser-48 in a proton relay system. As determined by X-ray refinement with no restraints on bond distances and planarity, the nicotinamide rings in the two complexes are slightly puckered (quasi-boat conformation, with torsion angles of 5.9° for C4N and 4.8° for N1N relative to the plane of the other atoms) and have bond distances that are somewhat different compared to those found for NAD(P)(+). It appears that the nicotinamide ring is strained toward the transition state on the path to alcohol oxidation.
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Affiliation(s)
- Bryce V Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA.
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25
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Abdel-Azeim S, Li X, Chung LW, Morokuma K. Zinc-Homocysteine binding in cobalamin-dependent methionine synthase and its role in the substrate activation: DFT, ONIOM, and QM/MM molecular dynamics studies. J Comput Chem 2011; 32:3154-67. [DOI: 10.1002/jcc.21895] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2011] [Revised: 06/16/2011] [Accepted: 06/28/2011] [Indexed: 12/20/2022]
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26
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LI X, WANG C. Theoretical Study on the Mechanism of Ethanol Oxidation to Acetaldehyde Catalyzed by Liver Alcohol Dehydrogenase. CHINESE JOURNAL OF CATALYSIS 2010. [DOI: 10.3724/sp.j.1088.2010.00208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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27
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Superfamilies SDR and MDR: From early ancestry to present forms. Emergence of three lines, a Zn-metalloenzyme, and distinct variabilities. Biochem Biophys Res Commun 2010; 396:125-30. [DOI: 10.1016/j.bbrc.2010.03.094] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 03/16/2010] [Indexed: 11/19/2022]
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29
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Dołęga A, Pladzyk A, Baranowska K, Jezierska J. Biomimetic zinc(II) and cobalt(II) complexes with tri-tert-butoxysilanethiolate and imidazole ligands – Structural and spectroscopic studies. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2009.08.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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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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31
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Dołęga A, Baranowska K, Gudat D, Herman A, Stangret J, Konitz A, Śmiechowski M, Godlewska S. Modeling of the Alcohol Dehydrogenase Active Site: Two Different Modes of Alcohol Binding in Crystals of Zinc and Cadmium Tri-tert-butoxysilanethiolates Evidenced by X-ray Diffraction and Solid-State Vibrational Spectroscopy. Eur J Inorg Chem 2009. [DOI: 10.1002/ejic.200900106] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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32
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Limphong P, McKinney RM, Adams NE, Bennett B, Makaroff CA, Gunasekera T, Crowder MW. Human glyoxalase II contains an Fe(II)Zn(II) center but is active as a mononuclear Zn(II) enzyme. Biochemistry 2009; 48:5426-34. [PMID: 19413286 DOI: 10.1021/bi9001375] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human glyoxalase II (Glx2) was overexpressed in rich medium and in minimal medium containing zinc, iron, or cobalt, and the resulting Glx2 analogues were characterized using metal analyses, steady-state and pre-steady-state kinetics, and NMR and EPR spectroscopies to determine the nature of the metal center in the enzyme. Recombinant human Glx2 tightly binds nearly 1 equiv each of Zn(II) and Fe. In contrast to previous reports, this study demonstrates that an analogue containing 2 equiv of Zn(II) cannot be prepared. EPR studies suggest that most of the iron in recombinant Glx2 is Fe(II). NMR studies show that Fe(II) binds to the consensus Zn(2) site in Glx2 and that this site can also bind Co(II) and Ni(II), suggesting that Zn(II) binds to the consensus Zn(1) site. The NMR studies also reveal the presence of a dinuclear Co(II) center in Co(II)-substituted Glx2. Steady-state and pre-steady-state kinetic studies show that Glx2 containing only 1 equiv of Zn(II) is catalytically active and that the metal ion in the consensus Zn(2) site has little effect on catalytic activity. Taken together, these studies suggest that Glx2 contains a Fe(II)Zn(II) center in vivo but that the catalytic activity is due to Zn(II) in the Zn(1) site.
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Affiliation(s)
- Pattraranee Limphong
- Department of Chemistry and Biochemistry, 160 Hughes Hall, Miami University, Oxford, Ohio 45056, USA
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Active site dynamics in the zinc-dependent medium chain alcohol dehydrogenase superfamily. Proc Natl Acad Sci U S A 2009; 106:779-84. [PMID: 19131516 DOI: 10.1073/pnas.0807529106] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite being the subject of intensive investigations, many aspects of the mechanism of the zinc-dependent medium chain alcohol dehydrogenase (MDR) superfamily remain contentious. We have determined the high-resolution structures of a series of binary and ternary complexes of glucose dehydrogenase, an MDR enzyme from Haloferax mediterranei. In stark contrast to the textbook MDR mechanism in which the zinc ion is proposed to remain stationary and attached to a common set of protein ligands, analysis of these structures reveals that in each complex, there are dramatic differences in the nature of the zinc ligation. These changes arise as a direct consequence of linked movements of the zinc ion, a zinc-bound bound water molecule, and the substrate during progression through the reaction. These results provide evidence for the molecular basis of proton traffic during catalysis, a structural explanation for pentacoordinate zinc ion intermediates, a unifying view for the observed patterns of metal ligation in the MDR family, and highlight the importance of dynamic fluctuations at the metal center in changing the electrostatic potential in the active site, thereby influencing the proton traffic and hydride transfer events.
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Meijers R, Cedergren-Zeppezauer E. A variety of electrostatic interactions and adducts can activate NAD(P) cofactors for hydride transfer. Chem Biol Interact 2008; 178:24-8. [PMID: 19028476 DOI: 10.1016/j.cbi.2008.10.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Revised: 10/14/2008] [Accepted: 10/15/2008] [Indexed: 11/17/2022]
Abstract
In NAD(P)-dependent enzymes the coenzyme gives or takes a hydride ion, but how the nicotinamide ring is activated to form the transition state for hydride transfer is not clear. On the basis of ultra-high resolution X-ray crystal structures of liver alcohol dehydrogenase (LADH) in complex with NADH and a number of substrate analogues we proposed that the activation of NADH is an integral part of the enzyme mechanism of aldehyde reduction [R. Meijers, R.J. Morris, H.W. Adolph, A. Merli, V.S. Lamzin, E.S. Cedergren-Zeppezauer, On the enzymatic activation of NADH, The Journal of Biological Chemistry 276(12) (2001) 9316-9321, %U http://www.ncbi.nlm.nih.gov/pubmed/11134046; R. Meijers, H.-W. Adolph, Z. Dauter, K.S. Wilson, V.S. Lamzin, E.S. Cedergren-Zeppezauer, Structural evidence for a ligand coordination switch in liver alcohol dehydrogenase, Biochemistry 46(18) (2007) 5446-5454, %U http://www.ncbi.nlm.nih.gov/pubmed/17429946]. We observed a nicotinamide with a severely distorted pyridine ring and a water molecule in close proximity to the ring. Quantum chemical calculations indicated that (de)protonation of the water molecule can be directly coupled to activation of NADH for hydride transfer. A systematic search of the Protein Data Bank (PDB) for atoms that come within van der Waals distance of the pyridine ring of the nicotinamide reveals that a large number of NAD(P)-containing protein complexes are involved in electrostatic interactions with the enzymatic environment. Using the deposited diffraction data to analyze the cofactor and its surroundings, we observe several adducts between protein atoms and the pyridine ring that were not previously reported. This further indicates that the enzymatic activation of NAD(P) induced by electrostatic interactions is an essential part of the hydride transfer mechanism.
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Affiliation(s)
- Rob Meijers
- Synchrotron Soleil, L'Orme des Merisiers, Saint Aubin, France.
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Self-assembly of zinc and cobalt complexes mimicking active site of alcohol dehydrogenase. INORG CHEM COMMUN 2008. [DOI: 10.1016/j.inoche.2008.04.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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