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Fujino Y, Miyagawa T, Torii M, Inoue M, Fujii Y, Okanishi H, Kanai Y, Masui R. Structural changes induced by ligand binding drastically increase the thermostability of the Ser/Thr protein kinase TpkD from Thermus thermophilus HB8. FEBS Lett 2020; 595:264-274. [PMID: 33159808 DOI: 10.1002/1873-3468.13996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/26/2020] [Accepted: 11/02/2020] [Indexed: 11/06/2022]
Abstract
Thermophilic proteins maintain their structure at high temperatures through a combination of various factors. Here, we report the ligand-induced stabilization of a thermophilic Ser/Thr protein kinase. Thermus thermophilus TpkD unfolds completely at 55 °C despite the optimum growth temperature of 75 °C. Unexpectedly, we found that the TpkD structure is drastically stabilized by its natural ligands ATP and ADP, as evidenced by the increase in the melting temperature to 80 °C. Such a striking effect of a substrate on thermostability has not been reported for other protein kinases. Conformational changes upon ATP binding were observed in fluorescence quenching and limited proteolysis experiments. Urea denaturation of Trp mutants suggested that ATP binding affects not only the ATP-binding site, but also the remote regions. Our findings shed light on thermoadaptation of thermophilic proteins.
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Affiliation(s)
- Yusuke Fujino
- Graduate School of Science, Osaka City University, Japan
| | - Takero Miyagawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Masayuki Torii
- Graduate School of Science, Osaka City University, Japan
| | - Masao Inoue
- Graduate School of Agriculture, Kyoto University, Japan
| | - Yuki Fujii
- Graduate School of Science, Osaka City University, Japan
| | | | - Yoshikatsu Kanai
- Graduate School of Medicine, Osaka University, Suita, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University, Suita, Japan
| | - Ryoji Masui
- Graduate School of Science, Osaka City University, Japan
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Boreikaite V, Wicky BIM, Watt IN, Clarke J, Walker JE. Extrinsic conditions influence the self-association and structure of IF 1, the regulatory protein of mitochondrial ATP synthase. Proc Natl Acad Sci U S A 2019; 116:10354-10359. [PMID: 31064873 PMCID: PMC6535023 DOI: 10.1073/pnas.1903535116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The endogenous inhibitor of ATP synthase in mitochondria, called IF1, conserves cellular energy when the proton-motive force collapses by inhibiting ATP hydrolysis. Around neutrality, the 84-amino-acid bovine IF1 is thought to self-assemble into active dimers and, under alkaline conditions, into inactive tetramers and higher oligomers. Dimerization is mediated by formation of an antiparallel α-helical coiled-coil involving residues 44-84. The inhibitory region of each monomer from residues 1-46 is largely α-helical in crystals, but disordered in solution. The formation of the inhibited enzyme complex requires the hydrolysis of two ATP molecules, and in the complex the disordered region from residues 8-13 is extended and is followed by an α-helix from residues 14-18 and a longer α-helix from residue 21, which continues unbroken into the coiled-coil region. From residues 21-46, the long α-helix binds to other α-helices in the C-terminal region of predominantly one of the β-subunits in the most closed of the three catalytic interfaces. The definition of the factors that influence the self-association of IF1 is a key to understanding the regulation of its inhibitory properties. Therefore, we investigated the influence of pH and salt-types on the self-association of bovine IF1 and the folding of its unfolded region. We identified the equilibrium between dimers and tetramers as a potential central factor in the in vivo modulation of the inhibitory activity and suggest that the intrinsically disordered region makes its inhibitory potency exquisitely sensitive and responsive to physiological changes that influence the capability of mitochondria to make ATP.
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Affiliation(s)
- Vytaute Boreikaite
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, CB2 0XY Cambridge, United Kingdom
- The Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - Basile I M Wicky
- The Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - Ian N Watt
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, CB2 0XY Cambridge, United Kingdom
| | - Jane Clarke
- The Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - John E Walker
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, CB2 0XY Cambridge, United Kingdom;
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Christensen DG, Meyer JG, Baumgartner JT, D'Souza AK, Nelson WC, Payne SH, Kuhn ML, Schilling B, Wolfe AJ. Identification of Novel Protein Lysine Acetyltransferases in Escherichia coli. mBio 2018; 9:e01905-18. [PMID: 30352934 PMCID: PMC6199490 DOI: 10.1128/mbio.01905-18] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 09/18/2018] [Indexed: 12/31/2022] Open
Abstract
Posttranslational modifications, such as Nε-lysine acetylation, regulate protein function. Nε-lysine acetylation can occur either nonenzymatically or enzymatically. The nonenzymatic mechanism uses acetyl phosphate (AcP) or acetyl coenzyme A (AcCoA) as acetyl donor to modify an Nε-lysine residue of a protein. The enzymatic mechanism uses Nε-lysine acetyltransferases (KATs) to specifically transfer an acetyl group from AcCoA to Nε-lysine residues on proteins. To date, only one KAT (YfiQ, also known as Pka and PatZ) has been identified in Escherichia coli Here, we demonstrate the existence of 4 additional E. coli KATs: RimI, YiaC, YjaB, and PhnO. In a genetic background devoid of all known acetylation mechanisms (most notably AcP and YfiQ) and one deacetylase (CobB), overexpression of these putative KATs elicited unique patterns of protein acetylation. We mutated key active site residues and found that most of them eliminated enzymatic acetylation activity. We used mass spectrometry to identify and quantify the specificity of YfiQ and the four novel KATs. Surprisingly, our analysis revealed a high degree of substrate specificity. The overlap between KAT-dependent and AcP-dependent acetylation was extremely limited, supporting the hypothesis that these two acetylation mechanisms play distinct roles in the posttranslational modification of bacterial proteins. We further showed that these novel KATs are conserved across broad swaths of bacterial phylogeny. Finally, we determined that one of the novel KATs (YiaC) and the known KAT (YfiQ) can negatively regulate bacterial migration. Together, these results emphasize distinct and specific nonenzymatic and enzymatic protein acetylation mechanisms present in bacteria.IMPORTANCENε-Lysine acetylation is one of the most abundant and important posttranslational modifications across all domains of life. One of the best-studied effects of acetylation occurs in eukaryotes, where acetylation of histone tails activates gene transcription. Although bacteria do not have true histones, Nε-lysine acetylation is prevalent; however, the role of these modifications is mostly unknown. We constructed an E. coli strain that lacked both known acetylation mechanisms to identify four new Nε-lysine acetyltransferases (RimI, YiaC, YjaB, and PhnO). We used mass spectrometry to determine the substrate specificity of these acetyltransferases. Structural analysis of selected substrate proteins revealed site-specific preferences for enzymatic acetylation that had little overlap with the preferences of the previously reported acetyl-phosphate nonenzymatic acetylation mechanism. Finally, YiaC and YfiQ appear to regulate flagellum-based motility, a phenotype critical for pathogenesis of many organisms. These acetyltransferases are highly conserved and reveal deeper and more complex roles for bacterial posttranslational modification.
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Affiliation(s)
- David G Christensen
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, USA
| | - Jesse G Meyer
- Buck Institute for Research on Aging, Novato, California, USA
| | - Jackson T Baumgartner
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | | | - William C Nelson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Samuel H Payne
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | | | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, USA
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Gardner NW, McGinness SM, Panchal J, Topp EM, Park C. A Cooperative Folding Unit as the Structural Link for Energetic Coupling within a Protein. Biochemistry 2017; 56:6555-6564. [PMID: 29166011 DOI: 10.1021/acs.biochem.7b00850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Previously, we demonstrated that binding of a ligand to Escherichia coli cofactor-dependent phosphoglycerate mutase (dPGM), a homodimeric protein, is energetically coupled with dimerization. The equilibrium unfolding of dPGM occurs with a stable, monomeric intermediate. Binding of several nonsubstrate metabolites stabilizes the dimeric native form over the monomeric intermediate, reducing the population of the intermediate. Both the active site and the dimer interface appear to be unfolded in the intermediate. We hypothesized that a loop containing residues 118-152 was responsible for the energetic coupling between the dimer interface and the distal active site and was unfolded in the intermediate. Here, we investigated the structure of the dPGM intermediate by probing side-chain interactions and solvent accessibility of the peptide backbone. By comparing the effect of a mutation on the global stability and the stability of the intermediate, we determine an equilibrium φ value (φeq value), which provides information about whether side-chain interactions are retained or lost in the intermediate. Hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) was used to investigate differences in the solvent accessibility of the peptide backbone in the intermediate and native forms of dPGM. The results of φeq value analysis and HDX-MS reveal the least stable folding unit of dPGM, which is unfolded in the intermediate and links the active site to the dimer interface. The structure of the intermediate reveals how the cooperative network of residues in dPGM gives rise to the observed energetic coupling between dimerization and ligand binding.
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Affiliation(s)
- Nathan W Gardner
- Department of Medicinal Chemistry and Molecular Pharmacology, ‡Interdisciplinary Life Science Graduate Program, §Department of Industrial and Physical Pharmacy, and ∥Bindley Bioscience Center, Purdue University , West Lafayette, Indiana 47907, United States
| | - Sarah M McGinness
- Department of Medicinal Chemistry and Molecular Pharmacology, ‡Interdisciplinary Life Science Graduate Program, §Department of Industrial and Physical Pharmacy, and ∥Bindley Bioscience Center, Purdue University , West Lafayette, Indiana 47907, United States
| | - Jainik Panchal
- Department of Medicinal Chemistry and Molecular Pharmacology, ‡Interdisciplinary Life Science Graduate Program, §Department of Industrial and Physical Pharmacy, and ∥Bindley Bioscience Center, Purdue University , West Lafayette, Indiana 47907, United States
| | - Elizabeth M Topp
- Department of Medicinal Chemistry and Molecular Pharmacology, ‡Interdisciplinary Life Science Graduate Program, §Department of Industrial and Physical Pharmacy, and ∥Bindley Bioscience Center, Purdue University , West Lafayette, Indiana 47907, United States
| | - Chiwook Park
- Department of Medicinal Chemistry and Molecular Pharmacology, ‡Interdisciplinary Life Science Graduate Program, §Department of Industrial and Physical Pharmacy, and ∥Bindley Bioscience Center, Purdue University , West Lafayette, Indiana 47907, United States
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Liu YK, Lin TH, Liu PF. ATP alters protein folding and function of Escherichia coli uridine phosphorylase. Arch Biochem Biophys 2017; 634:11-20. [PMID: 28917600 DOI: 10.1016/j.abb.2017.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/06/2017] [Accepted: 09/11/2017] [Indexed: 01/07/2023]
Abstract
Uridine phosphorylase is one of the critical enzymes in the pyrimidine salvage pathway. Cells regenerate uridine for nucleotide metabolism by incorporating uracil with ribose-1-phosphate with this enzyme. Recent studies indicate that Escherichia coli uridine phosphorylase is destabilized in the presence of ATP. However, the mechanism underlying the destabilization process and its influence on uridine phosphorylase function remain to be established. Here, we comprehensively investigated the effects of ATP on protein folding and function of Escherichia coli uridine phosphorylase. Our results demonstrate that ATP apparently decreases the stability of uridine phosphorylase in a concentration-dependent manner. Additionally, simply increasing the level of ATP led to a reduction of enzymatic activity to complete inhibition. Further studies showed that uridine phosphorylase accumulates as a partially unfolded state in the presence of ATP. Moreover, ATP specifically accelerated the unfolding rate of uridine phosphorylase with no observable effects on the refolding process. Our preliminary findings suggest that ATP can alter the protein folding and function of enzymes via apparent destabilization. This mechanism may be significant for proteins functioning under conditions of high levels of ATP, such as cancer cell environments.
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Affiliation(s)
- Yi-Kai Liu
- Department of Food Science and Biotechnology, National Chung Hsing University, 145 Xingda Rd., South Dist., Taichung City 402, Taiwan, ROC
| | - Tzu-Hsuan Lin
- Department of Food Science and Biotechnology, National Chung Hsing University, 145 Xingda Rd., South Dist., Taichung City 402, Taiwan, ROC
| | - Pei-Fen Liu
- Department of Food Science and Biotechnology, National Chung Hsing University, 145 Xingda Rd., South Dist., Taichung City 402, Taiwan, ROC.
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