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Berndsen CE, Bell JK. The structural biology and dynamics of malate dehydrogenases. Essays Biochem 2024; 68:57-72. [PMID: 39113569 DOI: 10.1042/ebc20230082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 10/04/2024]
Abstract
Malate dehydrogenase (MDH) enzymes catalyze the reversible oxidoreduction of malate to oxaloacetate using NAD(P) as a cofactor. This reaction is vital for metabolism and the exchange of reducing equivalents between cellular compartments. There are more than 100 structures of MDH in the Protein Data Bank, representing species from archaea, bacteria, and eukaryotes. This conserved family of enzymes shares a common nucleotide-binding domain, substrate-binding domain, and subunits associate to form a dimeric or a tetrameric enzyme. Despite the variety of crystallization conditions and ligands in the experimental structures, the conformation and configuration of MDH are similar. The quaternary structure and active site dynamics account for most conformational differences in the experimental MDH structures. Oligomerization appears essential for activity despite each subunit having a structurally independent active site. There are two dynamic regions within the active site that influence substrate binding and possibly catalysis, with one of these regions adjoining the subunit interface. In this review, we introduce the reader to the general structural framework of MDH highlighting the conservation of certain features and pointing out unique differences that regulate MDH enzyme activity.
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Affiliation(s)
- Christopher E Berndsen
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, U.S.A
| | - Jessica K Bell
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, U.S.A
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2
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Li S, Wang N, Li X. Enhancement of poly‑γ‑L‑diaminobutanoic acid production in Bacillus pumilus by repeated pH shocks. Bioprocess Biosyst Eng 2024; 47:1547-1554. [PMID: 38904716 DOI: 10.1007/s00449-024-03050-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 06/17/2024] [Indexed: 06/22/2024]
Abstract
This study investigated the effect of pH on poly-γ-L-diaminobutanoic acid (γ-PAB) production by Bacillus pumilus in batch fermentation. In the natural fermentation where pH was not controlled, pH decreased from initial 7.0 to 3.0 in 18 h and γ-PAB production was 428.6 mg/L. In the pH-controlled fermentation, B. pumilus tended to proliferation at higher pH, while γ-PAB synthesis was favorable at lower pH, in which the optimal pH for γ-PAB production was 4.2, and γ-PAB yield reached 2284.5 mg/L. Adopting a pH shock strategy which lasted 9 h in the pre-fermentation phase, biomass (OD600) and γ-PAB yield of B. pumilus were obtained as 61.3 and 2794.6 mg/L, respectively, which were 10.8% and 22.4% higher than those in batch fermentation without pH shock. Subsequent fermentation of repeated pH shocks showed that a further higher productivity could be achieved, in which the final OD600 reached 65.1, and γ-PAB production reached as high as 3482.3 mg/L, which were increased by 6.2% and 17.1% compared with those in single pH shock, respectively. This study demonstrated that B. pumilus can synthesize more γ-PAB at suboptimal pH and provided a novel approach to regulate γ-PAB synthesis.
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Affiliation(s)
- Shu Li
- Marine College, Shandong University, Weihai, 264209, Shandong, China.
| | - Nan Wang
- Food and Drug Inspection, Testing Institute at Weihai, Weihai, 264210, Shandong, China
| | - Xiaoting Li
- Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, Shandong, China
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3
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Block MF, Delley CL, Keller LML, Stuehlinger TT, Weber-Ban E. Electrostatic interactions guide substrate recognition of the prokaryotic ubiquitin-like protein ligase PafA. Nat Commun 2023; 14:5266. [PMID: 37644028 PMCID: PMC10465538 DOI: 10.1038/s41467-023-40807-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Pupylation, a post-translational modification found in Mycobacterium tuberculosis and other Actinobacteria, involves the covalent attachment of prokaryotic ubiquitin-like protein (Pup) to lysines on target proteins by the ligase PafA (proteasome accessory factor A). Pupylated proteins, like ubiquitinated proteins in eukaryotes, are recruited for proteasomal degradation. Proteomic studies suggest that hundreds of potential pupylation targets are modified by the sole existing ligase PafA. This raises intriguing questions regarding the selectivity of this enzyme towards a diverse range of substrates. Here, we show that the availability of surface lysines alone is not sufficient for interaction between PafA and target proteins. By identifying the interacting residues at the pupylation site, we demonstrate that PafA recognizes authentic substrates via a structural recognition motif centered around exposed lysines. Through a combination of computational analysis, examination of available structures and pupylated proteomes, and biochemical experiments, we elucidate the mechanism by which PafA achieves recognition of a wide array of substrates while retaining selective protein turnover.
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Affiliation(s)
- Matthias F Block
- ETH Zurich, Institute of Molecular Biology & Biophysics, Zurich, Switzerland
| | - Cyrille L Delley
- ETH Zurich, Institute of Molecular Biology & Biophysics, Zurich, Switzerland
- University of California, San Francisco, USA
| | - Lena M L Keller
- ETH Zurich, Institute of Molecular Biology & Biophysics, Zurich, Switzerland
| | - Timo T Stuehlinger
- ETH Zurich, Institute of Molecular Biology & Biophysics, Zurich, Switzerland
| | - Eilika Weber-Ban
- ETH Zurich, Institute of Molecular Biology & Biophysics, Zurich, Switzerland.
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4
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Pathirage R, Favrot L, Petit C, Yamsek M, Singh S, Mallareddy JR, Rana S, Natarajan A, Ronning DR. Mycobacterium tuberculosis CitA activity is modulated by cysteine oxidation and pyruvate binding. RSC Med Chem 2023; 14:921-933. [PMID: 37252106 PMCID: PMC10211323 DOI: 10.1039/d3md00058c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 04/05/2023] [Indexed: 11/12/2023] Open
Abstract
As an adaptation for survival during infection, Mycobacterium tuberculosis becomes dormant, reducing its metabolism and growth. Two types of citrate synthases have been identified in Mycobacterium tuberculosis, GltA2 and CitA. Previous work shows that overexpression of CitA, the secondary citrate synthase, stimulates the growth of Mycobacterium tuberculosis under hypoxic conditions without showing accumulation of triacylglycerols and makes mycobacteria more sensitive to antibiotics, suggesting that CitA may play a role as a metabolic switch during infection and may be an interesting TB drug target. To assess the druggability and possible mechanisms of targeting CitA with small-molecule compounds, the CitA crystal structure was solved to 2.1 Å by X-ray crystallography. The solved structure shows that CitA lacks an NADH binding site that would afford allosteric regulation, which is atypical of most citrate synthases. However, a pyruvate molecule is observed within the analogous domain, suggesting pyruvate may instead be the allosteric regulator for CitA. The R149 and R153 residues forming the charged portion of the pyruvate binding pocket were mutated to glutamate and methionine, respectively, to assess the effect of mutations on activity. Protein thermal shift assay shows thermal stabilization of CitA in the presence of pyruvate compared to the two CitA variants designed to decrease pyruvate affinity. Solved crystal structures of both variants show no significant structural changes. However, the catalytic efficiency of the R153M variant increases by 2.6-fold. Additionally, we show that covalent modification of C143 of CitA by Ebselen completely arrests enzyme activity. Similar inhibition is observed using two spirocyclic Michael acceptor containing compounds, which inhibit CitA with ICapp50 values of 6.6 and 10.9 μM. A crystal structure of CitA modified by Ebselen was solved, but significant structural changes were lacking. Considering that covalent modification of C143 inactivates CitA and the proximity of C143 to the pyruvate binding site, this suggests that structural and/or chemical changes in this sub-domain are responsible for regulating CitA enzymatic activity.
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Affiliation(s)
- Rasangi Pathirage
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center Omaha NE 68198 USA
| | - Lorenza Favrot
- Department of Chemistry and Biochemistry, University of Toledo Toledo OH 43606 USA
| | - Cecile Petit
- Department of Chemistry and Biochemistry, University of Toledo Toledo OH 43606 USA
| | - Melvin Yamsek
- Department of Chemistry and Biochemistry, University of Toledo Toledo OH 43606 USA
| | - Sarbjit Singh
- Eppley Institute for Cancer Research, University of Nebraska Medical Center Omaha NE 68198 USA
| | | | - Sandeep Rana
- Eppley Institute for Cancer Research, University of Nebraska Medical Center Omaha NE 68198 USA
| | - Amarnath Natarajan
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center Omaha NE 68198 USA
- Eppley Institute for Cancer Research, University of Nebraska Medical Center Omaha NE 68198 USA
- Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center Omaha NE 68198 USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center Omaha NE USA
| | - Donald R Ronning
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center Omaha NE 68198 USA
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Wang T, Yin Y, Zhang J, Guan H, Xu J, Liu X. Extracellular vesicles as a strategy for cadmium secretion in bacteria SH225. CHEMOSPHERE 2023; 324:138373. [PMID: 36906001 DOI: 10.1016/j.chemosphere.2023.138373] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/17/2023] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
Cadmium (Cd), as one of the most carcinogenic substances, poses a great threat to human health. With the development of microbial remediation technology, the necessity for urgent research into the mechanism of Cd toxicity to bacteria has arisen. In this study, a highly Cd-tolerant strain (up to 225 mg/L) was isolated and purified from Cd-contaminated soil, which was identified by 16S rRNA as a strain of Stenotrophomonas sp., thus manually designated as SH225. By testing OD600 of the strain, we indicated that Cd concentrations below 100 mg/L had no discernible impact on the biomass of SH225. When the Cd concentration was over 100 mg/L, the cell growth was significantly inhibited, while the number of extracellular vesicles (EVs) was greatly elevated. After extraction, cell-secreted EVs were confirmed to contain large amounts of Cd cations, highlighting the crucial function of EVs in the Cd detoxification of SH225. Meanwhile, the TCA cycle was vastly enhanced, suggesting that the cells provided adequate energy supply for EVs transport. Thus, these findings emphasized the crucial role played by vesicles and TCA cycle in Cd detoxification.
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Affiliation(s)
- Tong Wang
- College of Environmental & Natural Resources, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Yiran Yin
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiawen Zhang
- College of Environmental & Natural Resources, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Haoran Guan
- College of Environmental & Natural Resources, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Jianming Xu
- College of Environmental & Natural Resources, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Xingmei Liu
- College of Environmental & Natural Resources, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China.
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Chen Y, Yang H, Shen Z, Ye J. Whole-Genome Sequencing and Potassium-Solubilizing Mechanism of Bacillus aryabhattai SK1-7. Front Microbiol 2022; 12:722379. [PMID: 35058888 PMCID: PMC8764406 DOI: 10.3389/fmicb.2021.722379] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 11/08/2021] [Indexed: 12/26/2022] Open
Abstract
To analyze the whole genome of Bacillus aryabhattai strain SK1-7 and explore its potassium solubilization characteristics and mechanism, thus providing a theoretical basis for analyzing the utilization and improvement of insoluble potassium resources in soil. Genome information for Bacillus aryabhattai SK1-7 was obtained by using Illumina NovaSeq second-generation sequencing and GridION Nanopore ONT third-generation sequencing technology. The contents of organic acids and polysaccharides in fermentation broth of Bacillus aryabhattai SK1-7 were determined by high-performance liquid chromatography and the anthrone sulfuric acid method, and the expression levels of the potassium solubilization-related genes ackA, epsB, gltA, mdh and ppc were compared by real-time fluorescence quantitative PCR under different potassium source culture conditions. The whole genome of the strain consisted of a complete chromosome sequence and four plasmid sequences. The sequence sizes of the chromosomes and plasmids P1, P2, P3 and P4 were 5,188,391 bp, 136,204 bp, 124,862 bp, 67,200 bp and 12,374 bp, respectively. The GC contents were 38.2, 34.4, 33.6, 32.8, and 33.7%. Strain SK1-7 mainly secreted malic, formic, acetic and citric acids under culture with an insoluble potassium source. The polysaccharide content produced with an insoluble potassium source was higher than that with a soluble potassium source. The expression levels of five potassium solubilization-related genes with the insoluble potassium source were higher than those with the soluble potassium source.
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Affiliation(s)
- Yifan Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Hui Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Zizhu Shen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Jianren Ye
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
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McCue W, Finzel BC. Structural Characterization of the Human Cytosolic Malate Dehydrogenase I. ACS OMEGA 2022; 7:207-214. [PMID: 35036692 PMCID: PMC8756447 DOI: 10.1021/acsomega.1c04385] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
The first crystal structure of the human cytosolic malate dehydrogenase I (MDH1) is described. Structure determination at a high resolution (1.65 Å) followed production, isolation, and purification of human MDH1 using a bacterial expression system. The structure is a binary complex of MDH1 with only a bound malonate molecule in the substrate binding site. Comparisons of this structure with malate dehydrogenase enzymes from other species confirm that the human enzyme adopts similar secondary, tertiary, and quaternary structures and that the enzyme retains a similar conformation even when nicotinamide adenine dinucleotide (NAD+) is not bound. A comparison to the highly homologous porcine (sus scrofa) MDH1 ternary structures leads to the conclusion that only small conformational differences are needed to accommodate binding by NAD+ or other NAD+ mimetics. Conformational differences observed in the second subunit show that the NAD+ binding elements are nevertheless quite flexible. Comparison of hMDH1 to the human mitochondrial malate dehydrogenase (hMDH2) reveals some key differences in the α7-α8 loop, which lies directly beneath the substrate binding pocket. These differences might be exploited in the structure-assisted design of selective small molecule inhibitors of hMDH1, an emerging target for the development of anticancer therapeutics.
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8
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Association of the malate dehydrogenase-citrate synthase metabolon is modulated by intermediates of the Krebs tricarboxylic acid cycle. Sci Rep 2021; 11:18770. [PMID: 34548590 PMCID: PMC8455617 DOI: 10.1038/s41598-021-98314-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/07/2021] [Indexed: 12/25/2022] Open
Abstract
Mitochondrial malate dehydrogenase (MDH)-citrate synthase (CS) multi-enzyme complex is a part of the Krebs tricarboxylic acid (TCA) cycle ‘metabolon’ which is enzyme machinery catalyzing sequential reactions without diffusion of reaction intermediates into a bulk matrix. This complex is assumed to be a dynamic structure involved in the regulation of the cycle by enhancing metabolic flux. Microscale Thermophoresis analysis of the porcine heart MDH-CS complex revealed that substrates of the MDH and CS reactions, NAD+ and acetyl-CoA, enhance complex association while products of the reactions, NADH and citrate, weaken the affinity of the complex. Oxaloacetate enhanced the interaction only when it was present together with acetyl-CoA. Structural modeling using published CS structures suggested that the binding of these substrates can stabilize the closed format of CS which favors the MDH-CS association. Two other TCA cycle intermediates, ATP, and low pH also enhanced the association of the complex. These results suggest that dynamic formation of the MDH-CS multi-enzyme complex is modulated by metabolic factors responding to respiratory metabolism, and it may function in the feedback regulation of the cycle and adjacent metabolic pathways.
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Park SH, Lee CW, Bae DW, Do H, Jeong CS, Hwang J, Cha SS, Lee JH. Structural basis of the cooperative activation of type II citrate synthase (HyCS) from Hymenobacter sp. PAMC 26554. Int J Biol Macromol 2021; 183:213-221. [PMID: 33910038 DOI: 10.1016/j.ijbiomac.2021.04.141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 12/01/2022]
Abstract
Citrate synthase (CS) catalyzes the formation of citrate and coenzyme A from acetyl-CoA and oxaloacetate. CS exists in two forms: type I and type II. We determined the citrate-bound crystal structure of type II CS from the Hymenobacter sp. PAMC 26554 bacterium (HyCS; isolated from Antarctic lichen). Citrate molecules bound to a cleft between the large and small domains of HyCS. Structural comparison of HyCS with other type II CSs revealed that type II CSs have a highly conserved flexible hinge region (residues G264-P265 in HyCS), enabling correct positioning of active site residues. Notably, the catalytic His266 residue of HyCS interacted with Trp262 in the inactive (unliganded open) state of other type II CSs, whereas the His266 residue moved to the active site via a small-domain swing motion, interacting with the bound citrate in the closed conformation of HyCS. However, type I CSs lack this tryptophan residue and face-to-edge interactions. Thus, type II CSs might have a unique domain-motion control mechanism enabling a tight allosteric regulation. An activity assay using a W262A mutant showed a Hill coefficient of 2.4; thus, the interaction between Trp262 and His266 was closely related to the positive cooperative ligand binding of type II CS.
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Affiliation(s)
- Sun-Ha Park
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Chang Woo Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Da-Woon Bae
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hackwon Do
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Chang-Sook Jeong
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Jisub Hwang
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Sun-Shin Cha
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea.
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10
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Targeting NAD-dependent dehydrogenases in drug discovery against infectious diseases and cancer. Biochem Soc Trans 2021; 48:693-707. [PMID: 32311017 DOI: 10.1042/bst20191261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/10/2020] [Accepted: 03/16/2020] [Indexed: 12/24/2022]
Abstract
Dehydrogenases are oxidoreductase enzymes that play a variety of fundamental functions in the living organisms and have primary roles in pathogen survival and infection processes as well as in cancer development. We review here a sub-set of NAD-dependent dehydrogenases involved in human diseases and the recent advancements in drug development targeting pathogen-associated NAD-dependent dehydrogenases. We focus also on the molecular aspects of the inhibition process listing the structures of the most relevant molecules targeting this enzyme family. Our aim is to review the most impacting findings regarding the discovery of novel inhibitory compounds targeting the selected NAD-dependent dehydrogenases involved in cancer and infectious diseases.
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11
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Ferrario E, Miggiano R, Rizzi M, Ferraris DM. Structure of Thermococcus litoralis Δ 1-pyrroline-2-carboxylate reductase in complex with NADH and L-proline. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:496-505. [PMID: 32355045 DOI: 10.1107/s2059798320004866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/05/2020] [Indexed: 11/10/2022]
Abstract
L-Hydroxyproline (L-Hyp) is a nonstandard amino acid that is present in certain proteins, in some antibiotics and in the cell-wall components of plants. L-Hyp is the product of the post-translational modification of protein prolines by prolyl hydroxylase enzymes, and the isomers trans-3-hydroxy-L-proline (T3LHyp) and trans-4-hydroxy-L-proline (T4LHyp) are major components of mammalian collagen. T4LHyp follows two distinct degradation pathways in bacteria and mammals, while T3LHyp is metabolized by a two-step metabolic pathway that is conserved in bacteria and mammals, which involves a T3LHyp dehydratase and a Δ1-pyrroline-2-carboxylate (Pyr2C) reductase. In order to shed light on the structure and catalysis of the enzyme involved in the second step of the T3LHyp degradation pathway, the crystal structure of Pyr2C reductase from the archaeon Thermococcus litoralis DSM 5473 complexed with NADH and L-proline is presented. The model allows the mapping of the residues involved in cofactor and product binding and represents a valid model for rationalizing the catalysis of Pyr2C reductases.
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Affiliation(s)
- Eugenio Ferrario
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Riccardo Miggiano
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Menico Rizzi
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Davide M Ferraris
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
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Miggiano R, Martignon S, Minassi A, Rossi F, Rizzi M. Crystal structure of Haemophilus influenzae 3-isopropylmalate dehydrogenase (LeuB) in complex with the inhibitor O-isobutenyl oxalylhydroxamate. Biochem Biophys Res Commun 2020; 524:996-1002. [DOI: 10.1016/j.bbrc.2020.02.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 02/04/2020] [Indexed: 11/25/2022]
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13
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Madani A, Ridenour JN, Martin BP, Paudel RR, Abdul Basir A, Le Moigne V, Herrmann JL, Audebert S, Camoin L, Kremer L, Spilling CD, Canaan S, Cavalier JF. Cyclipostins and Cyclophostin Analogues as Multitarget Inhibitors That Impair Growth of Mycobacterium abscessus. ACS Infect Dis 2019; 5:1597-1608. [PMID: 31299146 DOI: 10.1021/acsinfecdis.9b00172] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Twelve new Cyclophostin and Cyclipostins analogues (CyC19-30) were synthesized, thus extending our series to 38 CyCs. Their antibacterial activities were evaluated against four pathogenic mycobacteria (Mycobacterium abscessus, Mycobacterium marinum, Mycobacterium bovis BCG, and Mycobacterium tuberculosis) and two Gram negative bacteria. The CyCs displayed very low toxicity toward host cells and were only active against mycobacteria. Importantly, several CyCs were active against extracellular M. abscessus (CyC17/CyC18β/CyC25/CyC26) or intramacrophage residing mycobacteria (CyC7(α,β)/CyC8(α,β)) with minimal inhibitory concentrations (MIC50) values comparable to or better than those of amikacin or imipenem, respectively. An activity-based protein profiling combined with mass spectrometry allowed identification of the potential target enzymes of CyC17/CyC26, mostly being involved in lipid metabolism and/or in cell wall biosynthesis. Overall, these results strengthen the selective activity of the CyCs against mycobacteria, including the most drug-resistant M. abscessus, through the cumulative inhibition of a large number of Ser- and Cys-enzymes participating in key physiological processes.
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Affiliation(s)
- Abdeldjalil Madani
- Aix-Marseille Université, CNRS, LISM, Institut de Microbiologie de la Méditerranée, Marseille, France 13402 Cedex 20
| | - Jeremy N. Ridenour
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Benjamin P. Martin
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Rishi R. Paudel
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Anosha Abdul Basir
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Vincent Le Moigne
- APHP, GHU PIFO, Hôpital Raymond-Poincaré−Hôpital Ambroise-Paré, 92100 Boulogne-Billancourt, France
| | - Jean-Louis Herrmann
- APHP, GHU PIFO, Hôpital Raymond-Poincaré−Hôpital Ambroise-Paré, 92100 Boulogne-Billancourt, France
- 2I, UVSQ, INSERM UMR 1173, Université Paris-Saclay, 78035 Versailles, France
| | - Stéphane Audebert
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, 13273 Marseille Cedex 09, France
| | - Luc Camoin
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, 13273 Marseille Cedex 09, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, 34293 Montpellier, France
- IRIM, INSERM, 34293 Montpellier, France
| | - Christopher D. Spilling
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Stéphane Canaan
- Aix-Marseille Université, CNRS, LISM, Institut de Microbiologie de la Méditerranée, Marseille, France 13402 Cedex 20
| | - Jean-François Cavalier
- Aix-Marseille Université, CNRS, LISM, Institut de Microbiologie de la Méditerranée, Marseille, France 13402 Cedex 20
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14
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Rittershaus ESC, Baek SH, Krieger IV, Nelson SJ, Cheng YS, Nambi S, Baker RE, Leszyk JD, Shaffer SA, Sacchettini JC, Sassetti CM. A Lysine Acetyltransferase Contributes to the Metabolic Adaptation to Hypoxia in Mycobacterium tuberculosis. Cell Chem Biol 2018; 25:1495-1505.e3. [PMID: 30318462 PMCID: PMC6309504 DOI: 10.1016/j.chembiol.2018.09.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 05/14/2018] [Accepted: 09/12/2018] [Indexed: 01/07/2023]
Abstract
Upon inhibition of respiration, which occurs in hypoxic or nitric oxide-containing host microenvironments, Mycobacterium tuberculosis (Mtb) adopts a non-replicating "quiescent" state and becomes relatively unresponsive to antibiotic treatment. We used comprehensive mutant fitness analysis to identify regulatory and metabolic pathways that are essential for the survival of quiescent Mtb. This genetic study identified a protein acetyltransferase (Mt-Pat/Rv0998) that promoted survival and altered the flux of carbon from oxidative to reductive tricarboxylic acid (TCA) reactions. Reductive TCA requires malate dehydrogenase (MDH) and maintains the redox state of the NAD+/NADH pool. Genetic or chemical inhibition of MDH resulted in rapid cell death in both hypoxic cultures and in murine lung. These phenotypic data, in conjunction with significant structural differences between human and mycobacterial MDH enzymes that could be exploited for drug development, suggest a new strategy for eradicating quiescent bacteria.
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Affiliation(s)
- Emily S. C. Rittershaus
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School. Worcester, MA. 01650 USA
| | - Seung-Hun Baek
- Department of Microbiology, Yonsei University College of Medicine, Seoul Korea
| | - Inna V. Krieger
- Department of Biochemistry and Biophysics. Texas A&M University. College Station, TX. 77843 USA
| | - Samantha J. Nelson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School. Worcester, MA. 01650 USA
| | - Yu-Shan Cheng
- Department of Biochemistry and Biophysics. Texas A&M University. College Station, TX. 77843 USA
| | - Subhalaxmi Nambi
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School. Worcester, MA. 01650 USA
| | - Richard E. Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School. Worcester, MA. 01650 USA
| | - John D. Leszyk
- Proteomics and Mass Spectrometry Facility, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA. 01650 USA
| | - Scott A. Shaffer
- Proteomics and Mass Spectrometry Facility, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA. 01650 USA
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics. Texas A&M University. College Station, TX. 77843 USA
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School. Worcester, MA. 01650 USA
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15
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Brininger C, Spradlin S, Cobani L, Evilia C. The more adaptive to change, the more likely you are to survive: Protein adaptation in extremophiles. Semin Cell Dev Biol 2018; 84:158-169. [PMID: 29288800 DOI: 10.1016/j.semcdb.2017.12.016] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 12/25/2017] [Accepted: 12/25/2017] [Indexed: 12/22/2022]
Abstract
Discovering how organisms and their proteins adapt to extreme conditions is a complicated process. Every condition has its own set of adaptations that make it uniquely stable in its environment. The purpose of our review is to discuss what is known in the extremophilic community about protein adaptations. To simplify our mission, we broke the extremophiles into three broad categories: thermophiles, halophiles and psychrophiles. While there are crossover organisms- organisms that exist in two or more extremes, like heat plus acid or cold plus pressure, most of them have a primary adaptation that is within one of these categories which tends to be the most easily identifiable one. While the generally known adaptations are still accepted, like thermophilic proteins have increased ionic interactions and a hardier hydrophobic core, halophilic proteins have a large increase in acidic amino acids and amino acid/peptide insertions and psychrophiles have a much more open structure and reduced ionic interactions, some new information has come to light. Thermophilic stability can be improved by increased subunit-subunit or subunit-cofactor interactions. Halophilic proteins have reversible folding when in the presence of salt. Psychrophilic proteins have an increase in cavities that not only decrease the formation of ice, but also increase flexibility under low temperature conditions. In a proof of concept experiment, we applied what is currently known about adaptations to a well characterized protein, malate dehydrogenase (MDH). While this protein has been profiled in the literature, we are applying our adaptation predictions to its sequence and structure to see if the described adaptations apply. Our analysis demonstrates that thermophilic and halophilic adaptations fit the corresponding MDHs very well. However, because the number of psychrophiles MDH sequences and structures is low, our analysis on psychrophiles is inconclusive and needs more information. By discussing known extremophilic adaptations and applying them to a random, conserved protein, we have found that general adaptations are conserved and can be predicted in proposed extremophilic proteins. The present field of extremophile adaptations is discovering more and more ways organisms and their proteins have adapted. The more that is learned about protein adaptation, the closer we get to custom proteins, designed to fit any extreme and solve some of the world's most pressing environmental problems.
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Affiliation(s)
- C Brininger
- Department of Chemistry, Idaho State University, Pocatello, ID 83209, USA
| | - S Spradlin
- Department of Chemistry, Idaho State University, Pocatello, ID 83209, USA
| | - L Cobani
- Department of Chemistry, Idaho State University, Pocatello, ID 83209, USA
| | - C Evilia
- Department of Chemistry, Idaho State University, Pocatello, ID 83209, USA.
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16
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Ferraris DM, Miggiano R, Rossi F, Rizzi M. Mycobacterium tuberculosis Molecular Determinants of Infection, Survival Strategies, and Vulnerable Targets. Pathogens 2018; 7:E17. [PMID: 29389854 PMCID: PMC5874743 DOI: 10.3390/pathogens7010017] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/26/2018] [Accepted: 01/28/2018] [Indexed: 12/13/2022] Open
Abstract
Mycobacterium tuberculosis is the causative agent of tuberculosis, an ancient disease which, still today, represents a major threat for the world population. Despite the advances in medicine and the development of effective antitubercular drugs, the cure of tuberculosis involves prolonged therapies which complicate the compliance and monitoring of drug administration and treatment. Moreover, the only available antitubercular vaccine fails to provide an effective shield against adult lung tuberculosis, which is the most prevalent form. Hence, there is a pressing need for effective antitubercular drugs and vaccines. This review highlights recent advances in the study of selected M. tuberculosis key molecular determinants of infection and vulnerable targets whose structures could be exploited for the development of new antitubercular agents.
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Affiliation(s)
- Davide M Ferraris
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale "A. Avogadro", Largo Donegani 2, 28100 Novara, Italy.
| | - Riccardo Miggiano
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale "A. Avogadro", Largo Donegani 2, 28100 Novara, Italy.
| | - Franca Rossi
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale "A. Avogadro", Largo Donegani 2, 28100 Novara, Italy.
| | - Menico Rizzi
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale "A. Avogadro", Largo Donegani 2, 28100 Novara, Italy.
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17
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Ghiraldi-Lopes LD, Campanerut-Sá PAZ, Meneguello JE, Seixas FAV, Lopes-Ortiz MA, Scodro RBL, Pires CTA, da Silva RZ, Siqueira VLD, Nakamura CV, Cardoso RF. Proteomic profile of Mycobacterium tuberculosis after eupomatenoid-5 induction reveals potential drug targets. Future Microbiol 2017; 12:867-879. [DOI: 10.2217/fmb-2017-0023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: We investigated a proteome profile, protein–protein interaction and morphological changes of Mycobacterium tuberculosis after different times of eupomatenoid-5 (EUP-5) induction to evaluate the cellular response to the drug-induced damages. Methods: The bacillus was induced to sub-minimal inhibitory concentration of EUP-5 at 12 h, 24 h and 48 h. The proteins were separated by 2D gel electrophoresis, identified by LC/MS-MS. Scanning electron microscopy and Search Tool for the Retrieval of Interacting Genes/Proteins analyses were performed. Results: EUP-5 impacts mainly in M. tuberculosis proteins of intermediary metabolism and interactome suggests a multisite disturbance that contributes to bacilli death. Scanning electron microscopy revealed the loss of bacillary form. Conclusion: Some of the differentially expressed proteins have the potential to be drug targets such as citrate synthase (Rv0896), phosphoglycerate kinase (Rv1437), ketol-acid reductoisomerase (Rv3001c) and ATP synthase alpha chain (Rv1308).
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Affiliation(s)
- Luciana D Ghiraldi-Lopes
- Postgraduate Program in Health Sciences, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
- Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Paula AZ Campanerut-Sá
- Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Jean E Meneguello
- Postgraduate Program in Biosciences & Phisiopatology, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Flávio AV Seixas
- Department of Biochemistry, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Mariana A Lopes-Ortiz
- Postgraduate Program in Biosciences & Phisiopatology, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
- Uningá University Center, Rod PR 317, 6114, 87035-510, Maringá, Paraná, Brazil
| | - Regiane BL Scodro
- Postgraduate Program in Health Sciences, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
- Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Claudia TA Pires
- Postgraduate Program in Biosciences & Phisiopatology, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Rosi Z da Silva
- State University of Ponta Grossa, Avenida General Carlos Cavalcanti, 4748, 84030-900, Ponta Grossa, Paraná, Brazil
| | - Vera LD Siqueira
- Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
- Postgraduate Program in Biosciences & Phisiopatology, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Celso V Nakamura
- Postgraduate Program in Pharmaceutical Sciences, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Rosilene F Cardoso
- Postgraduate Program in Health Sciences, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
- Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
- Postgraduate Program in Biosciences & Phisiopatology, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
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18
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Kanamori E, Kawaguchi SI, Kuramitsu S, Kouyama T, Murakami M. Structural comparison between the open and closed forms of citrate synthase from Thermus thermophilus HB8. Biophys Physicobiol 2015; 12:47-56. [PMID: 27493854 PMCID: PMC4736845 DOI: 10.2142/biophysico.12.0_47] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/16/2015] [Indexed: 12/01/2022] Open
Abstract
The crystal structures of citrate synthase from the thermophilic eubacteria Thermus thermophilus HB8 (TtCS) were determined for an open form at 1.5 Å resolution and for closed form at 2.3 Å resolution, respectively. In the absence of ligands TtCS in the open form was crystalized into a tetragonal form with a single subunit in the asymmetric unit. TtCS was also co-crystallized with citrate and coenzyme-A to form an orthorhombic crystal with two homodimers in the asymmetric unit. Citrate and CoA are found in the active site situated between the large domain and the small domain in all subunit whereas the complex shows two distinct closed conformations, the fully closed form and partially closed form. Structural comparisons are performed to describe conformational changes associated with binding of products of TtCS. Upon binding of citrate, basic residues in the active site move toward citrate and make a hydrogen bond network in the active site, inducing a large-scale rotation of the small domain relative to the large domain. CoA is sandwiched between the small and large domains and then the cysteamine tail is inserted into the active site with a cooperative rotation around mainchain dihedrals in the hinge region connecting helices M and N. According to this rotation these helices are extended to close the active site completely. The considerable flexibility and structural rearrangements in the hinge region are crucial for an ordered bibi reaction in catalysis for microbial CSs.
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Affiliation(s)
- Eiji Kanamori
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Shin-Ichi Kawaguchi
- Graduate School Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Seiki Kuramitsu
- Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Tsutomu Kouyama
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Midori Murakami
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
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19
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Singhal A, Arora G, Virmani R, Kundu P, Khanna T, Sajid A, Misra R, Joshi J, Yadav V, Samanta S, Saini N, Pandey AK, Visweswariah SS, Hentschker C, Becher D, Gerth U, Singh Y. Systematic Analysis of Mycobacterial Acylation Reveals First Example of Acylation-mediated Regulation of Enzyme Activity of a Bacterial Phosphatase. J Biol Chem 2015; 290:26218-34. [PMID: 26350458 DOI: 10.1074/jbc.m115.687269] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Indexed: 02/02/2023] Open
Abstract
Protein lysine acetylation is known to regulate multiple aspects of bacterial metabolism. However, its presence in mycobacterial signal transduction and virulence-associated proteins has not been studied. In this study, analysis of mycobacterial proteins from different cellular fractions indicated dynamic and widespread occurrence of lysine acetylation. Mycobacterium tuberculosis proteins regulating diverse physiological processes were then selected and expressed in the surrogate host Mycobacterium smegmatis. The purified proteins were analyzed for the presence of lysine acetylation, leading to the identification of 24 acetylated proteins. In addition, novel lysine succinylation and propionylation events were found to co-occur with acetylation on several proteins. Protein-tyrosine phosphatase B (PtpB), a secretory phosphatase that regulates phosphorylation of host proteins and plays a critical role in Mycobacterium infection, is modified by acetylation and succinylation at Lys-224. This residue is situated in a lid region that covers the enzyme's active site. Consequently, acetylation and succinylation negatively regulate the activity of PtpB.
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Affiliation(s)
- Anshika Singhal
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Gunjan Arora
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India, the Translational Health Science and Technology Institute, Faridabad 121001, India
| | - Richa Virmani
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Parijat Kundu
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Tanya Khanna
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Andaleeb Sajid
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Richa Misra
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Jayadev Joshi
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Vikas Yadav
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Sintu Samanta
- the Indian Institute of Science, Bangalore 560012, India, and
| | - Neeru Saini
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Amit K Pandey
- the Translational Health Science and Technology Institute, Faridabad 121001, India,
| | | | - Christian Hentschker
- the Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, D-17487 Greifswald, Germany
| | - Dörte Becher
- the Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, D-17487 Greifswald, Germany
| | - Ulf Gerth
- the Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, D-17487 Greifswald, Germany
| | - Yogendra Singh
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India,
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