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Jackson SA, Duan M, Zhang P, Ihua MW, Stengel DB, Duan D, Dobson ADW. Isolation, identification, and biochemical characterization of a novel bifunctional phosphomannomutase/phosphoglucomutase from the metagenome of the brown alga Laminaria digitata. Front Microbiol 2022; 13:1000634. [PMID: 36212884 PMCID: PMC9537760 DOI: 10.3389/fmicb.2022.1000634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
Macroalgae host diverse epiphytic bacterial communities with potential symbiotic roles including important roles influencing morphogenesis and growth of the host, nutrient exchange, and protection of the host from pathogens. Macroalgal cell wall structures, exudates, and intra-cellular environments possess numerous complex and valuable carbohydrates such as cellulose, hemi-cellulose, mannans, alginates, fucoidans, and laminarin. Bacterial colonizers of macroalgae are important carbon cyclers, acquiring nutrition from living macroalgae and also from decaying macroalgae. Seaweed epiphytic communities are a rich source of diverse carbohydrate-active enzymes which may have useful applications in industrial bioprocessing. With this in mind, we constructed a large insert fosmid clone library from the metagenome of Laminaria digitata (Ochrophyta) in which decay was induced. Subsequent sequencing of a fosmid clone insert revealed the presence of a gene encoding a bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM) enzyme 10L6AlgC, closely related to a protein from the halophilic marine bacterium, Cobetia sp. 10L6AlgC was subsequently heterologously expressed in Escherichia coli and biochemically characterized. The enzyme was found to possess both PMM and PGM activity, which had temperature and pH optima of 45°C and 8.0, respectively; for both activities. The PMM activity had a K m of 2.229 mM and V max of 29.35 mM min-1 mg-1, while the PGM activity had a K m of 0.5314 mM and a V max of 644.7 mM min-1 mg-1. Overall characterization of the enzyme including the above parameters as well as the influence of various divalent cations on these activities revealed that 10L6AlgC has a unique biochemical profile when compared to previously characterized PMM/PGM bifunctional enzymes. Thus 10L6AlgC may find utility in enzyme-based production of biochemicals with different potential industrial applications, in which other bacterial PMM/PGMs have previously been used such as in the production of low-calorie sweeteners in the food industry.
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Affiliation(s)
- Stephen A. Jackson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Maohang Duan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Pengyan Zhang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Maureen W. Ihua
- School of Microbiology, University College Cork, Cork, Ireland
| | - Dagmar B. Stengel
- Botany and Plant Science, School of Natural Sciences, Ryan Institute for Environmental, Marine and Energy Research, University of Galway, Galway, Ireland
| | - Delin Duan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
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2
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Glucose-1,6-Bisphosphate, a Key Metabolic Regulator, Is Synthesized by a Distinct Family of α-Phosphohexomutases Widely Distributed in Prokaryotes. mBio 2022; 13:e0146922. [PMID: 35856562 PMCID: PMC9426568 DOI: 10.1128/mbio.01469-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The reactions of α-d-phosphohexomutases (αPHM) are ubiquitous, key to primary metabolism, and essential for several processes in all domains of life. The functionality of these enzymes relies on an initial phosphorylation step which requires the presence of α-d-glucose-1,6-bisphosphate (Glc-1,6-BP). While well investigated in vertebrates, the origin of this activator compound in bacteria is unknown. Here we show that the Slr1334 protein from the unicellular cyanobacterium Synechocysitis sp. PCC 6803 is a Glc-1,6-BP-synthase. Biochemical analysis revealed that Slr1334 efficiently converts fructose-1,6-bisphosphate (Frc-1,6-BP) and α-d-glucose-1-phosphate/α-d-glucose-6-phosphate into Glc-1,6-BP and also catalyzes the reverse reaction. As inferred from phylogenetic analysis, the slr1334 product belongs to a primordial subfamily of αPHMs that is present especially in deeply branching bacteria and also includes human commensals and pathogens. Remarkably, the homologue of Slr1334 in the human gut bacterium Bacteroides salyersiae catalyzes the same reaction, suggesting a conserved and essential role for the members of this αPHM subfamily.
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3
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Yan K, Stanley M, Kowalski B, Raimi OG, Ferenbach AT, Wei P, Fang W, van Aalten DMF. Genetic validation of Aspergillus fumigatus phosphoglucomutase as a viable therapeutic target in invasive aspergillosis. J Biol Chem 2022; 298:102003. [PMID: 35504355 PMCID: PMC9168620 DOI: 10.1016/j.jbc.2022.102003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 02/09/2023] Open
Abstract
Aspergillus fumigatus is the causative agent of invasive aspergillosis, an infection with mortality rates of up to 50%. The glucan-rich cell wall of A. fumigatus is a protective structure that is absent from human cells and is a potential target for antifungal treatments. Glucan is synthesized from the donor uridine diphosphate glucose, with the conversion of glucose-6-phosphate to glucose-1-phosphate by the enzyme phosphoglucomutase (PGM) representing a key step in its biosynthesis. Here, we explore the possibility of selectively targeting A. fumigatus PGM (AfPGM) as an antifungal treatment strategy. Using a promoter replacement strategy, we constructed a conditional pgm mutant and revealed that pgm is required for A. fumigatus growth and cell wall integrity. In addition, using a fragment screen, we identified the thiol-reactive compound isothiazolone fragment of PGM as targeting a cysteine residue not conserved in the human ortholog. Furthermore, through scaffold exploration, we synthesized a para-aryl derivative (ISFP10) and demonstrated that it inhibits AfPGM with an IC50 of 2 μM and exhibits 50-fold selectivity over the human enzyme. Taken together, our data provide genetic validation of PGM as a therapeutic target and suggest new avenues for inhibiting AfPGM using covalent inhibitors that could serve as tools for chemical validation.
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Affiliation(s)
- Kaizhou Yan
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Mathew Stanley
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Bartosz Kowalski
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Olawale G Raimi
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Andrew T Ferenbach
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Pingzhen Wei
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, China
| | - Wenxia Fang
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, China
| | - Daan M F van Aalten
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom.
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4
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Gustafsson R, Eckhard U, Ye W, Enbody ED, Pettersson M, Jemth P, Andersson L, Selmer M. Structure and Characterization of Phosphoglucomutase 5 from Atlantic and Baltic Herring-An Inactive Enzyme with Intact Substrate Binding. Biomolecules 2020; 10:E1631. [PMID: 33287293 PMCID: PMC7761743 DOI: 10.3390/biom10121631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 12/31/2022] Open
Abstract
Phosphoglucomutase 5 (PGM5) in humans is known as a structural muscle protein without enzymatic activity, but detailed understanding of its function is lacking. PGM5 belongs to the alpha-D-phosphohexomutase family and is closely related to the enzymatically active metabolic enzyme PGM1. In the Atlantic herring, Clupea harengus, PGM5 is one of the genes strongly associated with ecological adaptation to the brackish Baltic Sea. We here present the first crystal structures of PGM5, from the Atlantic and Baltic herring, differing by a single substitution Ala330Val. The structure of PGM5 is overall highly similar to structures of PGM1. The structure of the Baltic herring PGM5 in complex with the substrate glucose-1-phosphate shows conserved substrate binding and active site compared to human PGM1, but both PGM5 variants lack phosphoglucomutase activity under the tested conditions. Structure comparison and sequence analysis of PGM5 and PGM1 from fish and mammals suggest that the lacking enzymatic activity of PGM5 is related to differences in active-site loops that are important for flipping of the reaction intermediate. The Ala330Val substitution does not alter structure or biophysical properties of PGM5 but, due to its surface-exposed location, could affect interactions with protein-binding partners.
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Affiliation(s)
- Robert Gustafsson
- Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, SE-751 24 Uppsala, Sweden; (R.G.); (U.E.)
| | - Ulrich Eckhard
- Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, SE-751 24 Uppsala, Sweden; (R.G.); (U.E.)
| | - Weihua Ye
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, SE-751 23 Uppsala, Sweden; (W.Y.); (E.D.E.); (M.P.); (P.J.); (L.A.)
| | - Erik D. Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, SE-751 23 Uppsala, Sweden; (W.Y.); (E.D.E.); (M.P.); (P.J.); (L.A.)
| | - Mats Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, SE-751 23 Uppsala, Sweden; (W.Y.); (E.D.E.); (M.P.); (P.J.); (L.A.)
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, SE-751 23 Uppsala, Sweden; (W.Y.); (E.D.E.); (M.P.); (P.J.); (L.A.)
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, SE-751 23 Uppsala, Sweden; (W.Y.); (E.D.E.); (M.P.); (P.J.); (L.A.)
- Department of Veterinary Integrative Biosciences, Texas A & M University, College Station, TX 77843, USA
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Maria Selmer
- Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, SE-751 24 Uppsala, Sweden; (R.G.); (U.E.)
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5
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Structural basis for substrate and product recognition in human phosphoglucomutase-1 (PGM1) isoform 2, a member of the α-D-phosphohexomutase superfamily. Sci Rep 2020; 10:5656. [PMID: 32221390 PMCID: PMC7101342 DOI: 10.1038/s41598-020-62548-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/13/2020] [Indexed: 01/01/2023] Open
Abstract
Human phosphoglucomutase 1 (PGM1) is an evolutionary conserved enzyme that belongs to the ubiquitous and ancient α-d-phosphohexomutases, a large enzyme superfamily with members in all three domains of life. PGM1 catalyzes the bi-directional interconversion between α-d-glucose 1-phosphate (G1P) and α-d-glucose 6-phosphate (G6P), a reaction that is essential for normal carbohydrate metabolism and also important in the cytoplasmic biosynthesis of nucleotide sugars needed for glycan biosynthesis. Clinical studies have shown that mutations in the PGM1 gene may cause PGM1 deficiency, an inborn error of metabolism previously classified as a glycogen storage disease, and PGM1 deficiency was recently also shown to be a congenital disorder of glycosylation. Here we present three crystal structures of the isoform 2 variant of PGM1, both as a free enzyme and in complex with its substrate and product. The structures show the longer N-terminal of this PGM1 variant, and the ligand complex structures reveal for the first time the detailed structural basis for both G1P substrate and G6P product recognition by human PGM1. We also show that PGM1 and the paralogous gene PGM5 are the results of a gene duplication event in a common ancestor of jawed vertebrates, and, importantly, that both PGM1 isoforms are conserved and of functional significance in all vertebrates. Our finding that PGM1 encodes two equally conserved and functionally important isoforms in the human organism should be taken into account in the evaluation of disease-related missense mutations in patients in the future.
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6
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Zhu JS, Stiers KM, Soleimani E, Groves BR, Beamer LJ, Jakeman DL. Inhibitory Evaluation of αPMM/PGM from Pseudomonas aeruginosa: Chemical Synthesis, Enzyme Kinetics, and Protein Crystallographic Study. J Org Chem 2019; 84:9627-9636. [DOI: 10.1021/acs.joc.9b01305] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jian-She Zhu
- College of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
| | - Kyle M. Stiers
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Ebrahim Soleimani
- College of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- Department of Chemistry, Razi University, Kermanshah 67149-67346, Iran
| | - Brandon R. Groves
- College of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
| | - Lesa J. Beamer
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - David L. Jakeman
- College of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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7
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Zhu JS, Stiers KM, Winter SM, Garcia AD, Versini AF, Beamer LJ, Jakeman DL. Synthesis, Derivatization, and Structural Analysis of Phosphorylated Mono-, Di-, and Trifluorinated d-Gluco-heptuloses by Glucokinase: Tunable Phosphoglucomutase Inhibition. ACS OMEGA 2019; 4:7029-7037. [PMID: 31179410 PMCID: PMC6547622 DOI: 10.1021/acsomega.9b00008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/08/2019] [Indexed: 05/16/2023]
Abstract
Glucokinase phosphorylated a series of C-1 fluorinated α-d-gluco-heptuloses. These phosphorylated products were discovered to be inhibitors of α-phosphomannomutase/phosphoglucomutase (αPMM/PGM) and β-phosphoglucomutase (βPGM). Inhibition potency with both mutases inversely correlated to the degree of fluorination. Structural analysis with αPMM demonstrated the inhibitor binding to the active site, with the phosphate in the phosphate binding site and the anomeric hydroxyl directed to the catalytic site.
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Affiliation(s)
- Jian-She Zhu
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
| | - Kyle M. Stiers
- Biochemistry
Department, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Sherany M. Winter
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- Department
of Chemistry, Hogeschool Leiden (UAS Leiden), Zernikedreef 11, CK Leiden 2333, The Netherlands
| | - Anthony D. Garcia
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- École
Nationale Supérieure de Chimie de Rennes, 11 Allée de Beaulieu, CS 50837, Rennes Cedex 7 35708, France
| | - Antoine F. Versini
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- École
Supérieure de Physique et de Chimie Industrielles de la Ville
de Paris, 10 rue Vauquelin, Paris 75005, France
| | - Lesa J. Beamer
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- E-mail: (L.J.B.)
| | - David L. Jakeman
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- E-mail: (D.L.J.)
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8
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Stiers KM, Graham AC, Zhu JS, Jakeman DL, Nix JC, Beamer LJ. Structural and dynamical description of the enzymatic reaction of a phosphohexomutase. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:024703. [PMID: 31041362 PMCID: PMC6443537 DOI: 10.1063/1.5092803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Enzymes are known to adopt various conformations at different points along their catalytic cycles. Here, we present a comprehensive analysis of 15 isomorphous, high resolution crystal structures of the enzyme phosphoglucomutase from the bacterium Xanthomonas citri. The protein was captured in distinct states critical to function, including enzyme-substrate, enzyme-product, and enzyme-intermediate complexes. Key residues in ligand recognition and regions undergoing conformational change are identified and correlated with the various steps of the catalytic reaction. In addition, we use principal component analysis to examine various subsets of these structures with two goals: (1) identifying sites of conformational heterogeneity through a comparison of room temperature and cryogenic structures of the apo-enzyme and (2) a priori clustering of the enzyme-ligand complexes into functionally related groups, showing sensitivity of this method to structural features difficult to detect by traditional methods. This study captures, in a single system, the structural basis of diverse substrate recognition, the subtle impact of covalent modification, and the role of ligand-induced conformational change in this representative enzyme of the α-D-phosphohexomutase superfamily.
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Affiliation(s)
- Kyle M. Stiers
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, USA
| | - Abigail C. Graham
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, USA
| | - Jian-She Zhu
- College of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 3J5, Canada
| | | | - Jay C. Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Lesa J. Beamer
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, USA
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9
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Evidence for substrate-assisted catalysis in N-acetylphosphoglucosamine mutase. Biochem J 2018; 475:2547-2557. [PMID: 29967067 PMCID: PMC6096347 DOI: 10.1042/bcj20180172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 07/02/2018] [Accepted: 07/02/2018] [Indexed: 11/17/2022]
Abstract
N-acetylphosphoglucosamine mutase (AGM1) is a key component of the hexosamine biosynthetic pathway that produces UDP-GlcNAc, an essential precursor for a wide range of glycans in eukaryotes. AGM belongs to the α-d-phosphohexomutase metalloenzyme superfamily and catalyzes the interconversion of N-acetylglucosamine-6-phosphate (GlcNAc-6P) to N-acetylglucosamine-1-phosphate (GlcNAc-1P) through N-acetylglucosamine-1,6-bisphosphate (GlcNAc-1,6-bisP) as the catalytic intermediate. Although there is an understanding of the phosphoserine-dependent catalytic mechanism at enzymatic and structural level, the identity of the requisite catalytic base in AGM1/phosphoglucomutases is as yet unknown. Here, we present crystal structures of a Michaelis complex of AGM1 with GlcNAc-6P and Mg2+, and a complex of the inactive Ser69Ala mutant together with glucose-1,6-bisphosphate (Glc-1,6-bisP) that represents key snapshots along the reaction co-ordinate. Together with mutagenesis, these structures reveal that the phosphate group of the hexose-1,6-bisP intermediate may act as the catalytic base.
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10
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Stiers KM, Beamer LJ. Assessment and Impacts of Phosphorylation on Protein Flexibility of the α-d-Phosphohexomutases. Methods Enzymol 2018; 607:241-267. [DOI: 10.1016/bs.mie.2018.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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11
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Rexer TFT, Schildbach A, Klapproth J, Schierhorn A, Mahour R, Pietzsch M, Rapp E, Reichl U. One pot synthesis of GDP-mannose by a multi-enzyme cascade for enzymatic assembly of lipid-linked oligosaccharides. Biotechnol Bioeng 2017; 115:192-205. [PMID: 28922469 PMCID: PMC5765510 DOI: 10.1002/bit.26454] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 12/22/2022]
Abstract
Glycosylation of proteins is a key function of the biosynthetic‐secretory pathway in the endoplasmic reticulum (ER) and Golgi apparatus. Glycosylated proteins play a crucial role in cell trafficking and signaling, cell‐cell adhesion, blood‐group antigenicity, and immune response. In addition, the glycosylation of proteins is an important parameter in the optimization of many glycoprotein‐based drugs such as monoclonal antibodies. In vitro glycoengineering of proteins requires glycosyltransferases as well as expensive nucleotide sugars. Here, we present a designed pathway consisting of five enzymes, glucokinase (Glk), phosphomannomutase (ManB), mannose‐1‐phosphate‐guanyltransferase (ManC), inorganic pyrophosphatase (PmPpA), and 1‐domain polyphosphate kinase 2 (1D‐Ppk2) expressed in E. coli for the cell‐free production and regeneration of GDP‐mannose from mannose and polyphosphate with catalytic amounts of GDP and ADP. It was shown that GDP‐mannose is produced at various conditions, that is pH 7–8, temperature 25–35°C and co‐factor concentrations of 5–20 mM MgCl2. The maximum reaction rate of GDP‐mannose achieved was 2.7 μM/min at 30°C and 10 mM MgCl2 producing 566 nmol GDP‐mannose after a reaction time of 240 min. With respect to the initial GDP concentration (0.8 mM) this is equivalent to a yield of 71%. Additionally, the cascade was coupled to purified, transmembrane‐deleted Alg1 (ALG1ΔTM), the first mannosyltransferase in the ER‐associated lipid‐linked oligosaccharide (LLO) assembly. Thereby, in a one‐pot reaction, phytanyl‐PP‐(GlcNAc)2‐Man1 was produced with efficient nucleotide sugar regeneration for the first time. Phytanyl‐PP‐(GlcNAc)2‐Man1 can serve as a substrate for the synthesis of LLO for the cell‐free in vitro glycosylation of proteins. A high‐performance anion exchange chromatography method with UV and conductivity detection (HPAEC‐UV/CD) assay was optimized and validated to determine the enzyme kinetics. The established kinetic model enabled the optimization of the GDP‐mannose regenerating cascade and can further be used to study coupling of the GDP‐mannose cascade with glycosyltransferases. Overall, the study envisages a first step towards the development of a platform for the cell‐free production of LLOs as precursors for in vitro glycoengineering of proteins.
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Affiliation(s)
- Thomas F T Rexer
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Anna Schildbach
- Department of Downstream Processing, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Jan Klapproth
- Department of Downstream Processing, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Angelika Schierhorn
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Reza Mahour
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Markus Pietzsch
- Department of Downstream Processing, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.,Otto-von-Guericke University Magdeburg, Chair of Bioprocess Engineering, Magdeburg, Germany
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12
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Multiple Ligand-Bound States of a Phosphohexomutase Revealed by Principal Component Analysis of NMR Peak Shifts. Sci Rep 2017; 7:5343. [PMID: 28706231 PMCID: PMC5509744 DOI: 10.1038/s41598-017-05557-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/31/2017] [Indexed: 11/08/2022] Open
Abstract
Enzymes sample multiple conformations during their catalytic cycles. Chemical shifts from Nuclear Magnetic Resonance (NMR) are hypersensitive to conformational changes and ensembles in solution. Phosphomannomutase/phosphoglucomutase (PMM/PGM) is a ubiquitous four-domain enzyme that catalyzes phosphoryl transfer across phosphohexose substrates. We compared states the enzyme visits during its catalytic cycle. Collective responses of Pseudomonas PMM/PGM to phosphosugar substrates and inhibitor were assessed using NMR-detected titrations. Affinities were estimated from binding isotherms obtained by principal component analysis (PCA). Relationships among phosphosugar-enzyme associations emerge from PCA comparisons of the titrations. COordiNated Chemical Shifts bEhavior (CONCISE) analysis provides novel discrimination of three ligand-bound states of PMM/PGM harboring a mutation that suppresses activity. Enzyme phosphorylation and phosphosugar binding appear to drive the open dephosphorylated enzyme to the free phosphorylated state, and on toward ligand-closed states. Domain 4 appears central to collective responses to substrate and inhibitor binding. Hydrogen exchange reveals that binding of a substrate analogue enhances folding stability of the domains to a uniform level, establishing a globally unified structure. CONCISE and PCA of NMR spectra have discovered novel states of a well-studied enzyme and appear ready to discriminate other enzyme and ligand binding states.
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13
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Stiers KM, Muenks AG, Beamer LJ. Biology, Mechanism, and Structure of Enzymes in the α-d-Phosphohexomutase Superfamily. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 109:265-304. [PMID: 28683921 PMCID: PMC5802415 DOI: 10.1016/bs.apcsb.2017.04.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enzymes in the α-d-phosphohexomutases superfamily catalyze the reversible conversion of phosphosugars, such as glucose 1-phosphate and glucose 6-phosphate. These reactions are fundamental to primary metabolism across the kingdoms of life and are required for a myriad of cellular processes, ranging from exopolysaccharide production to protein glycosylation. The subject of extensive mechanistic characterization during the latter half of the 20th century, these enzymes have recently benefitted from biophysical characterization, including X-ray crystallography, NMR, and hydrogen-deuterium exchange studies. This work has provided new insights into the unique catalytic mechanism of the superfamily, shed light on the molecular determinants of ligand recognition, and revealed the evolutionary conservation of conformational flexibility. Novel associations with inherited metabolic disease and the pathogenesis of bacterial infections have emerged, spurring renewed interest in the long-appreciated functional roles of these enzymes.
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Affiliation(s)
| | | | - Lesa J Beamer
- University of Missouri, Columbia, MO, United States.
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14
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Lee Y, Furdui C, Beamer LJ. Data on the phosphorylation state of the catalytic serine of enzymes in the α-D-phosphohexomutase superfamily. Data Brief 2016; 10:398-405. [PMID: 28050582 PMCID: PMC5192239 DOI: 10.1016/j.dib.2016.12.017] [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: 11/14/2016] [Revised: 12/06/2016] [Accepted: 12/08/2016] [Indexed: 01/28/2023] Open
Abstract
Most enzymes in the α-D-phosphohexomutase superfamily catalyze the reversible conversion of 1- to 6-phosphosugars. They play important roles in carbohydrate and sugar nucleotide metabolism, and participate in the biosynthesis of polysaccharides, glycolipids, and other exoproducts. Mutations in genes encoding these enzymes are associated with inherited metabolic diseases in humans, including glycogen storage disease and congenital disorders of glycosylation. Enzymes in the superfamily share a highly conserved active site serine that participates in the multi-step phosphoryl transfer reaction. Here we provide data on the effects of various phosphosugar ligands on the phosphorylation of this serine, as monitored by electrospray ionization mass spectrometry (ESI-MS) data on the intact proteins. We also show data on the longevity of the phospho-enzyme under various solution conditions in one member of the superfamily from Pseudomonas aeruginosa, and present inhibition data for several ligands. These data should be useful for the production of homogeneous samples of phosphorylated or unphosphorylated proteins, which are essential for biophysical characterization of these enzymes.
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Affiliation(s)
- Yingying Lee
- Departments of Biochemistry and Chemistry, University of Missouri-Columbia, Columbia, MO 65211, United States
| | - Cristina Furdui
- Department of Internal Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Lesa J. Beamer
- Departments of Biochemistry and Chemistry, University of Missouri-Columbia, Columbia, MO 65211, United States
- Corresponding author.
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15
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Waugh B, Sen U, Banerjee R. Crystal structure of phosphoglucomutase from Leishmania major at 3.5 Å resolution. Biochimie 2015; 121:102-11. [PMID: 26607241 DOI: 10.1016/j.biochi.2015.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/17/2015] [Indexed: 10/22/2022]
Abstract
The crystal structure of phosphoglucomutase (LmPGM) from the parasite Leishmania major has been solved at 3.5 Å resolution. Although the active form of the enzyme is monomeric in solution, four molecules (A, B, C, D) were found in the asymmetric unit, of which the pairs (A,D) and (B,C) were of identical inter-subunit geometry. The parasitic enzyme constituted of four domains exhibited the canonical 'heart' shape of the protein, with domains I to III having a conserved α|β core, while the fourth (IV) domain being structurally distinct from the rest. Conformational variability of the IVth domain, postulated to be responsible for the catalytic function of the enzyme has been studied by normal mode analysis (NMA) and the conformational features responsible for domain movement in the 'hinge region' analyzed in detail. Although the active site of phosphoglucomutase is highly conserved from parasite to human, initial calculations show that a ligand binding pocket could exist near the hinge region, which is unique to the parasite. The enzymatic parameters of LmPGM have been determined and compared with other PGMs from orthologous species in addition to elucidating its mechanism of action by docking the substrate, intermediate onto the active site.
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Affiliation(s)
- Barnali Waugh
- Saha Institute of Nuclear Physics, Crystallography and Molecular Biology Division, Sector 1, Block AF, Bidhannagar, Kolkata, West Bengal, India.
| | - Udayaditya Sen
- Saha Institute of Nuclear Physics, Crystallography and Molecular Biology Division, Sector 1, Block AF, Bidhannagar, Kolkata, West Bengal, India.
| | - Rahul Banerjee
- Saha Institute of Nuclear Physics, Crystallography and Molecular Biology Division, Sector 1, Block AF, Bidhannagar, Kolkata, West Bengal, India.
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16
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Xu J, Lee Y, Beamer LJ, Van Doren SR. Phosphorylation in the catalytic cleft stabilizes and attracts domains of a phosphohexomutase. Biophys J 2015; 108:325-37. [PMID: 25606681 DOI: 10.1016/j.bpj.2014.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 11/22/2014] [Accepted: 12/03/2014] [Indexed: 11/18/2022] Open
Abstract
Phosphorylation can modulate the activities of enzymes. The phosphoryl donor in the catalytic cleft of α-D-phosphohexomutases is transiently dephosphorylated while the reaction intermediate completes a 180° reorientation within the cleft. The phosphorylated form of 52 kDa bacterial phosphomannomutase/phosphoglucomutase is less accessible to dye or protease, more stable to chemical denaturation, and widely stabilized against NMR-detected hydrogen exchange across the core of domain 3 to juxtaposed domain 4 (each by ≥ 1.3 kcal/mol) and parts of domains 1 and 2. However, phosphorylation accelerates hydrogen exchange in specific regions of domains 1 and 2, including a metal-binding residue in the active site. Electrostatic field lines reveal attraction across the catalytic cleft between phosphorylated Ser-108 and domain 4, but repulsion when Ser-108 is dephosphorylated. Molecular dynamics (MD) simulated the dephosphorylated form to be expanded due to enhanced rotational freedom of domain 4. The contacts and fluctuations of the MD trajectories enabled correct simulation of more than 80% of sites that undergo either protection or deprotection from hydrogen exchange due to phosphorylation. Electrostatic attraction in the phosphorylated enzyme accounts for 1) domain 4 drawing closer to domains 1 and 3; 2) decreased accessibility; and 3) increased stability within these domains. The electrostriction due to phosphorylation may help capture substrate, whereas the opening of the cleft upon transient dephosphorylation allows rotation of the intermediate. The long-range effects of phosphorylation on hydrogen exchange parallel reports on protein kinases, suggesting a conceptual link among these multidomain, phosphoryl transfer enzymes.
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Affiliation(s)
- Jia Xu
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Yingying Lee
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Lesa J Beamer
- Department of Biochemistry, University of Missouri, Columbia, Missouri
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17
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Wei Y, Marcink TC, Xu J, Sirianni AG, Sarma AVS, Prior SH, Beamer LJ, Van Doren SR. Chemical shift assignments of domain 4 from the phosphohexomutase from Pseudomonas aeruginosa suggest that freeing perturbs its coevolved domain interface. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:329-333. [PMID: 23893395 PMCID: PMC3905050 DOI: 10.1007/s12104-013-9511-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/18/2013] [Indexed: 06/02/2023]
Abstract
A domain needed for the catalytic efficiency of an enzyme model of simple processivity and domain-domain interactions has been characterized by NMR. This domain 4 from phosphomannomutase/phosphoglucomutase (PMM/PGM) closes upon glucose phosphate and mannose phosphate ligands in the active site, and can modestly reconstitute activity of enzyme truncated to domains 1-3. This enzyme supports biosynthesis of the saccharide-derived virulence factors (rhamnolipids, lipopolysaccharides, and alginate) of the opportunistic bacterial pathogen Pseudomonas aeruginosa. (1)H, (13)C, and (15)N NMR chemical shift assignments of domain 4 of PMM/PGM suggest preservation and independence of its structure when separated from domains 1-3. The face of domain 4 that packs with domain 3 is perturbed in NMR spectra without disrupting this fold. The perturbed residues overlap both the most highly coevolved positions in the interface and residues lining a cavity at the domain interface.
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18
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Bazzi W, Sabra A, Zahreddine L, Khairallah MT, Baroud M, Hadi U, Matar GM. The inhibitory effect of micafungin on biofilm formation by Pseudomonas aeruginosa. BIOFOULING 2013; 29:909-915. [PMID: 23879871 DOI: 10.1080/08927014.2013.816299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This study assesses the potential effect of micafungin, an antifungal agent known to inhibit 1,3-β-D-glucan synthesis in Candida albicans, on biofilm formation of selected Pseudomonas aeruginosa isolates by decreasing the synthesis of extracellular matrix β-D-glucan forming units. The effect of an optimal therapeutic dose of 10 mg ml(-1) micafungin on the production of biofilm was monitored in vitro using a microtiter plate assay. Phenotypic reduction in the formation of biofilm was significant (based on average optical density; p < 0.05) in most of the isolates. Moreover, the relative gene expression of biofilm encoding genes for alginate and pellicles (algC and pelC, respectively), and the cell wall 1,3-β-D-glucan encoding gene (ndvB) was evaluated using quantitative reverse transcription PCR. For all the genes tested, the levels of mRNA transcription were also decreased significantly (p < 0.05) in micafungin-treated samples cf. their untreated counterparts. In conclusion, this study presents micafungin as a potential agent for disrupting the structure of a biofilm of P. aeruginosa allowing the possible exposure and treatment of core-planktonic cells.
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Affiliation(s)
- Wael Bazzi
- Department of Experimental Pathology, Immunology and Microbiology, American University of Beirut, Beirut, Lebanon
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Lee Y, Mehra-Chaudhary R, Furdui C, Beamer LJ. Identification of an essential active-site residue in the α-D-phosphohexomutase enzyme superfamily. FEBS J 2013; 280:2622-32. [PMID: 23517223 DOI: 10.1111/febs.12249] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 03/12/2013] [Accepted: 03/14/2013] [Indexed: 12/01/2022]
Abstract
UNLABELLED Enzymes in the α-d-phosphohexomutase superfamily catalyze the conversion of 1-phosphosugars to their 6-phospho counterparts. Their phosphoryl transfer reaction has long been proposed to require general acid-base catalysts, but candidate residues for these key roles have not been identified. In this study, we show through mutagenesis and kinetic studies that a histidine (His329) in the active site is critical for enzyme activity in a well-studied member of the superfamily, phosphomannomutase/phosphoglucomutase from Pseudomonas aeruginosa. Crystallographic characterization of an H329A mutant protein showed no significant changes from the wild-type enzyme, excluding structural disruption as the source of its compromised activity. Mutation of the structurally analogous lysine residue in a related protein, phosphoglucomutase from Salmonella typhimurium, also results in significant catalytic impairment. Analyses of protein-ligand complexes of the P. aeruginosa enzyme show that His329 is appropriately positioned to abstract a proton from the O1/O6 hydroxyl of the phosphosugar substrates, and thus may serve as the general base in the reaction. Histidine is strongly conserved at this position in many proteins in the superfamily, and lysine is also often conserved at a structurally corresponding position, particularly in the phosphoglucomutase enzyme sub-group. These studies shed light on the mechanism of this important enzyme superfamily, and may facilitate the design of mechanism-based inhibitors. DATABASE Structural data have been deposited in the Protein Data Bank with accession number 4IL8.
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Affiliation(s)
- Yingying Lee
- Chemistry Department, University of Missouri, Columbia, MO 65211, USA
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20
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Conservation of functionally important global motions in an enzyme superfamily across varying quaternary structures. J Mol Biol 2012; 423:831-46. [PMID: 22935436 DOI: 10.1016/j.jmb.2012.08.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 08/16/2012] [Accepted: 08/17/2012] [Indexed: 11/21/2022]
Abstract
The α-d-phosphohexomutase superfamily comprises enzymes involved in carbohydrate metabolism that are found in all kingdoms of life. Recent biophysical studies have shown for the first time that several of these enzymes exist as dimers in solution, prompting an examination of the oligomeric state of all proteins of known structure in the superfamily (11 different proteins; 31 crystal structures) via computational and experimental analyses. We find that these proteins range in quaternary structure from monomers to tetramers, with 6 of the 11 known structures being likely oligomers. The oligomeric state of these proteins not only is associated in some cases with enzyme subgroup (i.e., substrate specificity) but also appears to depend on domain of life, with the two archaeal proteins existing as higher-order oligomers. Within the oligomers, three distinct interfaces are observed, one of which is found in both archaeal and bacterial proteins. Normal mode analysis shows that the topological arrangement of the oligomers permits domain 4 of each protomer to move independently as required for catalysis. Our analysis suggests that the advantages associated with protein flexibility in this enzyme family are of sufficient importance to be maintained during the evolution of multiple independent oligomers. This study is one of the first showing that global motions may be conserved not only within protein families but also across members of a superfamily with varying oligomeric structures.
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21
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Lee Y, Mick J, Furdui C, Beamer LJ. A coevolutionary residue network at the site of a functionally important conformational change in a phosphohexomutase enzyme family. PLoS One 2012; 7:e38114. [PMID: 22685552 PMCID: PMC3369874 DOI: 10.1371/journal.pone.0038114] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 05/01/2012] [Indexed: 11/26/2022] Open
Abstract
Coevolution analyses identify residues that co-vary with each other during evolution, revealing sequence relationships unobservable from traditional multiple sequence alignments. Here we describe a coevolutionary analysis of phosphomannomutase/phosphoglucomutase (PMM/PGM), a widespread and diverse enzyme family involved in carbohydrate biosynthesis. Mutual information and graph theory were utilized to identify a network of highly connected residues with high significance. An examination of the most tightly connected regions of the coevolutionary network reveals that most of the involved residues are localized near an interdomain interface of this enzyme, known to be the site of a functionally important conformational change. The roles of four interface residues found in this network were examined via site-directed mutagenesis and kinetic characterization. For three of these residues, mutation to alanine reduces enzyme specificity to ∼10% or less of wild-type, while the other has ∼45% activity of wild-type enzyme. An additional mutant of an interface residue that is not densely connected in the coevolutionary network was also characterized, and shows no change in activity relative to wild-type enzyme. The results of these studies are interpreted in the context of structural and functional data on PMM/PGM. Together, they demonstrate that a network of coevolving residues links the highly conserved active site with the interdomain conformational change necessary for the multi-step catalytic reaction. This work adds to our understanding of the functional roles of coevolving residue networks, and has implications for the definition of catalytically important residues.
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Affiliation(s)
- Yingying Lee
- Department of Chemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Jacob Mick
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Cristina Furdui
- Department of Internal Medicine, Wake Forest University Health Sciences Winston-Salem, North Carolina, United States of America
| | - Lesa J. Beamer
- Department of Chemistry, University of Missouri, Columbia, Missouri, United States of America
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
- * E-mail:
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22
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Sarma AVS, Anbanandam A, Kelm A, Mehra-Chaudhary R, Wei Y, Qin P, Lee Y, Berjanskii MV, Mick JA, Beamer LJ, Van Doren SR. Solution NMR of a 463-residue phosphohexomutase: domain 4 mobility, substates, and phosphoryl transfer defect. Biochemistry 2012; 51:807-19. [PMID: 22242625 DOI: 10.1021/bi201609n] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phosphomannomutase/phosphoglucomutase contributes to the infectivity of Pseudomonas aeruginosa, retains and reorients its intermediate by 180°, and rotates domain 4 to close the deep catalytic cleft. Nuclear magnetic resonance (NMR) spectra of the backbone of wild-type and S108C-inactivated enzymes were assigned to at least 90%. (13)C secondary chemical shifts report excellent agreement of solution and crystallographic structure over the 14 α-helices, C-capping motifs, and 20 of the 22 β-strands. Major and minor NMR peaks implicate substates affecting 28% of assigned residues. These can be attributed to the phosphorylation state and possibly to conformational interconversions. The S108C substitution of the phosphoryl donor and acceptor slowed transformation of the glucose 1-phosphate substrate by impairing k(cat). Addition of the glucose 1,6-bisphosphate intermediate accelerated this reaction by 2-3 orders of magnitude, somewhat bypassing the defect and apparently relieving substrate inhibition. The S108C mutation perturbs the NMR spectra and electron density map around the catalytic cleft while preserving the secondary structure in solution. Diminished peak heights and faster (15)N relaxation suggest line broadening and millisecond fluctuations within four loops that can contact phosphosugars. (15)N NMR relaxation and peak heights suggest that domain 4 reorients slightly faster in solution than domains 1-3, and with a different principal axis of diffusion. This adds to the crystallographic evidence of domain 4 rotations in the enzyme, which were previously suggested to couple to reorientation of the intermediate, substrate binding, and product release.
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Affiliation(s)
- Akella V S Sarma
- Biochemistry Department, University of Missouri, Columbia, Missouri 65211, United States
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23
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Crystal structure of Bacillus anthracis phosphoglucosamine mutase, an enzyme in the peptidoglycan biosynthetic pathway. J Bacteriol 2011; 193:4081-7. [PMID: 21685296 DOI: 10.1128/jb.00418-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phosphoglucosamine mutase (PNGM) is an evolutionarily conserved bacterial enzyme that participates in the cytoplasmic steps of peptidoglycan biosynthesis. As peptidoglycan is essential for bacterial survival and is absent in humans, enzymes in this pathway have been the focus of intensive inhibitor design efforts. Many aspects of the structural biology of the peptidoglycan pathway have been elucidated, with the exception of the PNGM structure. We present here the crystal structure of PNGM from the human pathogen and bioterrorism agent Bacillus anthracis. The structure reveals key residues in the large active site cleft of the enzyme which likely have roles in catalysis and specificity. A large conformational change of the C-terminal domain of PNGM is observed when comparing two independent molecules in the crystal, shedding light on both the apo- and ligand-bound conformers of the enzyme. Crystal packing analyses and dynamic light scattering studies suggest that the enzyme is a dimer in solution. Multiple sequence alignments show that residues in the dimer interface are conserved, suggesting that many PNGM enzymes adopt this oligomeric state. This work lays the foundation for the development of inhibitors for PNGM enzymes from human pathogens.
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24
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Going Beyond Continuous Glucose Monitoring with Boronic Acid-Appended Bipyridinium Salts. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/978-1-4419-9672-5_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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25
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Mehra-Chaudhary R, Mick J, Tanner JJ, Henzl MT, Beamer LJ. Crystal structure of a bacterial phosphoglucomutase, an enzyme involved in the virulence of multiple human pathogens. Proteins 2011; 79:1215-29. [PMID: 21246636 PMCID: PMC3066478 DOI: 10.1002/prot.22957] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 11/12/2010] [Accepted: 11/24/2010] [Indexed: 11/11/2022]
Abstract
The crystal structure of the enzyme phosphoglucomutase from Salmonella typhimurium (StPGM) is reported at 1.7 A resolution. This is the first high-resolution structural characterization of a bacterial protein from this large enzyme family, which has a central role in metabolism and is also important to bacterial virulence and infectivity. A comparison of the active site of StPGM with that of other phosphoglucomutases reveals conserved residues that are likely involved in catalysis and ligand binding for the entire enzyme family. An alternate crystal form of StPGM and normal mode analysis give insights into conformational changes of the C-terminal domain that occur upon ligand binding. A novel observation from the StPGM structure is an apparent dimer in the asymmetric unit of the crystal, mediated largely through contacts in an N-terminal helix. Analytical ultracentrifugation and small-angle X-ray scattering confirm that StPGM forms a dimer in solution. Multiple sequence alignments and phylogenetic studies show that a distinct subset of bacterial PGMs share the signature dimerization helix, while other bacterial and eukaryotic PGMs are likely monomers. These structural, biochemical, and bioinformatic studies of StPGM provide insights into the large α-D-phosphohexomutase enzyme superfamily to which it belongs, and are also relevant to the design of inhibitors specific to the bacterial PGMs.
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Affiliation(s)
- Ritcha Mehra-Chaudhary
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211
| | - Jacob Mick
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211
| | - John J. Tanner
- Department of Chemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211
| | - Michael T. Henzl
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211
| | - Lesa J. Beamer
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211
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26
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Chuang GY, Mehra-Chaudhary R, Ngan CH, Zerbe BS, Kozakov D, Vajda S, Beamer LJ. Domain motion and interdomain hot spots in a multidomain enzyme. Protein Sci 2011; 19:1662-72. [PMID: 20589904 DOI: 10.1002/pro.446] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The aim of this article is to analyze conformational changes by comparing 10 different structures of Pseudomonas aeruginosa phosphomannomutase/phosphoglucomutase (PMM/PGM), a four-domain enzyme in which both substrate binding and catalysis require substantial movement of the C-terminal domain. We focus on changes in interdomain and active site crevices using a method called computational solvent mapping rather than superimposing the structures. The method places molecular probes (i.e., small organic molecules containing various functional groups) around the protein to find hot spots. One of the most important hot spots is in the active site, consistent with the ability of the enzyme to bind both glucose and mannose phosphosugar substrates. The protein has eight additional hot spots at domain-domain interfaces and hinge regions. The locations and nature of six of these hot spots vary between the open, half-open, and closed conformers of the enzyme, in good agreement with the ligand-induced conformational changes. In the closed structures the number of probe clusters at the hinge region significantly depends on the position of the phosphorylated oxygen in the substrate (e.g., glucose 1-phosphate versus glucose 6-phosphate), but the protein remains almost unchanged in terms of the overall RMSD, indicating that computational solvent mapping is a more sensitive approach to detect changes in binding sites and interdomain crevices. Focusing on multidomain proteins we show that the subresolution conformational differences revealed by the mapping are in fact significant, and present a general statistical method of analysis to determine the significance of rigid body domain movements in X-ray structures.
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Affiliation(s)
- Gwo-Yu Chuang
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
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27
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DFT investigation on the reaction mechanism catalyzed by α-phosphomannomutase1 in protonated/deprotonated states. J Mol Model 2011; 17:577-85. [DOI: 10.1007/s00894-010-0743-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2009] [Accepted: 05/04/2010] [Indexed: 10/19/2022]
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28
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Schramm AM, Karr D, Mehra-Chaudhary R, Van Doren SR, Furdui CM, Beamer LJ. Breaking the covalent connection: Chain connectivity and the catalytic reaction of PMM/PGM. Protein Sci 2010; 19:1235-42. [PMID: 20512975 DOI: 10.1002/pro.402] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Fragment complementation has been used to investigate the role of chain connectivity in the catalytic reaction of phosphomannomutase/phosphoglucomutase (PMM/PGM) from Pseudomonas aeruginosa, a human pathogen. A heterodimer of PMM/PGM, created from fragments corresponding to its first three and fourth domains, was constructed and enzyme activity reconstituted. NMR spectra demonstrate that the fragment corresponding to the fourth (C-terminal) domain exists as a highly structured, independent folding domain, consistent with its varied conformation observed in enzyme-substrate complexes. Steady-state kinetics and thermodynamics studies reported here show that complete conformational freedom of Domain 4, because of the break in the polypeptide chain, is deleterious to catalytic efficiency primarily as a consequence of increased entropy. This extends observations from studies of the intact enzyme, which showed that the degree of flexibility of a hinge region is controlled by the precise sequence of amino acids optimized through evolutionary constraints. This work also sheds light on the functional advantage gained by combining separate folding domains into a single polypeptide chain.
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Affiliation(s)
- Andrew M Schramm
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
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29
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Phosphoglucomutase of Yersinia pestis is required for autoaggregation and polymyxin B resistance. Infect Immun 2009; 78:1163-75. [PMID: 20028810 DOI: 10.1128/iai.00997-09] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yersinia pestis, the causative agent of plague, autoaggregates within a few minutes of cessation of shaking when grown at 28 degrees C. To identify the autoaggregation factor of Y. pestis, we performed mariner-based transposon mutagenesis. Autoaggregation-defective mutants from three different pools were identified, each with a transposon insertion at a different position within the gene encoding phosphoglucomutase (pgmA; y1258). Targeted deletion of pgmA in Y. pestis KIM5 also resulted in loss of autoaggregation. Given the previously defined role for phosphoglucomutase in antimicrobial peptide resistance in other organisms, we tested the KIM5 DeltapgmA mutant for antimicrobial peptide sensitivity. The DeltapgmA mutant displayed >1,000-fold increased sensitivity to polymyxin B compared to the parental Y. pestis strain, KIM5. This sensitivity is not due to changes in lipopolysaccharide (LPS) since the LPSs from both Y. pestis KIM5 and the DeltapgmA mutant are identical based on a comparison of their structures by mass spectrometry (MS), tandem MS, and nuclear magnetic resonance analyses. Furthermore, the ability of polymyxin B to neutralize LPS toxicity was identical for LPS purified from both KIM5 and the DeltapgmA mutant. Our results indicate that increased polymyxin B sensitivity of the DeltapgmA mutant is due to changes in surface structures other than LPS. Experiments with mice via the intravenous and intranasal routes did not demonstrate any virulence defect for the DeltapgmA mutant, nor was flea colonization or blockage affected. Our findings suggest that the activity of PgmA results in modification and/or elaboration of a surface component of Y. pestis responsible for autoaggregation and polymyxin B resistance.
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30
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Enzyme assays with boronic acid appended bipyridinium salts. Anal Chim Acta 2009; 649:246-51. [DOI: 10.1016/j.aca.2009.07.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Revised: 07/09/2009] [Accepted: 07/14/2009] [Indexed: 11/19/2022]
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31
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Dai J, Finci L, Zhang C, Lahiri S, Zhang G, Peisach E, Allen KN, Dunaway-Mariano D. Analysis of the structural determinants underlying discrimination between substrate and solvent in beta-phosphoglucomutase catalysis. Biochemistry 2009; 48:1984-95. [PMID: 19154134 DOI: 10.1021/bi801653r] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tauhe beta-phosphoglucomutase (beta-PGM) of the haloacid dehalogenase enzyme superfamily (HADSF) catalyzes the conversion of beta-glucose 1-phosphate (betaG1P) to glucose 6-phosphate (G6P) using Asp8 of the core domain active site to mediate phosphoryl transfer from beta-glucose 1,6-(bis)phosphate (betaG1,6bisP) to betaG1P. Herein, we explore the mechanism by which hydrolysis of the beta-PGM phospho-Asp8 is avoided during the time that the active site must remain open to solvent to allow the exchange of the bound product G6P with the substrate betaG1P. On the basis of structural information, a model of catalysis is proposed in which the general acid/base (Asp10) side chain moves from a position where it forms a hydrogen bond to the Thr16-Ala17 portion of the domain-domain linker to a functional position where it forms a hydrogen bond to the substrate leaving group O and a His20-Lys76 pair of the cap domain. This repositioning of the general acid/base within the core domain active site is coordinated with substrate-induced closure of the cap domain over the core domain. The model predicts that Asp10 is required for general acid/base catalysis and for stabilization of the enzyme in the cap-closed conformation. It also predicts that hinge residue Thr16 plays a key role in productive domain-domain association, that hydrogen bond interaction with the Thr16 backbone amide NH group is required to prevent phospho-Asp8 hydrolysis in the cap-open conformation, and that the His20-Lys76 pair plays an important role in substrate-induced cap closure. The model is examined via kinetic analyses of Asp10, Thr16, His20, and Lys76 site-directed mutants. Replacement of Asp10 with Ala, Ser, Cys, Asn, or Glu resulted in no observable activity. The kinetic consequences of the replacement of linker residue Thr16 with Pro include a reduced rate of Asp8 phosphorylation by betaG1,6bisP, a reduced rate of cycling of the phosphorylated enzyme to convert betaG1P to G6P, and an enhanced rate of phosphoryl transfer from phospho-Asp8 to water. The X-ray crystal structure of the T16P mutant at 2.7 A resolution provides a snapshot of the enzyme in an unnatural cap-open conformation where the Asp10 side chain is located in the core domain active site. The His20 and Lys76 site-directed mutants exhibit reduced activity in catalysis of the Asp8-mediated phosphoryl transfer between betaG1,6bisP and betaG1P but no reduction in the rate of phospho-Asp8 hydrolysis. Taken together, the results support a substrate induced-fit model of catalysis in which betaG1P binding to the core domain facilitates recruitment of the general acid/base Asp10 to the catalytic site and induces cap closure.
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Affiliation(s)
- Jianying Dai
- Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, USA
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32
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Unusual starch degradation pathway via cyclodextrins in the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus strain 7324. J Bacteriol 2007; 189:8901-13. [PMID: 17921308 DOI: 10.1128/jb.01136-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hyperthermophilic archaeon Archaeoglobus fulgidus strain 7324 has been shown to grow on starch and sulfate and thus represents the first sulfate reducer able to degrade polymeric sugars. The enzymes involved in starch degradation to glucose 6-phosphate were studied. In extracts of starch-grown cells the activities of the classical starch degradation enzymes, alpha-amylase and amylopullulanase, could not be detected. Instead, evidence is presented here that A. fulgidus utilizes an unusual pathway of starch degradation involving cyclodextrins as intermediates. The pathway comprises the combined action of an extracellular cyclodextrin glucanotransferase (CGTase) converting starch to cyclodextrins and the intracellular conversion of cyclodextrins to glucose 6-phosphate via cyclodextrinase (CDase), maltodextrin phosphorylase (Mal-P), and phosphoglucomutase (PGM). These enzymes, which are all induced after growth on starch, were characterized. CGTase catalyzed the conversion of starch to mainly beta-cyclodextrin. The gene encoding CGTase was cloned and sequenced and showed highest similarity to a glucanotransferase from Thermococcus litoralis. After transport of the cyclodextrins into the cell by a transport system to be defined, these molecules are linearized via a CDase, catalyzing exclusively the ring opening of the cyclodextrins to the respective maltooligodextrins. These are degraded by a Mal-P to glucose 1-phosphate. Finally, PGM catalyzes the conversion of glucose 1-phosphate to glucose 6-phosphate, which is further degraded to pyruvate via the modified Embden-Meyerhof pathway.
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Regni C, Shackelford GS, Beamer LJ. Complexes of the enzyme phosphomannomutase/phosphoglucomutase with a slow substrate and an inhibitor. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:722-6. [PMID: 16880541 PMCID: PMC2242917 DOI: 10.1107/s1744309106025887] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Accepted: 07/04/2006] [Indexed: 11/10/2022]
Abstract
Two complexes of the enzyme phosphomannomutase/phosphoglucomutase (PMM/PGM) from Pseudomonas aeruginosa with a slow substrate and with an inhibitor have been characterized by X-ray crystallography. Both ligands induce an interdomain rearrangement in the enzyme that creates a highly buried active site. Comparisons with enzyme-substrate complexes show that the inhibitor xylose 1-phosphate utilizes many of the previously observed enzyme-ligand interactions. In contrast, analysis of the ribose 1-phosphate complex reveals a combination of new and conserved enzyme-ligand interactions for binding. The ability of PMM/PGM to accommodate these two pentose phosphosugars in its active site may be relevant for future efforts towards inhibitor design.
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Affiliation(s)
- Catherine Regni
- Department of Structural Biology, St Jude Children’s Research Hospital, 332 North Lauderdale M/S 311, Memphis, TN 38105, USA
| | - Grant S. Shackelford
- Department of Biopharmaceutical Sciences, University of California, 1700 Fourth Street, San Francisco, CA 94158, USA
| | - Lesa J. Beamer
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri-Columbia, Columbia, MO 65211, USA
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Regni C, Schramm AM, Beamer LJ. The Reaction of Phosphohexomutase from Pseudomonas aeruginosa. J Biol Chem 2006; 281:15564-71. [PMID: 16595672 DOI: 10.1074/jbc.m600590200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The enzyme phosphomannomutase/phosphoglucomutase (PMM/PGM) from Pseudomonas aeruginosa catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars. The reaction entails two phosphoryl transfers, with an intervening 180 degrees reorientation of the reaction intermediate (e.g. glucose 1,6-bisphosphate) during catalysis. Reorientation of the intermediate occurs without dissociation from the active site of the enzyme and is, thus, a simple example of processivity, as defined by multiple rounds of catalysis without release of substrate. Structural characterization of two PMM/PGM-intermediate complexes with glucose 1,6-bisphosphate provides new insights into the reaction catalyzed by the enzyme, including the reorientation of the intermediate. Kinetic analyses of site-directed mutants prompted by the structural studies reveal active site residues critical for maintaining association with glucose 1,6-bisphosphate during its unique dynamic reorientation in the active site of PMM/PGM.
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Affiliation(s)
- Catherine Regni
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
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35
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Nishitani Y, Maruyama D, Nonaka T, Kita A, Fukami TA, Mio T, Yamada-Okabe H, Yamada-Okabe T, Miki K. Crystal structures of N-acetylglucosamine-phosphate mutase, a member of the alpha-D-phosphohexomutase superfamily, and its substrate and product complexes. J Biol Chem 2006; 281:19740-7. [PMID: 16651269 DOI: 10.1074/jbc.m600801200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
N-acetylglucosamine-phosphate mutase (AGM1) is an essential enzyme in the synthetic process of UDP-N-acetylglucosamine (UDP-GlcNAc). UDP-GlcNAc is a UDP sugar that serves as a biosynthetic precursor of glycoproteins, mucopolysaccharides, and the cell wall of bacteria. Thus, a specific inhibitor of AGM1 from pathogenetic fungi could be a new candidate for an antifungal reagent that inhibits cell wall synthesis. AGM1 catalyzes the conversion of N-acetylglucosamine 6-phosphate (GlcNAc-6-P) into N-acetylglucosamine 1-phosphate (GlcNAc-1-P). This enzyme is a member of the alpha-D-phosphohexomutase superfamily, which catalyzes the intramolecular phosphoryl transfer of sugar substrates. Here we report the crystal structures of AGM1 from Candida albicans for the first time, both in the apoform and in the complex forms with the substrate and the product, and discuss its catalytic mechanism. The structure of AGM1 consists of four domains, of which three domains have essentially the same fold. The overall structure is similar to those of phosphohexomutases; however, there are two additional beta-strands in domain 4, and a circular permutation occurs in domain 1. The catalytic cleft is formed by four loops from each domain. The N-acetyl group of the substrate is recognized by Val-370 and Asn-389 in domain 3, from which the substrate specificity arises. By comparing the substrate and product complexes, it is suggested that the substrate rotates about 180 degrees on the axis linking C-4 and the midpoint of the C-5-O-5 bond in the reaction.
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Affiliation(s)
- Yuichi Nishitani
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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36
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Silvaggi NR, Zhang C, Lu Z, Dai J, Dunaway-Mariano D, Allen KN. The X-ray Crystal Structures of Human α-Phosphomannomutase 1 Reveal the Structural Basis of Congenital Disorder of Glycosylation Type 1a. J Biol Chem 2006; 281:14918-26. [PMID: 16540464 DOI: 10.1074/jbc.m601505200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Congenital disorder of glycosylation type 1a (CDG-1a) is a congenital disease characterized by severe defects in nervous system development. It is caused by mutations in alpha-phosphomannomutase (of which there are two isozymes, alpha-PMM1 and alpha-PPM2). Here we report the x-ray crystal structures of human alpha-PMM1 in the open conformation, with and without the bound substrate, alpha-D-mannose 1-phosphate. Alpha-PMM1, like most haloalkanoic acid dehalogenase superfamily (HADSF) members, consists of two domains, the cap and core, which open to bind substrate and then close to provide a solvent-exclusive environment for catalysis. The substrate phosphate group is observed at a positively charged site of the cap domain, rather than at the core domain phosphoryl-transfer site defined by the Asp(19) nucleophile and Mg(2+) cofactor. This suggests that substrate binds first to the cap and then is swept into the active site upon cap closure. The orientation of the acid/base residue Asp(21) suggests that alpha-phosphomannomutase (alpha-PMM) uses a different method of protecting the aspartylphosphate from hydrolysis than the HADSF member beta-phosphoglucomutase. It is hypothesized that the electrostatic repulsion of positive charges at the interface of the cap and core domains stabilizes alpha-PMM1 in the open conformation and that the negatively charged substrate binds to the cap, thereby facilitating its closure over the core domain. The two isozymes, alpha-PMM1 and alpha-PMM2, are shown to have a conserved active-site structure and to display similar kinetic properties. Analysis of the known mutation sites in the context of the structures reveals the genotype-phenotype relationship underlying CDG-1a.
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Affiliation(s)
- Nicholas R Silvaggi
- Department of Physiology and Biophysics, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118, USA
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37
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Akutsu JI, Zhang Z, Tsujimura M, Sasaki M, Yohda M, Kawarabayasi Y. Characterization of a Thermostable Enzyme with Phosphomannomutase/Phosphoglucomutase Activities from the Hyperthermophilic Archaeon Pyrococcus horikoshii OT3. ACTA ACUST UNITED AC 2005; 138:159-66. [PMID: 16091590 DOI: 10.1093/jb/mvi115] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The phosphomannomutase/phosphoglucomutase (PMM/PGM) enzyme catalyzes reversibly the intra-molecular phosphoryl interconverting reaction of mannose-6-phosphate and mannose-1-phosphate or glucose-6-phosphate and glucose-1-phosphate. Glucose-6-phosphate and glucose-1-phosphate are known to be utilized for energy metabolism and cell surface construction, respectively. PMM/PGM has been isolated from many microorganisms. By performing similarity searches using existing PMM/PGM sequences, the homologous ORFs PH0923 and PH1210 were identified from the genomic data of Pyrococcus horikoshii OT3. Since PH0923 appears to be part of an operon consisting of four carbohydrate metabolic enzymes, PH0923 was selected as the first target for the investigation of PMM/PGM activity in P. horikoshii OT3. The coding region of PH0923 was cloned and the purified recombinant protein was utilized for an examination of its biochemical properties. The enzyme retained half its initial activity after treatment at 95 degrees C for 90 min. Detailed analyses of activities showed that this protein is capable of utilizing a variety of metal ions that are not utilized by previously characterized PMM/PGM proteins. A mutated protein with an alanine residue replacing the active site serine residue indicated that this residue plays an important but non-essential role in PMM/PGM activity.
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Affiliation(s)
- Jun-ichi Akutsu
- National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki
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38
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Ray WK, Keith SM, DeSantis AM, Hunt JP, Larson TJ, Helm RF, Kennelly PJ. A phosphohexomutase from the archaeon Sulfolobus solfataricus is covalently modified by phosphorylation on serine. J Bacteriol 2005; 187:4270-5. [PMID: 15937189 PMCID: PMC1151728 DOI: 10.1128/jb.187.12.4270-4275.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A phosphoserine-containing peptide was identified from tryptic digests from Sulfolobus solfataricus P1 by liquid chromatography-tandem mass spectrometry. Its amino acid sequence closely matched that bracketing Ser-309 in the predicted protein product of open reading frame sso0207, a putative phosphohexomutase, in the genome of S. solfataricus P2. Open reading frame sso0207 was cloned, and its protein product expressed in Escherichia coli. The recombinant protein proved capable of interconverting mannose 1-phosphate and mannose 6-phosphate, as well as glucose 1-phosphate and glucose 6-phosphate, in vitro. It displayed no catalytic activity toward glucosamine 6-phosphate or N-acetylglucosamine 6-phosphate. Models constructed using the X-ray crystal structure of a homologous phosphohexomutase from Pseudomonas aeruginosa predicted that Ser-309 of the archaeal protein lies within the substrate binding site. The presence of a phosphoryl group at this location would be expected to electrostatically interfere with the binding of negatively charged phosphohexose substrates, thus attenuating the catalytic efficiency of the enzyme. Using site-directed mutagenesis, Ser-309 was substituted by aspartic acid to mimic the presence of a phosphoryl group. The V(max) of the mutationally altered protein was only 4% that of the unmodified form. Substitution of Ser-309 with larger, but uncharged, amino acids, including threonine, also decreased catalytic efficiency, but to a lesser extent--three- to fivefold. We therefore predict that phosphorylation of the enzyme in vivo serves to regulate its catalytic activity.
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Affiliation(s)
- W Keith Ray
- Department of Biochemistry and Virginia Institute for Genomics, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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39
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Rashid N, Kanai T, Atomi H, Imanaka T. Among multiple phosphomannomutase gene orthologues, only one gene encodes a protein with phosphoglucomutase and phosphomannomutase activities in Thermococcus kodakaraensis. J Bacteriol 2004; 186:6070-6. [PMID: 15342576 PMCID: PMC515153 DOI: 10.1128/jb.186.18.6070-6076.2004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Four orthologous genes (TK1108, TK1404, TK1777, and TK2185) that can be annotated as phosphomannomutase (PMM) genes (COG1109) have been identified in the genome of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. We previously found that TK1777 actually encodes a phosphopentomutase. In order to determine which of the remaining three orthologues encodes a phosphoglucomutase (PGM), we examined the PGM activity in T. kodakaraensis cells and identified the gene responsible for this activity. Heterologous gene expression and purification and characterization of the recombinant protein indicated that TK1108 encoded a protein with high levels of PGM activity (690 U mg(-1)), along with high levels of PMM activity (401 U mg(-1)). Similar analyses of the remaining two orthologues revealed that their protein products exhibited neither PGM nor PMM activity. PGM activity and transcription of TK1108 in T. kodakaraensis were found to be higher in cells grown on starch than in cells grown on pyruvate. Our results clearly indicate that, among the four PMM gene orthologues in T. kodakaraensis, only one gene, TK1108, actually encodes a protein with PGM and PMM activities.
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Affiliation(s)
- Naeem Rashid
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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40
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Shackelford GS, Regni CA, Beamer LJ. Evolutionary trace analysis of the alpha-D-phosphohexomutase superfamily. Protein Sci 2004; 13:2130-8. [PMID: 15238632 PMCID: PMC2279825 DOI: 10.1110/ps.04801104] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The alpha-D-phosphohexomutase superfamily is composed of four related enzymes that catalyze a reversible, intramolecular phosphoryl transfer on their sugar substrates. The enzymes in this superfamily play important and diverse roles in carbohydrate metabolism in organisms from bacteria to humans. Recent structural and mechanistic studies of one member of this superfamily, phosphomannomutase/phosphoglucomutase (PMM/PGM) from Pseudomonas aeruginosa, have provided new insights into enzyme mechanism and substrate recognition. Here we use sequence-sequence and sequence-structure comparisons via evolutionary trace analysis to examine 71 members of the alpha-D-phosphohexomutase superfamily. These analyses show that key residues in the active site, including many of those involved in substrate contacts in the P. aeruginosa PMM/PGM complexes, are conserved throughout the enzyme family. Several important regions show class-specific differences in sequence that appear to be correlated with differences in substrate specificity exhibited by subgroups of the family. In addition, we describe the translocation of a 20-residue segment containing the catalytic phosphoserine of phosphoacetylglucosamine mutase, which uniquely identifies members of this subgroup.
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Affiliation(s)
- Grant S Shackelford
- Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211, USA
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41
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Regni C, Naught L, Tipton PA, Beamer LJ. Structural Basis of Diverse Substrate Recognition by the Enzyme PMM/PGM from P. aeruginosa. Structure 2004; 12:55-63. [PMID: 14725765 DOI: 10.1016/j.str.2003.11.015] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Enzyme-substrate complexes of phosphomannomutase/phosphoglucomutase (PMM/PGM) reveal the structural basis of the enzyme's ability to use four different substrates in catalysis. High-resolution structures with glucose 1-phosphate, glucose 6-phosphate, mannose 1-phosphate, and mannose 6-phosphate show that the position of the phosphate group of each substrate is held constant by a conserved network of hydrogen bonds. This produces two distinct, and mutually exclusive, binding orientations for the sugar rings of the 1-phospho and 6-phospho sugars. Specific binding of both orientations is accomplished by key contacts with the O3 and O4 hydroxyls of the sugar, which must occupy equatorial positions. Dual recognition of glucose and mannose phosphosugars uses a combination of specific protein contacts and nonspecific solvent contacts. The ability of PMM/PGM to accommodate these four diverse substrates in a single active site is consistent with its highly reversible phosphoryl transfer reaction and allows it to function in multiple biosynthetic pathways in P. aeruginosa.
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Affiliation(s)
- Catherine Regni
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri-Columbia, Columbia, MO 65211, USA
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42
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Basu NK, Ciotti M, Hwang MS, Kole L, Mitra PS, Cho JW, Owens IS. Differential and special properties of the major human UGT1-encoded gastrointestinal UDP-glucuronosyltransferases enhance potential to control chemical uptake. J Biol Chem 2003; 279:1429-41. [PMID: 14557274 DOI: 10.1074/jbc.m306439200] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
UDP-glucuronosyltransferase (UGT) isozymes detoxify metabolites, drugs, toxins, and environmental chemicals via conjugation to glucuronic acid. Based on the extended UGT1 locus combined with Northern blot analysis and in situ hybridization, we determined the distribution of UGT1A1 and UGT1A7 through UGT1A10 mRNAs and found them for the first time segmentally distributed in the mucosal epithelia layer of the gastrointestinal tract. Biochemically, recombinant isozymes exhibited pH optima of 5.5, 6.4, 7.6, 8.5, and/or a broad pH range, and activities were found to be unaffected or progressively inhibited by increasing substrate concentrations after attaining Vmax for certain chemicals. Under different optimal conditions, all exhibited wide substrate selections for dietary and environmentally associated chemicals. Evidence also suggests tandem effects of isozymes in the time for completion of reactions when comparing short- and long-term incubations. Moreover, treatment of colon cells with certain diet-associated constituents, curcumin and nordihydroguaiaretic acid, reversibly targets UGTs causing inhibition without affecting protein levels; there is no direct inhibition of control UGT using curcumin as substrate in the in vitro assay. In summary, we demonstrate that UGTs are located in gastrointestinal mucosa, have vast overlapping activities under differential optimal conditions, and exhibit marked sensitivity to certain dietary substrates/constituents, representing a first comprehensive study of critical properties concerning glucuronidating isozymes in alimentary tissues. Additionally, the highly dynamic, complex, and variable properties necessarily impact absorption of ingested chemicals and therapeutic drugs.
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Affiliation(s)
- Nikhil K Basu
- Heritable Disorders Branch, NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA
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43
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Lahiri SD, Zhang G, Dunaway-Mariano D, Allen KN. The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction. Science 2003; 299:2067-71. [PMID: 12637673 DOI: 10.1126/science.1082710] [Citation(s) in RCA: 265] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Enzymes provide enormous rate enhancements, unmatched by any other type of catalyst. The stabilization of high-energy states along the reaction coordinate is the crux of the catalytic power of enzymes. We report the atomic-resolution structure of a high-energy reaction intermediate stabilized in the active site of an enzyme. Crystallization of phosphorylated beta-phosphoglucomutase in the presence of the Mg(II) cofactor and either of the substrates glucose 1-phosphate or glucose 6-phosphate produced crystals of the enzyme-Mg(II)-glucose 1,6-(bis)phosphate complex, which diffracted x-rays to 1.2 and 1.4 angstroms, respectively. The structure reveals a stabilized pentacovalent phosphorane formed in the phosphoryl transfer from the C(1)O of glucose 1,6-(bis)phosphate to the nucleophilic Asp8 carboxylate.
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Affiliation(s)
- Sushmita D Lahiri
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118-2394, USA
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44
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Regni C, Tipton PA, Beamer LJ. Crystal structure of PMM/PGM: an enzyme in the biosynthetic pathway of P. aeruginosa virulence factors. Structure 2002; 10:269-79. [PMID: 11839312 DOI: 10.1016/s0969-2126(02)00705-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The enzyme phosphomannomutase/phosphoglucomutase (PMM/PGM) from P. aeruginosa is required for the biosynthesis of two bacterial exopolysaccharides: alginate and lipopolysaccharide (LPS). Both of these molecules play a role in the virulence of P. aeruginosa, an important human pathogen known for its ability to develop antibiotic resistance and cause chronic lung infections in cystic fibrosis patients. The crystal structure of PMM/PGM shows that the enzyme has four domains, three of which have a similar three-dimensional fold. Residues from all four domains of the protein contribute to the formation of a large active site cleft in the center of the molecule. Detailed information on the active site of PMM/PGM lays the foundation for structure-based inhibitor design. Inhibitors of sufficient potency and specificity should impair the biosynthesis of alginate and LPS, and may facilitate clearance of the bacteria by the host immune system and increase the efficacy of conventional antibiotic treatment against chronic P. aeruginosa infections.
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Affiliation(s)
- Catherine Regni
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri-Columbia, Columbia, MO 65211, USA
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