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Maqsood A, Shakir NA, Aslam M, Rahman M, Rashid N. Structural and functional investigations of Pcal_0606, a bifunctional phosphoglucose/phosphomannose isomerase from Pyrobaculum calidifontis. Int J Biol Macromol 2024; 279:135127. [PMID: 39208883 DOI: 10.1016/j.ijbiomac.2024.135127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 08/26/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
We are investigating the glycolytic pathway in Pyrobaculum calidifontis whose genome sequence contains homologues of all the enzymes involved in this pathway. We have characterized most of them. An open reading frame, Pcal_0606, annotated as a putative phosphoglucose/phosphomannose isomerase has to be characterized yet. In silico analysis indicated the presence of more than one substrate binding pockets at the dimeric interface of Pcal_0606. The gene encoding Pcal_0606 was cloned and expressed in Escherichia coli. Recombinant Pcal_0606, produced in soluble form, exhibited highest enzyme activity at 90 °C and pH 8.5. Presence or absence of metal ions or EDTA did not significantly affect the enzyme activity. Under optimal conditions, Pcal_0606 displayed apparent Km values of 0.33, 0.34, and 0.29 mM against glucose 6-phosphate, mannose 6-phosphate and fructose 6-phosphate, respectively. In the same order, Vmax values against these substrates were 290, 235, and 240 μmol min-1 mg-1, indicating that Pcal_0606 catalyzed the reversible isomerization of these substrates with nearly same catalytic efficiency. These results characterize Pcal_0606 a bifunctional phosphoglucose/phosphomannose isomerase, which displayed high thermostability with a half-life of ∼50 min at 100 °C. To the best of our knowledge, Pcal_0606 is the most active and thermostable bifunctional phosphoglucose/phosphomannose isomerase characterized to date.
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Affiliation(s)
- Amina Maqsood
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Nisar Ahmed Shakir
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Mehwish Aslam
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Moazur Rahman
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan.
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2
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Boteva E, Doychev K, Kirilov K, Handzhiyski Y, Tsekovska R, Gatev E, Mironova R. Deglycation activity of the Escherichia coli glycolytic enzyme phosphoglucose isomerase. Int J Biol Macromol 2024; 257:128541. [PMID: 38056730 DOI: 10.1016/j.ijbiomac.2023.128541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/24/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023]
Abstract
Glycation is a spontaneous chemical reaction, which affects the structure and function of proteins under normal physiological conditions. Therefore, organisms have evolved diverse mechanisms to combat glycation. In this study, we show that the Escherichia coli glycolytic enzyme phosphoglucose isomerase (Pgi) exhibits deglycation activity. We found that E. coli Pgi catalyzes the breakdown of glucose 6-phosphate (G6P)-derived Amadori products (APs) in chicken lysozyme. The affinity of Pgi to the glycated lysozyme (Km, 1.1 mM) was ten times lower than the affinity to its native substrate, fructose 6-phosphate (Km, 0.1 mM). However, the high kinetic constants of the enzyme with the glycated lysozyme (kcat, 396 s-1 and kcat/Km, 3.6 × 105 M-1 s-1) indicated that the Pgi amadoriase activity may have physiological implications. Indeed, when using total E. coli protein (20 mg/mL) as a substrate in the deglycation reaction, we observed a release of G6P from the bacterial protein at a Pgi specific activity of 33 μmol/min/mg. Further, we detected 11.4 % lower APs concentration in protein extracts from Pgi-proficient vs. deficient cells (p = 0.0006) under conditions where the G6P concentration in Pgi-proficient cells was four times higher than in Pgi-deficient cells (p = 0.0001). Altogether, these data point to physiological relevance of the Pgi deglycation activity.
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Affiliation(s)
- Elitsa Boteva
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Konstantin Doychev
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Kiril Kirilov
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Yordan Handzhiyski
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Rositsa Tsekovska
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Evan Gatev
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Roumyana Mironova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria.
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3
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Jiao J, Gao F, Liu J, Lv Z, Liu C. A structural basis for the functional differences between the cytosolic and plastid phosphoglucose isomerase isozymes. PLoS One 2022; 17:e0272647. [PMID: 36048814 PMCID: PMC9436075 DOI: 10.1371/journal.pone.0272647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/22/2022] [Indexed: 11/23/2022] Open
Abstract
Phosphoglucose isomerase (PGI) catalyzes the interconversion between glucose-6-phosphate (G6P) and fructose-6-phosphate (F6P), thereby regulating sucrose synthesis in plant cells. In general, plants contain a pair of PGI isozymes located in two distinct compartments of the cell (cytosol and plastid) with differences in both the primary structure and the higher-order structure. Previously, we showed that the activity of cytosolic PGI (PGIc) is more robust (activity, thermal stability, substrate turnover rate, etc.) than that of the plastid counterpart (PGIp) in multiple organisms, including wheat, rice, and Arabidopsis. The crystal structures of apoTaPGIc (an isotype cytosol PGIc in Triticum aestivum), TaPGIc-G6P complex, and apoTaPGIp (an isotype plastid PGIp in Triticum aestivum) were first solved in higher plants, especially in crops. In this study, we detailed the structural characteristics related to the biochemical properties and functions of TaPGIs in different plant organelles. We found that the C-terminal domains (CTDs) of TaPGIc and TaPGIp are very different, which affects the stability of the dimerized enzyme, and that Lys213TaPGIc/Lys193TaPGIp and its surrounding residues at the binding pocket gateway may participate in the entrance and exit of substrates. Our findings provide a good example illuminating the evolution of proteins from primary to higher structures as a result of physical barriers and adaptation to the biochemical environment.
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Affiliation(s)
- Juan Jiao
- Department of Clinical Laboratory, 7th Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Fei Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Beijing, China
- Department of Research and development, Beijing IPE Center for Clinical Laboratory CO., Ltd, Beijing, China
- * E-mail: (FG); (CL); (ZL)
| | - Jie Liu
- Department of Clinical Laboratory, 7th Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zongyang Lv
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
- * E-mail: (FG); (CL); (ZL)
| | - Cuimin Liu
- Department of Clinical Laboratory, 7th Medical Center of Chinese PLA General Hospital, Beijing, China
- * E-mail: (FG); (CL); (ZL)
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4
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Zhou Y, Yan K, Qin Q, Raimi OG, Du C, Wang B, Ahamefule CS, Kowalski B, Jin C, van Aalten DMF, Fang W. Phosphoglucose Isomerase Is Important for Aspergillus fumigatus Cell Wall Biogenesis. mBio 2022; 13:e0142622. [PMID: 35913157 PMCID: PMC9426556 DOI: 10.1128/mbio.01426-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aspergillus fumigatus is a devastating opportunistic fungal pathogen causing hundreds of thousands of deaths every year. Phosphoglucose isomerase (PGI) is a glycolytic enzyme that converts glucose-6-phosphate to fructose-6-phosphate, a key precursor of fungal cell wall biosynthesis. Here, we demonstrate that the growth of A. fumigatus is repressed by the deletion of pgi, which can be rescued by glucose and fructose supplementation in a 1:10 ratio. Even under these optimized growth conditions, the Δpgi mutant exhibits severe cell wall defects, retarded development, and attenuated virulence in Caenorhabditis elegans and Galleria mellonella infection models. To facilitate exploitation of A. fumigatus PGI as an antifungal target, we determined its crystal structure, revealing potential avenues for developing inhibitors, which could potentially be used as adjunctive therapy in combination with other systemic antifungals. IMPORTANCE Aspergillus fumigatus is an opportunistic fungal pathogen causing deadly infections in immunocompromised patients. Enzymes essential for fungal survival and cell wall biosynthesis are considered potential drug targets against A. fumigatus. PGI catalyzes the second step of the glycolysis pathway, linking glycolysis and the pentose phosphate pathway. As such, PGI has been widely considered as a target for metabolic regulation and therefore a therapeutic target against hypoxia-related diseases. Our study here reveals that PGI is important for A. fumigatus survival and exhibit pleiotropic functions, including development, cell wall glucan biosynthesis, and virulence. We also solved the crystal structure of PGI, thus providing the genetic and structural groundwork for the exploitation of PGI as a potential antifungal target.
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Affiliation(s)
- Yao Zhou
- Guangxi Biological Sciences and Biotechnology Center, Guangxi Academy of Sciencesgrid.418329.5, Nanning, Guangxi, China
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Kaizhou Yan
- School of Life Sciences, University of Dundeegrid.8241.f, Dundee, United Kingdom
| | - Qijian Qin
- Guangxi Biological Sciences and Biotechnology Center, Guangxi Academy of Sciencesgrid.418329.5, Nanning, Guangxi, China
| | - Olawale G. Raimi
- School of Life Sciences, University of Dundeegrid.8241.f, Dundee, United Kingdom
| | - Chao Du
- Guangxi Biological Sciences and Biotechnology Center, Guangxi Academy of Sciencesgrid.418329.5, Nanning, Guangxi, China
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Bin Wang
- Guangxi Biological Sciences and Biotechnology Center, Guangxi Academy of Sciencesgrid.418329.5, Nanning, Guangxi, China
| | - Chukwuemeka Samson Ahamefule
- Guangxi Biological Sciences and Biotechnology Center, Guangxi Academy of Sciencesgrid.418329.5, Nanning, Guangxi, China
| | - Bartosz Kowalski
- School of Life Sciences, University of Dundeegrid.8241.f, Dundee, United Kingdom
| | - Cheng Jin
- Guangxi Biological Sciences and Biotechnology Center, Guangxi Academy of Sciencesgrid.418329.5, Nanning, Guangxi, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | | | - Wenxia Fang
- Guangxi Biological Sciences and Biotechnology Center, Guangxi Academy of Sciencesgrid.418329.5, Nanning, Guangxi, China
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
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5
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Iyengar SM, Barnsley KK, Xu R, Prystupa A, Ondrechen MJ. Electrostatic fingerprints of catalytically active amino acids in enzymes. Protein Sci 2022; 31:e4291. [PMID: 35481659 PMCID: PMC8994506 DOI: 10.1002/pro.4291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/14/2022] [Accepted: 02/22/2022] [Indexed: 11/06/2022]
Abstract
The computed electrostatic and proton transfer properties are studied for 20 enzymes that represent all six major enzyme commission classes and a variety of different folds. The properties of aspartate, glutamate, and lysine residues that have been previously experimentally determined to be catalytically active are reported. The catalytic aspartate and glutamate residues studied here are strongly coupled to at least one other aspartate or glutamate residue and often to multiple other carboxylate residues with intrinsic pKa differences less than 1 pH unit. Sometimes these catalytic acidic residues are also coupled to a histidine residue, such that the intrinsic pKa of the acidic residue is higher than that of the histidine. All catalytic lysine residues studied here are strongly coupled to tyrosine or cysteine residues, wherein the intrinsic pKa of the anion-forming residue is higher than that of the lysine. Some catalytic lysines are also coupled to other lysines with intrinsic pKa differences within 1 pH unit. Some evidence of the possible types of interactions that facilitate nucleophilicity is discussed. The interactions reported here provide important clues about how side chain functional groups that are weak Brønsted acids or bases for the free amino acid in solution can achieve catalytic potency and become strong acids, bases or nucleophiles in the enzymatic environment.
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Affiliation(s)
- Suhasini M. Iyengar
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | - Kelly K. Barnsley
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | - Rholee Xu
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | - Aleksandr Prystupa
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | - Mary Jo Ondrechen
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
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6
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Meek RW, Cadby IT, Lovering AL. Bdellovibrio bacteriovorus phosphoglucose isomerase structures reveal novel rigidity in the active site of a selected subset of enzymes upon substrate binding. Open Biol 2021; 11:210098. [PMID: 34375548 PMCID: PMC8354745 DOI: 10.1098/rsob.210098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Glycolysis and gluconeogenesis are central pathways of metabolism across all domains of life. A prominent enzyme in these pathways is phosphoglucose isomerase (PGI), which mediates the interconversion of glucose-6-phosphate and fructose-6-phosphate. The predatory bacterium Bdellovibrio bacteriovorus leads a complex life cycle, switching between intraperiplasmic replicative and extracellular 'hunter' attack-phase stages. Passage through this complex life cycle involves different metabolic states. Here we present the unliganded and substrate-bound structures of the B. bacteriovorus PGI, solved to 1.74 Å and 1.67 Å, respectively. These structures reveal that an induced-fit conformational change within the active site is not a prerequisite for the binding of substrates in some PGIs. Crucially, we suggest a phenylalanine residue, conserved across most PGI enzymes but substituted for glycine in B. bacteriovorus and other select organisms, is central to the induced-fit mode of substrate recognition for PGIs. This enzyme also represents the smallest conventional PGI characterized to date and probably represents the minimal requirements for a functional PGI.
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Affiliation(s)
- R W Meek
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - I T Cadby
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - A L Lovering
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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7
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Gao F, Zhang H, Zhang W, Wang N, Zhang S, Chu C, Liu C. Engineering of the cytosolic form of phosphoglucose isomerase into chloroplasts improves plant photosynthesis and biomass. THE NEW PHYTOLOGIST 2021; 231:315-325. [PMID: 33774822 DOI: 10.1111/nph.17368] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/20/2021] [Indexed: 06/12/2023]
Abstract
Starch is the most abundant carbohydrate synthesized in plant chloroplast as the product of photosynthetic carbon assimilation, serving a crucial role in the carbon budget as storage energy. Phosphoglucose isomerase (PGI) catalyzes the interconversion between glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P), which are important metabolic molecules in starch synthesis within chloroplasts and sucrose synthesis in cytosol. Here, we found that the specific activity of recombinantly purified PGI localized in cytosolic PGI (PGIc) was much higher than its plastidic isoenzyme counterpart (PGIp) originated from wheat, rice and Arabidopsis, with wheat PGIc having by far the highest activity. Crystal structures of wheat TaPGIc and TaPGIp proteins were solved and the functional units were homodimers. The active sites of PGIc and PGIp, constituted by the same amino acids, formed different binding pockets. Moreover, PGIc showed slightly lower affinity to the substrate F6P but with much faster turnover rates. Engineering of TaPGIc into chloroplasts of a pgip mutant of Arabidopsis thaliana (atpgip) resulted in starch overaccumulation, increased CO2 assimilation, up to 19% more plant biomass and 27% seed yield productivity. These results show that manipulating starch metabolic pathways in chloroplasts can improve plant biomass and yield productivity.
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Affiliation(s)
- Fei Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Huijun Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenjuan Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Ning Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Shijia Zhang
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Chengcai Chu
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cuimin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100101, China
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8
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Coulther TA, Ko J, Ondrechen MJ. Amino acid interactions that facilitate enzyme catalysis. J Chem Phys 2021; 154:195101. [PMID: 34240918 DOI: 10.1063/5.0041156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Interactions in enzymes between catalytic and neighboring amino acids and how these interactions facilitate catalysis are examined. In examples from both natural and designed enzymes, it is shown that increases in catalytic rates may be achieved through elongation of the buffer range of the catalytic residues; such perturbations in the protonation equilibria are, in turn, achieved through enhanced coupling of the protonation equilibria of the active ionizable residues with those of other ionizable residues. The strongest coupling between protonation states for a pair of residues that deprotonate to form an anion (or a pair that accept a proton to form a cation) is achieved when the difference in the intrinsic pKas of the two residues is approximately within 1 pH unit. Thus, catalytic aspartates and glutamates are often coupled to nearby acidic residues. For an anion-forming residue coupled to a cation-forming residue, the elongated buffer range is achieved when the intrinsic pKa of the anion-forming residue is higher than the intrinsic pKa of the (conjugate acid of the) cation-forming residue. Therefore, the high pKa, anion-forming residues tyrosine and cysteine make good coupling partners for catalytic lysine residues. For the anion-cation pairs, the optimum difference in intrinsic pKas is a function of the energy of interaction between the residues. For the energy of interaction ε expressed in units of (ln 10)RT, the optimum difference in intrinsic pKas is within ∼1 pH unit of ε.
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Affiliation(s)
- Timothy A Coulther
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Jaeju Ko
- Department of Chemistry, Indiana University of Pennsylvania, Indiana, Pennsylvania 15705, USA
| | - Mary Jo Ondrechen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
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9
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Phosphate sugar isomerases and their potential for rare sugar bioconversion. J Microbiol 2020; 58:725-733. [PMID: 32583284 DOI: 10.1007/s12275-020-0226-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 10/23/2022]
Abstract
Phosphate sugar isomerases, catalyzing the isomerization between ketopentose/ketohexose phosphate and aldopentose/aldohexose phosphate, play an important role in microbial sugar metabolism. They are present in a wide range of microorganisms. They have attracted increasing research interest because of their broad substrate specificity and great potential in the enzymatic production of various rare sugars. Here, the enzymatic properties of various phosphate sugar isomerases are reviewed in terms of their substrate specificities and their applications in the production of valuable rare sugars because of their functions such as low-calorie sweeteners, bulking agents, and pharmaceutical precursor. Specifically, we focused on the industrial applications of D-ribose-5-phosphate isomerase and D-mannose-6-phosphate isomerase to produce D-allose and L-ribose, respectively.
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10
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Zhang N, Meng X, Wu Y, Song H, Huang H, Wang F, Lv J. Highly Selective Isomerization of Glucose into Fructose Catalyzed by a Mimic Glucose Isomerase. ChemCatChem 2019. [DOI: 10.1002/cctc.201900143] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ni Zhang
- Key Laboratory of Green Chemistry and Technology College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Xiang‐Guang Meng
- Key Laboratory of Green Chemistry and Technology College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Yan‐Yan Wu
- Key Laboratory of Green Chemistry and Technology College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Hong‐Jin Song
- Key Laboratory of Green Chemistry and Technology College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Hong Huang
- Key Laboratory of Green Chemistry and Technology College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Fei Wang
- Key Laboratory of Green Chemistry and Technology College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Jing Lv
- Key Laboratory of Green Chemistry and Technology College of ChemistrySichuan University Chengdu 610064 P.R. China
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11
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Finelli MJ, Paramo T, Pires E, Ryan BJ, Wade-Martins R, Biggin PC, McCullagh J, Oliver PL. Oxidation Resistance 1 Modulates Glycolytic Pathways in the Cerebellum via an Interaction with Glucose-6-Phosphate Isomerase. Mol Neurobiol 2018; 56:1558-1577. [PMID: 29905912 PMCID: PMC6368252 DOI: 10.1007/s12035-018-1174-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/01/2018] [Indexed: 12/13/2022]
Abstract
Glucose metabolism is essential for the brain: it not only provides the required energy for cellular function and communication but also participates in balancing the levels of oxidative stress in neurons. Defects in glucose metabolism have been described in neurodegenerative disease; however, it remains unclear how this fundamental process contributes to neuronal cell death in these disorders. Here, we investigated the molecular mechanisms driving the selective neurodegeneration in an ataxic mouse model lacking oxidation resistance 1 (Oxr1) and discovered an unexpected function for this protein as a regulator of the glycolytic enzyme, glucose-6-phosphate isomerase (GPI/Gpi1). Initially, we present a dysregulation of metabolites of glucose metabolism at the pre-symptomatic stage in the Oxr1 knockout cerebellum. We then demonstrate that Oxr1 and Gpi1 physically and functionally interact and that the level of Gpi1 oligomerisation is disrupted when Oxr1 is deleted in vivo. Furthermore, we show that Oxr1 modulates the additional and less well-understood roles of Gpi1 as a cytokine and neuroprotective factor. Overall, our data identify a new molecular function for Oxr1, establishing this protein as important player in neuronal survival, regulating both oxidative stress and glucose metabolism in the brain.
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Affiliation(s)
- Mattéa J Finelli
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, UK
| | - Teresa Paramo
- Department of Biochemistry, University of Oxford, Parks Road, Oxford, OX1 3QU, UK
| | - Elisabete Pires
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Brent J Ryan
- Oxford Parkinson's Disease Centre, University of Oxford, South Parks Road, Oxford, OX1 3QX, UK
| | - Richard Wade-Martins
- Department of Biochemistry, University of Oxford, Parks Road, Oxford, OX1 3QU, UK
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Parks Road, Oxford, OX1 3QU, UK
| | - James McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Peter L Oliver
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, UK. .,MRC Harwell Institute, Harwell Campus, South Parks Road, Oxford, Oxfordshire, OX11 0RD, UK.
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12
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Vulcano R, Pengo P, Velari S, Wouters J, De Vita A, Tecilla P, Bonifazi D. Toward Fractioning of Isomers through Binding-Induced Acceleration of Azobenzene Switching. J Am Chem Soc 2017; 139:18271-18280. [PMID: 29064236 DOI: 10.1021/jacs.7b09568] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The E/Z isomerization process of a uracil-azobenzene derivative in which the nucleobase is conjugated to a phenyldiazene tail is studied in view of its ability to form triply H-bonded complexes with a suitably complementary 2,6-diacetylamino-4-pyridine ligand. UV-vis and 1H NMR investigations of the photochemical and thermal isomerization kinetics show that the thermal Z → E interconversion is 4-fold accelerated upon formation of the H-bonded complex. DFT calculations show that the formation of triple H-bonds triggers a significant elongation of the N═N double bond, caused by an increase of its πg* antibonding character. This results in a reduction of the N═N torsional barrier and thus in accelerated thermal Z → E isomerization. Combined with light-controlled E → Z isomerization, this enables controllable fractional tuning of the two configurational isomers.
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Affiliation(s)
- Rosaria Vulcano
- Department of Chemistry, University of Namur (UNamur) , Rue de Bruxelles 61, Namur, 5000, Belgium
| | | | | | - Johan Wouters
- Department of Chemistry, University of Namur (UNamur) , Rue de Bruxelles 61, Namur, 5000, Belgium
| | - Alessandro De Vita
- Department of Physics, King's College London , Strand, London WC2R 2LS, United Kingdom
| | | | - Davide Bonifazi
- Department of Chemistry, University of Namur (UNamur) , Rue de Bruxelles 61, Namur, 5000, Belgium.,School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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Ma H, Szeler K, Kamerlin SCL, Widersten M. Linking coupled motions and entropic effects to the catalytic activity of 2-deoxyribose-5-phosphate aldolase (DERA). Chem Sci 2015; 7:1415-1421. [PMID: 29910900 PMCID: PMC5975929 DOI: 10.1039/c5sc03666f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/17/2015] [Indexed: 12/13/2022] Open
Abstract
Local mutations in the phosphate binding group of DERA alter global conformation dynamics, catalytic activities and reaction entropies.
DERA, 2-deoxyribose-5-phosphate aldolase, catalyzes the retro-aldol cleavage of 2-deoxy-ribose-5-phosphate (dR5P) into glyceraldehyde-3-phosphate (G3P) and acetaldehyde in a branch of the pentose phosphate pathway. In addition to the physiological reaction, DERA also catalyzes the reverse addition reaction and, hence, is an interesting candidate for bio-catalysis of carbo-ligation reactions, which are central to synthetic chemistry. An obstacle to overcome for this enzyme to become a truly useful biocatalyst, however, is to relax the very strict dependency of this enzyme on phosphorylated substrates. We have studied herein the role of the non-canonical phosphate-binding site of this enzyme, consisting of Ser238 and Ser239, by site-directed and site-saturation mutagenesis, coupled to kinetic analysis of mutants. In addition, we have performed molecular dynamics simulations on the wild-type and four mutant enzymes, to analyse how mutations at this phosphate-binding site may affect the protein structure and dynamics. Further examination of the S239P mutant revealed that this variant increases the enthalpy change at the transition state, relative to the wild-type enzyme, but concomitant loss in entropy causes an overall relative loss in the TS free energy change. This entropy loss, as measured by the temperature dependence of catalysed rates, was mirrored in both a drastic loss in dynamics of the enzyme, which contributes to phosphate binding, as well as an overall loss in anti-correlated motions distributed over the entire protein. Our combined data suggests that the degree of anticorrelated motions within the DERA structure is coupled to catalytic efficiency in the DERA-catalyzed retro-aldol cleavage reaction, and can be manipulated for engineering purposes.
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Affiliation(s)
- Huan Ma
- Department of Chemistry - BMC , Uppsala University , Box 576 , SE-751 23 Uppsala , Sweden .
| | - Klaudia Szeler
- Department of Cell and Molecular Biology , Uppsala University , Box 596 , SE-751 24 , Uppsala , Sweden .
| | - Shina C L Kamerlin
- Department of Cell and Molecular Biology , Uppsala University , Box 596 , SE-751 24 , Uppsala , Sweden .
| | - Mikael Widersten
- Department of Chemistry - BMC , Uppsala University , Box 576 , SE-751 23 Uppsala , Sweden .
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14
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Brodkin HR, DeLateur NA, Somarowthu S, Mills CL, Novak WR, Beuning PJ, Ringe D, Ondrechen MJ. Prediction of distal residue participation in enzyme catalysis. Protein Sci 2015; 24:762-78. [PMID: 25627867 PMCID: PMC4420525 DOI: 10.1002/pro.2648] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 01/10/2015] [Accepted: 01/26/2015] [Indexed: 11/09/2022]
Abstract
A scoring method for the prediction of catalytically important residues in enzyme structures is presented and used to examine the participation of distal residues in enzyme catalysis. Scores are based on the Partial Order Optimum Likelihood (POOL) machine learning method, using computed electrostatic properties, surface geometric features, and information obtained from the phylogenetic tree as input features. Predictions of distal residue participation in catalysis are compared with experimental kinetics data from the literature on variants of the featured enzymes; some additional kinetics measurements are reported for variants of Pseudomonas putida nitrile hydratase (ppNH) and for Escherichia coli alkaline phosphatase (AP). The multilayer active sites of P. putida nitrile hydratase and of human phosphoglucose isomerase are predicted by the POOL log ZP scores, as is the single-layer active site of P. putida ketosteroid isomerase. The log ZP score cutoff utilized here results in over-prediction of distal residue involvement in E. coli alkaline phosphatase. While fewer experimental data points are available for P. putida mandelate racemase and for human carbonic anhydrase II, the POOL log ZP scores properly predict the previously reported participation of distal residues.
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Affiliation(s)
- Heather R Brodkin
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
| | - Nicholas A DeLateur
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Srinivas Somarowthu
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Caitlyn L Mills
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Walter R Novak
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Dagmar Ringe
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
| | - Mary Jo Ondrechen
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
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15
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Lin HY, Liu JH, Cheng KL, Lin JY, Liu NR, Meng M. A novel binding of GTP stabilizes the structure and modulates the activities of human phosphoglucose isomerase/autocrine motility factor. Biochem Biophys Rep 2015; 2:14-22. [PMID: 29124141 PMCID: PMC5668625 DOI: 10.1016/j.bbrep.2015.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/13/2015] [Accepted: 04/13/2015] [Indexed: 11/29/2022] Open
Abstract
Phosphoglucose isomerase (PGI) catalyzes the interconversion between glucose 6-phosphate and fructose 6-phosphate in the glycolysis pathway. In mammals, the enzyme is also identical to the extracellular proteins neuroleukin, tumor-secreted autocrine motility factor (AMF) and differentiation and maturation mediator for myeloid leukemia. Hereditary deficiency of the enzyme causes non-spherocytic hemolytic anemia in human. In the present study, a novel interaction between GTP and human PGI was corroborated by UV-induced crosslinking, affinity purification and kinetic study. GTP not only inhibits the isomerization activity but also compromises the AMF function of the enzyme. Kinetic studies, including the Yonetani-Theorell method, suggest that GTP is a competitive inhibitor with a Ki value of 63 μM and the GTP-binding site partially overlaps with the catalytic site. In addition, GTP stabilizes the structure of human PGI against heat- and detergent-induced denaturation. Molecular modelling and dynamic simulation suggest that GTP is bound in a syn-conformation with the γ-phosphate group located near the phosphate-binding loop and the ribose moiety positioned away from the active-site residues.
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Affiliation(s)
- Hua-Yang Lin
- Graduate Institute of Biotechnology, National Chung Hsing University (NCHU), 250 Kuo-Kuang Road, Taichung, Taiwan 40227
| | - Jyung-Hurng Liu
- Graduate Institute of Genomics and Bioinformatics, NCHU, Taichung, Taiwan 40227.,Agricultural Biotechnology Center (ABC), NCHU, Taichung, Taiwan 40227.,Rong Hsing Research Center for Translational Medicine, NCHU, Taichung, Taiwan 40227
| | - Ka-Lik Cheng
- Graduate Institute of Biotechnology, National Chung Hsing University (NCHU), 250 Kuo-Kuang Road, Taichung, Taiwan 40227
| | - Jia-Yun Lin
- Graduate Institute of Biotechnology, National Chung Hsing University (NCHU), 250 Kuo-Kuang Road, Taichung, Taiwan 40227
| | - Ni-Rung Liu
- Graduate Institute of Biotechnology, National Chung Hsing University (NCHU), 250 Kuo-Kuang Road, Taichung, Taiwan 40227
| | - Menghsiao Meng
- Graduate Institute of Biotechnology, National Chung Hsing University (NCHU), 250 Kuo-Kuang Road, Taichung, Taiwan 40227
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16
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Perera J, Liu X, Zhou Y, Joseph NE, Meng L, Turner JR, Huang H. Insufficient autoantigen presentation and failure of tolerance in a mouse model of rheumatoid arthritis. ACTA ACUST UNITED AC 2014; 65:2847-56. [PMID: 23840022 DOI: 10.1002/art.38085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 07/02/2013] [Indexed: 01/09/2023]
Abstract
OBJECTIVE In the K/BxN mouse model of rheumatoid arthritis, T cells reactive for the self antigen glucose-6-phosphate isomerase (GPI) escape negative selection even though GPI expression is ubiquitous. We sought to determine whether insufficient GPI presentation could account for the failure of negative selection and for the development of arthritis. METHODS To increase the antigen presentation of GPI, we generated transgenic mice expressing a membrane-bound form of GPI (mGPI) and crossed them with K/BxN mice. A monoclonal antibody specific for the α-chain of the KRN T cell receptor was generated to examine the fate of GPI-specific T cells. RESULTS The mGPI-transgenic mice presented GPI more efficiently and showed a dramatic increase in negative selection and an inhibition of arthritis. Interestingly, thymic negative selection remained incomplete in these mice, and the escaped autoreactive T cells were anergic in the peripheral lymphoid organs, suggesting that enhanced antigen presentation also induces peripheral tolerance. Despite this apparent tolerance induction toward GPI, these mice developed a chronic wasting disease, characterized by colonic inflammation with epithelial dysplasia, as well as a dramatic reduction in Treg cells. CONCLUSION These data indicate that insufficient autoantigen expression or presentation results in defects of both central and peripheral tolerance in the K/BxN mice. Our findings also support the idea that insufficient autoantigen levels may underlie the development of autoimmunity.
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17
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Fujiwara T, Saburi W, Matsui H, Mori H, Yao M. Structural insights into the epimerization of β-1,4-linked oligosaccharides catalyzed by cellobiose 2-epimerase, the sole enzyme epimerizing non-anomeric hydroxyl groups of unmodified sugars. J Biol Chem 2013; 289:3405-15. [PMID: 24362032 DOI: 10.1074/jbc.m113.531251] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellobiose 2-epimerase (CE) reversibly converts d-glucose residues into d-mannose residues at the reducing end of unmodified β1,4-linked oligosaccharides, including β-1,4-mannobiose, cellobiose, and lactose. CE is responsible for conversion of β1,4-mannobiose to 4-O-β-d-mannosyl-d-glucose in mannan metabolism. However, the detailed catalytic mechanism of CE is unclear due to the lack of structural data in complex with ligands. We determined the crystal structures of halothermophile Rhodothermus marinus CE (RmCE) in complex with substrates/products or intermediate analogs, and its apo form. The structures in complex with the substrates/products indicated that the residues in the β5-β6 loop as well as those in the inner six helices form the catalytic site. Trp-322 and Trp-385 interact with reducing and non-reducing end parts of these ligands, respectively, by stacking interactions. The architecture of the catalytic site also provided insights into the mechanism of reversible epimerization. His-259 abstracts the H2 proton of the d-mannose residue at the reducing end, and consistently forms the cis-enediol intermediate by facilitated depolarization of the 2-OH group mediated by hydrogen bonding interaction with His-200. His-390 subsequently donates the proton to the C2 atom of the intermediate to form a d-glucose residue. The reverse reaction is mediated by these three histidines with the inverse roles of acid/base catalysts. The conformation of cellobiitol demonstrated that the deprotonation/reprotonation step is coupled with rotation of the C2-C3 bond of the open form of the ligand. Moreover, it is postulated that His-390 is closely related to ring opening/closure by transferring a proton between the O5 and O1 atoms of the ligand.
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Affiliation(s)
- Takaaki Fujiwara
- From the Faculty of Advanced Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo 060-0810 and
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18
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Walker JA, Hall AM, Kotsopoulou E, Espeli M, Nitschke L, Barker RN, Lyons PA, Smith KGC. Increased red cell turnover in a line of CD22-deficient mice is caused by Gpi1c: a model for hereditary haemolytic anaemia. Eur J Immunol 2012; 42:3212-22. [PMID: 22930244 DOI: 10.1002/eji.201242633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Revised: 08/02/2012] [Accepted: 08/24/2012] [Indexed: 11/06/2022]
Abstract
CD22, an inhibitory co-receptor of the BCR, has been identified as a potential candidate gene for the development of autoimmune haemolytic anaemia in mice. In this study, we have examined Cd22(tm1Msn) CD22-deficient mice and identified an increase in RBC turnover and stress erythropoiesis, which might be consistent with haemolysis. We then, however, eliminated CD22 deficiency as the cause of accelerated RBC turnover and established that enhanced RBC turnover occurs independently of B cells and anti-RBC autoanti-bodies. Accelerated RBC turnover in this particular strain of CD22-deficient mice is red cell intrinsic and appears to be the consequence of a defective allele of glucose phosphate isomerase, Gpi1(c). This form of Gpi1 was originally derived from wild mice and results in a substantial reduction in enzyme activity. We have identified the polymorphism that causes impaired catalytic activity in the Gpi1(c) allele, and biochemically confirmed an approximate 75% reduction of GPI1 activity in Cd22(-/-) RBCs. The Cd22(-/-).Gpi1(c) congenic mouse provides a novel animal model of GPI1-deficiency, which is one of the most common causes of chronic non-spherocytic haemolytic anaemia in humans.
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Affiliation(s)
- Jennifer A Walker
- Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
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19
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Granchi C, Minutolo F. Anticancer agents that counteract tumor glycolysis. ChemMedChem 2012; 7:1318-50. [PMID: 22684868 PMCID: PMC3516916 DOI: 10.1002/cmdc.201200176] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 05/04/2012] [Indexed: 12/12/2022]
Abstract
Can we consider cancer to be a "metabolic disease"? Tumors are the result of a metabolic selection, forming tissues composed of heterogeneous cells that generally express an overactive metabolism as a common feature. In fact, cancer cells have increased needs for both energy and biosynthetic intermediates to support their growth and invasiveness. However, their high proliferation rate often generates regions that are insufficiently oxygenated. Therefore, their carbohydrate metabolism must rely mostly on a glycolytic process that is uncoupled from oxidative phosphorylation. This metabolic switch, also known as the Warburg effect, constitutes a fundamental adaptation of tumor cells to a relatively hostile environment, and supports the evolution of aggressive and metastatic phenotypes. As a result, tumor glycolysis may constitute an attractive target for cancer therapy. This approach has often raised concerns that antiglycolytic agents may cause serious side effects toward normal cells. The key to selective action against cancer cells can be found in their hyperbolic addiction to glycolysis, which may be exploited to generate new anticancer drugs with minimal toxicity. There is growing evidence to support many glycolytic enzymes and transporters as suitable candidate targets for cancer therapy. Herein we review some of the most relevant antiglycolytic agents that have been investigated thus far for the treatment of cancer.
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Affiliation(s)
- Carlotta Granchi
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa (Italy)
| | - Filippo Minutolo
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa (Italy)
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20
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McFerrin LG, Atchley WR. A novel N-terminal domain may dictate the glucose response of Mondo proteins. PLoS One 2012; 7:e34803. [PMID: 22506051 PMCID: PMC3323566 DOI: 10.1371/journal.pone.0034803] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 03/08/2012] [Indexed: 01/13/2023] Open
Abstract
Glucose is a fundamental energy source for both prokaryotes and eukaryotes. The balance between glucose utilization and storage is integral for proper energy homeostasis, and defects are associated with several diseases, e.g. type II diabetes. In vertebrates, the transcription factor ChREBP is a major component in glucose metabolism, while its ortholog MondoA is involved in glucose uptake. Both MondoA and ChREBP contain five Mondo conserved regions (MCRI-V) that affect their cellular localization and transactivation ability. While phosphorylation has been shown to affect ChREBP function, the mechanisms controlling glucose response of both ChREBP and MondoA remain elusive. By incorporating sequence analysis techniques, structure predictions, and functional annotations, we synthesized data surrounding Mondo family proteins into a cohesive, accurate, and general model involving the MCRs and two additional domains that determine ChREBP and MondoA glucose response. Paramount, we identified a conserved motif within the transactivation region of Mondo family proteins and propose that this motif interacts with the phosphorylated form of glucose. In addition, we discovered a putative nuclear receptor box in non-vertebrate Mondo and vertebrate ChREBP sequences that reveals a potentially novel interaction with nuclear receptors. These interactions are likely involved in altering ChREBP and MondoA conformation to form an active complex and induce transcription of genes involved in glucose metabolism and lipogenesis.
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Affiliation(s)
- Lisa G McFerrin
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America.
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21
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Totir M, Echols N, Nanao M, Gee CL, Moskaleva A, Gradia S, Iavarone AT, Berger JM, May AP, Zubieta C, Alber T. Macro-to-micro structural proteomics: native source proteins for high-throughput crystallization. PLoS One 2012; 7:e32498. [PMID: 22393408 PMCID: PMC3290569 DOI: 10.1371/journal.pone.0032498] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 01/27/2012] [Indexed: 01/07/2023] Open
Abstract
Structural biology and structural genomics projects routinely rely on recombinantly expressed proteins, but many proteins and complexes are difficult to obtain by this approach. We investigated native source proteins for high-throughput protein crystallography applications. The Escherichia coli proteome was fractionated, purified, crystallized, and structurally characterized. Macro-scale fermentation and fractionation were used to subdivide the soluble proteome into 408 unique fractions of which 295 fractions yielded crystals in microfluidic crystallization chips. Of the 295 crystals, 152 were selected for optimization, diffraction screening, and data collection. Twenty-three structures were determined, four of which were novel. This study demonstrates the utility of native source proteins for high-throughput crystallography.
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Affiliation(s)
- Monica Totir
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Nathaniel Echols
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Max Nanao
- European Molecular Biology Laboratory, Grenoble, France
| | - Christine L. Gee
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Alisa Moskaleva
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Scott Gradia
- QB3 Institute, Berkeley, California, United States of America
| | | | - James M. Berger
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Andrew P. May
- Fluidigm Corporation, South San Francisco, California, United States of America
| | - Chloe Zubieta
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Tom Alber
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
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22
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Somarowthu S, Brodkin HR, D’Aquino JA, Ringe D, Ondrechen MJ, Beuning PJ. A Tale of Two Isomerases: Compact versus Extended Active Sites in Ketosteroid Isomerase and Phosphoglucose Isomerase. Biochemistry 2011; 50:9283-95. [DOI: 10.1021/bi201089v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Srinivas Somarowthu
- Department of Chemistry and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Heather R. Brodkin
- Departments of Biochemistry
and Chemistry and Rosenstiel Basic Medical Sciences Center, Brandeis University, Waltham, Massachusetts 02454-9110,
United States
| | - J. Alejandro D’Aquino
- Departments of Biochemistry
and Chemistry and Rosenstiel Basic Medical Sciences Center, Brandeis University, Waltham, Massachusetts 02454-9110,
United States
| | - Dagmar Ringe
- Departments of Biochemistry
and Chemistry and Rosenstiel Basic Medical Sciences Center, Brandeis University, Waltham, Massachusetts 02454-9110,
United States
| | - Mary Jo Ondrechen
- Department of Chemistry and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Center for
Interdisciplinary Research
on Complex Systems, Northeastern University, Boston, Massachusetts 02115, United States
| | - Penny J. Beuning
- Department of Chemistry and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Center for
Interdisciplinary Research
on Complex Systems, Northeastern University, Boston, Massachusetts 02115, United States
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23
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Roux C, Bhatt F, Foret J, de Courcy B, Gresh N, Piquemal JP, Jeffery CJ, Salmon L. The reaction mechanism of type I phosphomannose isomerases: new information from inhibition and polarizable molecular mechanics studies. Proteins 2011; 79:203-20. [PMID: 21058398 DOI: 10.1002/prot.22873] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Type I phosphomannose isomerases (PMIs) are zinc-dependent metalloenzymes involved in the reversible isomerization of D-mannose 6-phosphate (M6P) and D-fructose 6-phosphate (F6P). 5-Phospho-D-arabinonohydroxamic acid (5PAH), an inhibitor endowed with nanomolar affinity for yeast (Type I) and Pseudomonas aeruginosa (Type II) PMIs (Roux et al., Biochemistry 2004; 43:2926-2934), strongly inhibits human (Type I) PMI (for which we report an improved expression and purification procedure), as well as Escherichia coli (Type I) PMI. Its K(i) value of 41 nM for human PMI is the lowest value ever reported for an inhibitor of PMI. 5-Phospho-D-arabinonhydrazide, a neutral analogue of the reaction intermediate 1,2-cis-enediol, is about 15 times less efficient at inhibiting both enzymes, in accord with the anionic nature of the postulated high-energy reaction intermediate. Using the polarizable molecular mechanics, sum of interactions between fragments ab initio computed (SIBFA) procedure, computed structures of the complexes between Candida albicans (Type I) PMI and the cyclic substrate β-D-mannopyranose 6-phosphate (β-M6P) and between the enzyme and the high-energy intermediate analogue inhibitor 5PAH are reported. Their analysis allows us to identify clearly the nature of each individual active site amino acid and to formulate a hypothesis for the overall mechanism of the reaction catalyzed by Type I PMIs, that is, the ring-opening and isomerization steps, respectively. Following enzyme-catalyzed ring-opening of β-M6P by zinc-coordinated water and Gln111 ligands, Lys136 is identified as the probable catalytic base involved in proton transfer between the two carbon atoms C1 and C2 of the substrate D-mannose 6-phosphate.
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Affiliation(s)
- Céline Roux
- Laboratoire de Chimie Bioorganique et Bioinorganique, ICMMO, Univ Paris-Sud, UMR 8182, Orsay F-91405, France
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24
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Anand K, Mathur D, Anant A, Garg LC. Structural studies of phosphoglucose isomerase from Mycobacterium tuberculosis H37Rv. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:490-7. [PMID: 20445242 DOI: 10.1107/s1744309110011656] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Accepted: 03/27/2010] [Indexed: 01/17/2023]
Abstract
Phosphoglucose isomerase (PGI) plays a key role in both glycolysis and gluconeogenesis inside the cell, whereas outside the cell it exhibits cytokine properties. PGI is also known to act as an autocrine motility factor, a neuroleukin agent and a differentiation and maturation mediator. Here, the first crystal structure of PGI from Mycobacterium tuberculosis H37Rv (Mtb) is reported. The structure was refined at 2.25 A resolution and revealed the presence of one molecule in the asymmetric unit with two globular domains. As known previously, the active site of Mtb PGI contains conserved residues including Glu356, Glu216 and His387 (where His387 is from the neighbouring molecule). The crystal structure of Mtb PGI was observed to be rather more similar to human PGI than other nonbacterial PGIs, with only a few differences being detected in the loops, arm and hook regions of the human and Mtb PGIs, suggesting that the M. tuberculosis enzyme uses the same enzyme mechanism.
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Affiliation(s)
- Kanchan Anand
- European Molecular Biology Laboratory Heidelberg, Structural and Computational Biology Unit, Meyerhof Strasse 1, D-69117 Heidelberg, Germany. ,
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25
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Aoki KI, Tanaka N, Kusakabe Y, Fukumi C, Haga A, Nakanishi M, Kitade Y, Nakamura KT. Crystallization and preliminary X-ray crystallographic study of phosphoglucose isomerase from Plasmodium falciparum. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:333-6. [PMID: 20208175 PMCID: PMC2833051 DOI: 10.1107/s1744309110001740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2009] [Accepted: 01/14/2010] [Indexed: 11/10/2022]
Abstract
Phosphoglucose isomerase (PGI) is a key enzyme in glycolysis and glycogenesis that catalyses the interconversion of glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P). For crystallographic studies, PGI from the human malaria parasite Plasmodium falciparum (PfPGI) was overproduced in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data to 1.5 A resolution were collected from an orthorhombic crystal form belonging to space group P2(1)2(1)2(1) with unit-cell parameters a = 103.3, b = 104.1, c = 114.6 A. Structural analysis by molecular replacement is in progress.
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Affiliation(s)
- Ken-ichi Aoki
- School of Pharmacy, Showa University, Tokyo 142-8555, Japan
| | | | | | - Chiharu Fukumi
- School of Pharmacy, Showa University, Tokyo 142-8555, Japan
| | - Arayo Haga
- Gifu Prefectural Research Institute for Health and Environmental Science, Kakamigahara 504-0838, Japan
- Gifu Pharmaceutical University, Gifu 502-8585, Japan
| | - Masayuki Nakanishi
- College of Pharmaceutical Sciences, Matsuyama University, Ehime 790-8578, Japan
| | - Yukio Kitade
- Faculty of Engineering, Gifu University, Gifu 501-1193, Japan
- Center for Advanced Drug Research, Gifu University, Gifu 501-1193, Japan
- Center for Emerging Infectious Diseases, Gifu University, Gifu 501-1193, Japan
- Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
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Probing the molecular determinant for the catalytic efficiency of L-arabinose isomerase from Bacillus licheniformis. Appl Environ Microbiol 2010; 76:1653-60. [PMID: 20048061 DOI: 10.1128/aem.02254-09] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus licheniformis l-arabinose isomerase (l-AI) is distinguished from other l-AIs by its high degree of substrate specificity for l-arabinose and its high turnover rate. A systematic strategy that included a sequence alignment-based first screening of residues and a homology model-based second screening, followed by site-directed mutagenesis to alter individual screened residues, was used to study the molecular determinants for the catalytic efficiency of B. licheniformis l-AI. One conserved amino acid, Y333, in the substrate binding pocket of the wild-type B. licheniformis l-AI was identified as an important residue affecting the catalytic efficiency of B. licheniformis l-AI. Further insights into the function of residue Y333 were obtained by replacing it with other aromatic, nonpolar hydrophobic amino acids or polar amino acids. Replacing Y333 with the aromatic amino acid Phe did not alter catalytic efficiency toward l-arabinose. In contrast, the activities of mutants containing a hydrophobic amino acid (Ala, Val, or Leu) at position 333 decreased as the size of the hydrophobic side chain of the amino acid decreased. However, mutants containing hydrophilic and charged amino acids, such as Asp, Glu, and Lys, showed almost no activity with l-arabinose. These data and a molecular dynamics simulation suggest that Y333 is involved in the catalytic efficiency of B. licheniformis l-AI.
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Emergence of Complex Haplotypes from Microevolutionary Variation in Sequence and Structure of Colias Phosphoglucose Isomerase. J Mol Evol 2009; 68:433-47. [DOI: 10.1007/s00239-009-9237-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2008] [Revised: 03/03/2009] [Accepted: 04/08/2009] [Indexed: 10/20/2022]
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Lin HY, Kao YH, Chen ST, Meng M. Effects of inherited mutations on catalytic activity and structural stability of human glucose-6-phosphate isomerase expressed in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:315-23. [DOI: 10.1016/j.bbapap.2008.11.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Revised: 10/06/2008] [Accepted: 11/06/2008] [Indexed: 02/07/2023]
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Arsenieva D, Appavu BL, Mazock GH, Jeffery CJ. Crystal structure of phosphoglucose isomerase fromTrypanosoma bruceicomplexed with glucose-6-phosphate at 1.6 Å resolution. Proteins 2009; 74:72-80. [DOI: 10.1002/prot.22133] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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31
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Lee YL, Li TT. Crystallization and preliminary crystallographic study of the phosphoglucose isomerase from Bacillus subtilis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:1181-3. [PMID: 19052382 PMCID: PMC2593699 DOI: 10.1107/s1744309108037718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2008] [Accepted: 11/13/2008] [Indexed: 11/10/2022]
Abstract
Crystallization and preliminary crystallographic analysis of the phosphoglucose isomerase from a Bacillus subtilis native strain were carried out. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 145.7, b = 136.0, c = 109.1 A, beta = 119.4 degrees . The diffraction quality of the crystal was significantly improved from 2.4 A to greater than 1.9 A resolution by using the in situ flash-annealing method. A 98% complete data set with an overall R(merge) of 4.6% was collected using an R-AXIS IV(++) image-plate system and a copper rotating-anode X-ray generator. The crystals contained four molecules per asymmetric unit and the predicted solvent content and the Matthews coefficient (V(M)) were 46.8% and 2.3 A(3) Da(-1), respectively. Structure determination by the molecular-replacement method provided a reasonable solution for model building.
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Affiliation(s)
- Yian Liang Lee
- Institute of Biochemistry, National ChungHsing University, Taichung 40227, Taiwan
| | - TienHsiung Thomas Li
- Institute of Biochemistry, National ChungHsing University, Taichung 40227, Taiwan
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Wu R, Xie H, Cao Z, Mo Y. Combined Quantum Mechanics/Molecular Mechanics Study on the Reversible Isomerization of Glucose and Fructose Catalyzed by Pyrococcus furiosus Phosphoglucose Isomerase. J Am Chem Soc 2008; 130:7022-31. [DOI: 10.1021/ja710633c] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ruibo Wu
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, 361005, China, and Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008
| | - Hujun Xie
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, 361005, China, and Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008
| | - Zexing Cao
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, 361005, China, and Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008
| | - Yirong Mo
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, 361005, China, and Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008
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Roux C, Gresh N, Perera LE, Piquemal JP, Salmon L. Binding of 5-phospho-D-arabinonohydroxamate and 5-phospho-D-arabinonate inhibitors to zinc phosphomannose isomerase from Candida albicans studied by polarizable molecular mechanics and quantum mechanics. J Comput Chem 2007; 28:938-57. [PMID: 17253648 DOI: 10.1002/jcc.20586] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Type I phosphomannose isomerase (PMI) is a Zn-dependent metalloenzyme involved in the isomerization of D-fructose 6-phosphate to D-mannose 6-phosphate. One of our laboratories has recently designed and synthesized 5-phospho-D-arabinonohydroxamate (5PAH), an inhibitor endowed with a nanomolar affinity for PMI (Roux et al., Biochemistry 2004, 43, 2926). By contrast, the 5-phospho-D-arabinonate (5PAA), in which the hydroxamate moiety is replaced by a carboxylate one, is devoid of inhibitory potency. Subsequent biochemical studies showed that in its PMI complex, 5PAH binds Zn(II) through its hydroxamate moiety rather than through its phosphate. These results have stimulated the present theoretical investigation in which we resort to the SIBFA polarizable molecular mechanics procedure to unravel the structural and energetical aspects of 5PAH and 5PAA binding to a 164-residue model of PMI. Consistent with the experimental results, our theoretical studies indicate that the complexation of PMI by 5PAH is much more favorable than by 5PAA, and that in the 5PAH complex, Zn(II) ligation by hydroxamate is much more favorable than by phosphate. Validations by parallel quantum-chemical computations on model of the recognition site extracted from the PMI-inhibitor complexes, and totaling up to 140 atoms, showed the values of the SIBFA intermolecular interaction energies in such models to be able to reproduce the quantum-chemistry ones with relative errors < 3%. On the basis of the PMI-5PAH SIBFA energy-minimized structure, we report the first hypothesis of a detailed view of the active site of the zinc PMI complexed to the high-energy intermediate analogue inhibitor, which allows us to identify active site residues likely involved in the proton transfer between the two adjacent carbons of the substrates.
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Affiliation(s)
- Celine Roux
- Laboratoire de Chimie Bioorganique et Bioinorganique, CNRS-UMR 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, Bâtiment 420, Université Paris-Sud XI, 15 rue Georges Clémenceau, 91405 Orsay, France
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Mathur D, Anand K, Mathur D, Jagadish N, Suri A, Garg LC. Crystallization and preliminary X-ray characterization of phosphoglucose isomerase from Mycobacterium tuberculosis H37Rv. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:353-5. [PMID: 17401215 PMCID: PMC2330222 DOI: 10.1107/s1744309107013218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Accepted: 03/20/2007] [Indexed: 11/10/2022]
Abstract
Phosphoglucose isomerase is a ubiquitous enzyme that catalyzes the isomerization of D-glucopyranose-6-phosphate to D-fructofuranose-6-phosphate. The present investigation reports the expression, purification, crystallization and preliminary crystallographic studies of the phosphoglucose isomerase from Mycobacterium tuberculosis H37Rv, which shares 46% sequence identity with that of its human host. The recombinant protein, which was prepared using an Escherichia coli expression system, was crystallized by the hanging-drop vapour-diffusion method. The crystals diffracted to a resolution of 2.8 A and belonged to the orthorhombic space group I2(1)2(1)2(1), with unit-cell parameters a = 109.0, b = 119.8, c = 138.9 A.
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Affiliation(s)
- Divya Mathur
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India
| | - Kanchan Anand
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Deepika Mathur
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India
| | - Nirmala Jagadish
- Genes and Proteins Laboratory, National Institute of Immunology, New Delhi 110067, India
| | - Anil Suri
- Genes and Proteins Laboratory, National Institute of Immunology, New Delhi 110067, India
| | - Lalit C. Garg
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India
- Correspondence e-mail: ,
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Kooijman EE, Tieleman DP, Testerink C, Munnik T, Rijkers DTS, Burger KNJ, de Kruijff B. An electrostatic/hydrogen bond switch as the basis for the specific interaction of phosphatidic acid with proteins. J Biol Chem 2007; 282:11356-64. [PMID: 17277311 DOI: 10.1074/jbc.m609737200] [Citation(s) in RCA: 179] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphatidic acid (PA) is a minor but important phospholipid that, through specific interactions with proteins, plays a central role in several key cellular processes. The simple yet unique structure of PA, carrying just a phosphomonoester head group, suggests an important role for interactions with the positively charged essential residues in these proteins. We analyzed by solid-state magic angle spinning 31P NMR and molecular dynamics simulations the interaction of low concentrations of PA in model membranes with positively charged side chains of membrane-interacting peptides. Surprisingly, lysine and arginine residues increase the charge of PA, predominantly by forming hydrogen bonds with the phosphate of PA, thereby stabilizing the protein-lipid interaction. Our results demonstrate that this electrostatic/hydrogen bond switch turns the phosphate of PA into an effective and preferred docking site for lysine and arginine residues. In combination with the special packing properties of PA, PA may well be nature's preferred membrane lipid for interfacial insertion of positively charged membrane protein domains.
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Affiliation(s)
- Edgar E Kooijman
- Department Biochemistry of Membranes, Bijvoet Center, Institute of Biomembranes, Utrecht University, Utrecht 3584 CH, The Netherlands.
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Berrisford JM, Hounslow AM, Akerboom J, Hagen WR, Brouns SJJ, van der Oost J, Murray IA, Michael Blackburn G, Waltho JP, Rice DW, Baker PJ. Evidence Supporting a cis-enediol-based Mechanism for Pyrococcus furiosus Phosphoglucose Isomerase. J Mol Biol 2006; 358:1353-66. [PMID: 16580686 DOI: 10.1016/j.jmb.2006.03.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Revised: 03/06/2006] [Accepted: 03/08/2006] [Indexed: 11/16/2022]
Abstract
The enzymatic aldose ketose isomerisation of glucose and fructose sugars involves the transfer of a hydrogen between their C1 and C2 carbon atoms and, in principle, can proceed through either a direct hydride shift or via a cis-enediol intermediate. Pyrococcus furiosus phosphoglucose isomerase (PfPGI), an archaeal metalloenzyme, which catalyses the interconversion of glucose 6-phosphate and fructose 6-phosphate, has been suggested to operate via a hydride shift mechanism. In contrast, the structurally distinct PGIs of eukaryotic or bacterial origin are thought to catalyse isomerisation via a cis-enediol intermediate. We have shown by NMR that hydrogen exchange between substrate and solvent occurs during the reaction catalysed by PfPGI eliminating the possibility of a hydride-shift-based mechanism. In addition, kinetic measurements on this enzyme have shown that 5-phospho-d-arabinonohydroxamate, a stable analogue of the putative cis-enediol intermediate, is the most potent inhibitor of the enzyme yet discovered. Furthermore, determination and analysis of crystal structures of PfPGI with bound zinc and the substrate F6P, and with a number of competitive inhibitors, and EPR analysis of the coordination of the metal ion within PfPGI, have suggested that a cis-enediol intermediate-based mechanism is used by PfPGI with Glu97 acting as the catalytic base responsible for isomerisation.
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Affiliation(s)
- John M Berrisford
- The Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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Tanaka N, Haga A, Naba N, Shiraiwa K, Kusakabe Y, Hashimoto K, Funasaka T, Nagase H, Raz A, Nakamura KT. Crystal Structures of Mouse Autocrine Motility Factor in Complex with Carbohydrate Phosphate Inhibitors Provide Insight into Structure–Activity Relationship of the Inhibitors. J Mol Biol 2006; 356:312-24. [PMID: 16375918 DOI: 10.1016/j.jmb.2005.11.076] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Revised: 11/16/2005] [Accepted: 11/22/2005] [Indexed: 10/25/2022]
Abstract
Autocrine motility factor (AMF), a tumor-secreted cytokine, stimulates cell migration in vitro and metastasis in vivo. AMF is identical to the extracellular cytokines neuroleukin and maturation factor and, interestingly, to the intracellular enzyme phosphoglucose isomerase. The cytokine activity of AMF is inhibited by carbohydrate phosphate compounds as they compete for AMF binding with the carbohydrate moiety of the AMF receptor (AMFR), which is a glycosylated seven transmembrane helix protein. Here, we report the first comprehensive high-resolution crystal structure analyses of the inhibitor-free form and the eight types of inhibitor (phosphate, erythrose 4-phosphate (E4P), arabinose 5-phosphate (A5P), sorbitol 6-phosphate (S6P), 6-phosphogluconic acid (6PGA), fructose 6-phosphate (F6P), glucose 6-phosphate (G6P), or mannose 6-phosphate (M6P)) complexes of mouse AMF (mAMF). We assayed the inhibitory activities of these inhibitors against the cytokine activity of mAMF. The inhibitory activities of the six-carbon sugars (G6P, F6P, M6P, and 6PGA) were found to be significantly higher than those of the four or five-carbon sugars (E4P or A5P). The inhibitory activities clearly depend on the length of the inhibitor molecules. A structural comparison revealed that a water-mediated hydrogen bond between one end of the inhibitor and a rigid portion of the protein surface in the shorter-chain inhibitor (E4P) complex is replaced by a direct hydrogen bond in the longer-chain inhibitor (6PGA) complex. Thus, to obtain a new compound with higher inhibitory activities against AMF, water molecules at the inhibitor binding site of AMF should be replaced by a functional group of inhibitors in order to introduce direct interactions with the protein surface. The present structure-activity relationship studies will be valuable not only for designing more effective AMF inhibitors but also for studying general protein-inhibitor interactions.
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Affiliation(s)
- Nobutada Tanaka
- School of Pharmaceutical Sciences, Showa University, Shinagawa-ku, Tokyo, Japan.
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Hansen T, Schlichting B, Grötzinger J, Swan MK, Davies C, Schönheit P. Mutagenesis of catalytically important residues of cupin type phosphoglucose isomerase from Archaeoglobus fulgidus. FEBS J 2005; 272:6266-75. [PMID: 16336264 DOI: 10.1111/j.1742-4658.2005.05007.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Recently, cupin type phosphoglucose isomerases have been described as a novel protein family representing a separate lineage in the evolution of phosphoglucose isomerases. The importance of eight active site residues completely conserved within the cPGI family has been assessed by site-directed mutagenesis using the cPGI from Archaeoglobus fulgidus (AfcPGI) as a model. The mutants T63A, G79A, G79L, H80A, H80D, H82A, E93A, E93D, Y95F, Y95K, H136A, and Y160F were constructed, purified, and the impact of the respective mutation on catalysis and/or metal ion binding as well as thermostability was analyzed. The variants G79A, G79L, and Y95F exhibited a lower thermostability. The catalytic efficiency of the enzyme was reduced by more than 100-fold in the G79A, G79L, H80A, H80D, E93D, Y95F variants and more than 15-fold in the T63A, H82A, Y95K, Y160F variants, but remained about the same in the H136A variant at Ni2+ saturating conditions. Further, the Ni2+ content of the mutants H80A, H80D, H82A, E93A, E93D and their apparent Ni2+ binding ability was reduced, resulting in an almost complete loss of activity and thus underlining the crucial role of the metal ion for catalysis. Evidence is presented that H80, H82 and E93 play an additional role in catalysis besides metal ion binding. E93 appears to be the key catalytic residue of AfcPGI, as the E93A mutant did not show any catalytic activity at all.
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Affiliation(s)
- Thomas Hansen
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Germany
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Mathur D, Ahsan Z, Tiwari M, Garg LC. Biochemical characterization of recombinant phosphoglucose isomerase of Mycobacterium tuberculosis. Biochem Biophys Res Commun 2005; 337:626-32. [PMID: 16212940 DOI: 10.1016/j.bbrc.2005.09.092] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2005] [Accepted: 09/15/2005] [Indexed: 10/25/2022]
Abstract
Phosphoglucose isomerase (PGI) is a well-characterized ubiquitous enzyme involved in the glycolytic pathway. It catalyzes the reversible isomerization of D-glucopyranose-6-phosphate and D-fructofuranose-6-phosphate and is present in all living cells. However, there is interspecies variation at the level of the primary structure which sometimes produces heterogeneity at the structural and functional levels. In order to evaluate and characterize the mycobacterial PGI, the gene encoding the PGI from Mycobacterium tuberculosis H37Rv was cloned in pET-22b(+) vector and expressed in Escherichia coli. The target DNA was PCR amplified from the bacterial artificial chromosome using specific primers and cloned under the control of T7 promoter. Upon induction with IPTG, the recombinant PGI (rPGI) expressed partly as soluble protein and partly as inclusion bodies. The rPGI from the soluble fraction was purified to near homogeneity by ion-exchange chromatography. Mass spectrum analysis of the purified rPGI revealed its mass to be 61.45 kDa. The purified rPGI was enzymatically active and the specific activity was 600 U/mg protein. The K(m) of rPGI was determined to be 0.318 mM for fructose-6-phosphate and the K(i) was 0.8 mM for 6-phosphogluconate. The rPGI exhibited optimal activity at 37 degrees C and pH 9.0, and did not require mono- or divalent cations for its activity.
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Affiliation(s)
- Divya Mathur
- Gene Regulation Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
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