1
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Abuhammad A, Laurieri N, Rice A, Lowe ED, Singh N, Naser SM, Ratrout SS, Churchill GC. Structural and biochemical analysis of human inositol monophosphatase-1 inhibition by ebselen. J Biomol Struct Dyn 2023; 41:14036-14048. [PMID: 36762717 DOI: 10.1080/07391102.2023.2176925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023]
Abstract
Bipolar disorder is a major psychiatric disorder associated with cognitive impairment and a high suicide rate. Frontline therapy for this condition includes lithium (Li+)-containing treatments that can exert severe side effects. One target of Li+ is inositol monophosphatase-1 (IMPase1); inhibition of IMPase1 through small-molecule compounds may provide an alternative treatment for bipolar disorder. One such compound is the anti-inflammatory drug ebselen, which is well tolerated and safe; however, ebselen's exact mechanism of action in IMPase1 inhibition is not fully understood, preventing rational design of IMPase1 inhibitors. To fill this gap, we performed crystallographic and biochemical studies to investigate how ebselen inhibits IMPase1. We obtained a structure of IMPase1 in space group P21 after treatment with ebselen that revealed three key active-site loops (residues 33-44, 70-79, and 161-165) that are either disordered or in multiple conformations, supporting a hypothesis whereby dynamic conformational changes may be important for catalysis and ebselen inhibition. Using the thermal shift assay, we confirmed that ebselen significantly destabilizes the enzyme. Molecular docking suggests that ebselen could bind in the vicinity of His217. Investigation of the role of IMPase1 residues His217 and Cys218 suggests that inhibition of IMPase1 by ebselen may not be mediated via covalent modification of the active-site cysteine (Cys218) and is not affected by the covalent modification of other cysteine residues in the structure. Our results suggest that effects previously ascribed to ebselen-dependent inhibition likely result from disruption of essential active-site architecture, preventing activation of the IMPase1-Mg2+ complex.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Areej Abuhammad
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Nicola Laurieri
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Alistair Rice
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Edward D Lowe
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Nisha Singh
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Saleem M Naser
- Research and Development Department, APIs Division, Hikma Pharmaceutical Co. Ltd, Amman, Jordan
| | - Samer S Ratrout
- Research and Development Department, APIs Division, Hikma Pharmaceutical Co. Ltd, Amman, Jordan
| | - Grant C Churchill
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
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2
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Venkatachalam K, Ettrich RH. Role of aspartic acid residues D87 and D89 in APS kinase domain of human 3'-phosphoadenosine 5'-phosphosulfate synthase 1 and 2b: A commonality with phosphatases/kinases. Biochem Biophys Rep 2021; 28:101155. [PMID: 34712849 PMCID: PMC8528679 DOI: 10.1016/j.bbrep.2021.101155] [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: 06/25/2021] [Revised: 10/06/2021] [Accepted: 10/15/2021] [Indexed: 11/26/2022] Open
Abstract
3'-phosphoadenosine 5'-phosphosulfate (PAPS) is synthesized in two steps by PAPS synthase (PAPSS). PAPSS is comprised of ATP sulfurylase (ATPS) and APS kinase (APSK) domain activities. ATPS combines inorganic sulfate with α-phosphoryl of ATP to form adenosine 5'-phosphosulfate (APS) and PPi. In the second step APS is phosphorylated at 3'-OH using another mole of ATP to form PAPS and ADP catalyzed by APSK. The transfer of gamma-phosphoryl from ATP onto 3'-OH requires Mg2 + and purported to involve residues D87GD89N. We report that mutation of either aspartic residue to alanine completely abolishes APSK activity in PAPS formation. PAPSS is an, unique enzyme that binds to four different nucleotides: ATP and APS on both ATPS and APSK domains and ADP and PAPS exclusively on the APSK domain. The thermodynamic binding and the catalytic interplay must be very tightly controlled to form the end-product PAPS in the forward direction. Though APS binds to ATPS and APSK, in ATPS domain, the APS is a product and for APSK it is a substrate. DGDN motif is absent in ATPS and present in APSK. Mutation of D87 and D89 did not hamper ATPS activity however abolished APSK activity severely. Thus, D87GD89N region is required for stabilization of Mg2+-ATP, in the process of splitting the γ-phosphoryl from ATP and transfer of γ-phosphoryl onto 3'-OH of APS to form PAPS a process that cannot be achieved by ATPS domain. In addition, gamma32P-ATP, trapped phosphoryl enzyme intermediate more with PAPSS2 than with PAPSS1. This suggests inherent active site residues could control novel catalytic differences. Molecular docking studies of hPAPSS1with ATP + Mg2+ and APS of wild type and mutants supports the experimental results.
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Affiliation(s)
- K.V. Venkatachalam
- College of Allopathic Medicine, Nova Southeastern University, Ft. Lauderdale, FL, 33328, USA
| | - Rudiger H. Ettrich
- College of Biomedical Sciences, Larkin University, Miami, FL, 33169, USA
- Faculty of Mathematics and Physics, Charles University, 121 16, Prague, Czech Republic
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3
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Dollins DE, Xiong JP, Endo-Streeter S, Anderson DE, Bansal VS, Ponder JW, Ren Y, York JD. A structural basis for lithium and substrate binding of an inositide phosphatase. J Biol Chem 2021; 296:100059. [PMID: 33172890 PMCID: PMC7948987 DOI: 10.1074/jbc.ra120.014057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/29/2020] [Accepted: 11/10/2020] [Indexed: 01/07/2023] Open
Abstract
Inositol polyphosphate 1-phosphatase (INPP1) is a prototype member of metal-dependent/lithium-inhibited phosphomonoesterase protein family defined by a conserved three-dimensional core structure. Enzymes within this family function in distinct pathways including inositide signaling, gluconeogenesis, and sulfur assimilation. Using structural and biochemical studies, we report the effect of substrate and lithium on a network of metal binding sites within the catalytic center of INPP1. We find that lithium preferentially occupies a key site involved in metal-activation only when substrate or product is added. Mutation of a conserved residue that selectively coordinates the putative lithium-binding site results in a dramatic 100-fold reduction in the inhibitory constant as compared with wild-type. Furthermore, we report the INPP1/inositol 1,4-bisphosphate complex which illuminates key features of the enzyme active site. Our results provide insights into a structural basis for uncompetitive lithium inhibition and substrate recognition and define a sequence motif for metal binding within this family of regulatory phosphatases.
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Affiliation(s)
- D Eric Dollins
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA
| | - Jian-Ping Xiong
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA
| | - Stuart Endo-Streeter
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA
| | - David E Anderson
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA
| | - Vinay S Bansal
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Jay W Ponder
- Department of Chemistry, Washington University, St Louis, Missouri, USA
| | - Yi Ren
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - John D York
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA.
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4
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Réus GZ, de Moura AB, Borba LA, Abelaira HM, Quevedo J. Strategies for Treatment-Resistant Depression: Lessons Learned from Animal Models. MOLECULAR NEUROPSYCHIATRY 2019; 5:178-189. [PMID: 31768371 DOI: 10.1159/000500324] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/11/2019] [Indexed: 12/18/2022]
Abstract
Around 300 million individuals are affected by major depressive disorder (MDD) in the world. Despite this high number of affected individuals, more than 50% of patients do not respond to antidepressants approved to treat MDD. Patients with MDD that do not respond to 2 or more first-line antidepressant treatments are considered to have treatment-resistant depression (TRD). Animal models of depression are important tools to better understand the pathophysiology of MDD as well as to help in the development of novel and fast antidepressants for TRD patients. This review will emphasize some discovery strategies for TRD from studies on animal models, including, antagonists of N-methyl-D-aspartate (NMDA) receptor (ketamine and memantine), electroconvulsive therapy (ECT), lithium, minocycline, quetiapine, and deep brain stimulation. Animal models of depression are not sufficient to represent all the traits of TRD, but they greatly aid in understanding the mechanism by which therapies that work for TRD exert antidepressant effects. Interestingly, these innovative therapies have mechanisms of action different from those of classic antidepressants. These effects are mainly related to the regulation of neurotransmitter activity, including general glutamate and increased connectivity, synaptic capacity, and neuroplasticity.
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Affiliation(s)
- Gislaine Zilli Réus
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, Health Sciences Unit, University of Southern Santa Catarina, Criciúma, Brazil
| | - Airam Barbosa de Moura
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, Health Sciences Unit, University of Southern Santa Catarina, Criciúma, Brazil
| | - Laura Araújo Borba
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, Health Sciences Unit, University of Southern Santa Catarina, Criciúma, Brazil
| | - Helena Mendes Abelaira
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, Health Sciences Unit, University of Southern Santa Catarina, Criciúma, Brazil
| | - João Quevedo
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, Health Sciences Unit, University of Southern Santa Catarina, Criciúma, Brazil.,Center of Excellence on Mood Disorders, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA.,Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA.,Neuroscience Graduate Program, Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA
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5
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Catazaro J, Caprez A, Swanson D, Powers R. Functional Evolution of Proteins. Proteins 2019; 87:492-501. [PMID: 30714210 DOI: 10.1002/prot.25670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 11/02/2018] [Accepted: 01/31/2019] [Indexed: 11/12/2022]
Abstract
The functional evolution of proteins advances through gene duplication followed by functional drift, whereas molecular evolution occurs through random mutational events. Over time, protein active-site structures or functional epitopes remain highly conserved, which enables relationships to be inferred between distant orthologs or paralogs. In this study, we present the first functional clustering and evolutionary analysis of the RCSB Protein Data Bank (RCSB PDB) based on similarities between active-site structures. All of the ligand-bound proteins within the RCSB PDB were scored using our Comparison of Protein Active-site Structures (CPASS) software and database (http://cpass.unl.edu/). Principal component analysis was then used to identify 4431 representative structures to construct a phylogenetic tree based on the CPASS comparative scores (http://itol.embl.de/shared/jcatazaro). The resulting phylogenetic tree identified a sequential, step-wise evolution of protein active-sites and provides novel insights into the emergence of protein function or changes in substrate specificity based on subtle changes in geometry and amino acid composition.
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Affiliation(s)
- Jonathan Catazaro
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Adam Caprez
- Holland Computing Center, Office of Research, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - David Swanson
- Holland Computing Center, Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska.,Department of Chemistry, Nebraska Center for Integrated Biomolecular Communication, Lincoln, Nebraska
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6
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Wolf NM, Gutka HJ, Movahedzadeh F, Abad-Zapatero C. Structures of the Mycobacterium tuberculosis GlpX protein (class II fructose-1,6-bisphosphatase): implications for the active oligomeric state, catalytic mechanism and citrate inhibition. Acta Crystallogr D Struct Biol 2018; 74:321-331. [PMID: 29652259 PMCID: PMC5892879 DOI: 10.1107/s2059798318002838] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/16/2018] [Indexed: 11/19/2022] Open
Abstract
The crystal structures of native class II fructose-1,6-bisphosphatase (FBPaseII) from Mycobacterium tuberculosis at 2.6 Å resolution and two active-site protein variants are presented. The variants were complexed with the reaction product fructose 6-phosphate (F6P). The Thr84Ala mutant is inactive, while the Thr84Ser mutant has a lower catalytic activity. The structures reveal the presence of a 222 tetramer, similar to those described for fructose-1,6/sedoheptulose-1,7-bisphosphatase from Synechocystis (strain 6803) as well as the equivalent enzyme from Thermosynechococcus elongatus. This homotetramer corresponds to a homologous oligomer that is present but not described in the crystal structure of FBPaseII from Escherichia coli and is probably conserved in all FBPaseIIs. The constellation of amino-acid residues in the active site of FBPaseII from M. tuberculosis (MtFBPaseII) is conserved and is analogous to that described previously for the E. coli enzyme. Moreover, the structure of the active site of the partially active (Thr84Ser) variant and the analysis of the kinetics are consistent with the previously proposed catalytic mechanism. The presence of metabolites in the crystallization medium (for example citrate and malonate) and in the corresponding crystal structures of MtFBPaseII, combined with their observed inhibitory effect, could suggest the existence of an uncharacterized inhibition of this class of enzymes besides the allosteric inhibition by adenosine monophosphate observed for the Synechocystis enzyme. The structural and functional insights derived from the structure of MtFBPaseII will provide critical information for the design of lead inhibitors, which will be used to validate this target for future chemical intervention.
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Affiliation(s)
- Nina M. Wolf
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Hiten J. Gutka
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, USA
- Oncobiologics Inc., Cranbury, New Jersey, USA
| | - Farahnaz Movahedzadeh
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Celerino Abad-Zapatero
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
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7
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Bondoc JMG, Wolf NM, Ndichuck M, Abad-Zapatero C, Movahedzadeh F. Mutagenesis of threonine to serine in the active site of Mycobacterium tuberculosis fructose-1,6-bisphosphatase (Class II) retains partial enzyme activity. ACTA ACUST UNITED AC 2017; 15:48-54. [PMID: 28702369 PMCID: PMC5485559 DOI: 10.1016/j.btre.2017.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/08/2017] [Accepted: 06/08/2017] [Indexed: 01/08/2023]
Abstract
The glpX gene encodes for the Class II fructose-1,6-bisphosphatase enzyme in Mycobacterium tuberculosis (Mt), an essential enzyme for pathogenesis. We have performed site directed mutagenesis to introduce two mutations at residue Thr84, T84A and T84S, to explore the binding affinity of the substrate and the catalytic mechanism. The T84A mutant fully abolishes enzyme activity while retaining substrate binding affinity. In contrast, the T84S mutant retains some activity having a 10 times reduction in Vmax and exhibited similar sensitivity to lithium when compared to the wildtype. Homology modeling using the Escherichia coli enzyme structure suggests that the replacement of the critical nucleophile OH- in the Thr84 residue of the wildtype of MtFBPase by Ser84 results in subtle alterations of the position and orientation that reduce the catalytic efficiency. This mutant could be used to trap reaction intermediates, through crystallographic methods, facilitating the design of potent inhibitors via structure-based drug design.
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Affiliation(s)
- Jasper Marc G Bondoc
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
| | - Nina M Wolf
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
| | - Michael Ndichuck
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
| | - Celerino Abad-Zapatero
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
| | - Farahnaz Movahedzadeh
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States.,Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
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8
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Wang J, Wang Z, Ling B, Cao N, Wang W. Identification of a potential proton donor to the linking oxygen atom in a three-metal ion assisted catalysis pathway catalyzed by Fructose-1, 6-bisphosphatase. J Mol Graph Model 2017; 73:191-199. [PMID: 28301812 DOI: 10.1016/j.jmgm.2017.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/16/2016] [Accepted: 01/04/2017] [Indexed: 12/01/2022]
Abstract
In this paper, the dephosphorylation mechanism of FBP to F6P catalyzed by the Fructose-1, 6-bisphosphatase (St-Fbp) from Sulfolobus tokodaii was studied using quantum mechanical/molecular mechanical (QM/MM) approach. Based on the experimental results, total five possible catalytic mechanisms (path1-path4') were designed. The most possible dephosphorylation reaction follows a two-step mechanism (path2): a dephosphorylation process (with D12 being an base of W6 and residue K133 being the proton donor of the linking FBP:O4) and a proton exchange process (between K133 and the water W1). Furthermore, the three-step of path4 is also possible: a dephosphorylation process (with D54 being the base of W6 and residue K133 being the proton donor of the linking FBP:O4) and two proton exchange processes (first between residues D54 and D12 then between K133 and the water W1). The relative low energy of this pathway suggests that D54 might also be a base except D12. Our calculations indicate that K133 is the preferred proton donor during the breaking of the phosphate bond O4-P1, with the W1 being an alternative proton donor to access to a more stable product. Findings here give a new insight into the understanding of catalytic mechanism of FBPase.
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Affiliation(s)
- Jinhu Wang
- College of Chemistry, Chemical Engineering and Material Science, Zaozhuang University, Zaozhuang, Shandong 277160, China.
| | - Zhiguo Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou 311121, China.
| | - Baoping Ling
- College of Chemistry Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, China
| | - Nan Cao
- College of Chemistry, Chemical Engineering and Material Science, Zaozhuang University, Zaozhuang, Shandong 277160, China
| | - Wen Wang
- College of Chemistry, Chemical Engineering and Material Science, Zaozhuang University, Zaozhuang, Shandong 277160, China
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9
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Roux M, Dosseto A. From direct to indirect lithium targets: a comprehensive review of omics data. Metallomics 2017; 9:1326-1351. [DOI: 10.1039/c7mt00203c] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metal ions are critical to a wide range of biological processes.
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Affiliation(s)
| | - Anthony Dosseto
- Wollongong Isotope Geochronology Laboratory
- School of Earth & Environmental Sciences
- University of Wollongong
- Wollongong
- Australia
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10
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Erickson AI, Sarsam RD, Fisher AJ. Crystal Structures of Mycobacterium tuberculosis CysQ, with Substrate and Products Bound. Biochemistry 2015; 54:6830-41. [PMID: 26512869 DOI: 10.1021/acs.biochem.5b01000] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In many organisms, 3'-phosphoadenosine 5'-phosphate (PAP) is a product of two reactions in the sulfur activation pathway. The sulfurylation of biomolecules, catalyzed by sulfotransferases, uses 3'-phosphoadenosine 5'-phosphosulfate (PAPS) as a sulfate donor, producing the sulfated biomolecule and PAP product. Additionally, the first step in sulfate reduction for many bacteria and fungi reduces the sulfate moiety of PAPS, producing PAP and sulfite, which is subsequently reduced to sulfide. PAP is removed by the phosphatase activity of CysQ, a 3',5'-bisphosphate nucleotidase, yielding AMP and phosphate. Because excess PAP alters the equilibrium of the sulfur pathway and inhibits sulfotransferases, PAP concentrations can affect the levels of sulfur-containing metabolites. Therefore, CysQ, a divalent cation metal-dependent phosphatase, is a major regulator of this pathway. CysQ (Rv2131c) from Mycobacterium tuberculosis (Mtb) was successfully expressed, purified, and crystallized in a variety of ligand-bound states. Here we report six crystal structures of Mtb CysQ, including a ligand-free structure, a lithium-inhibited state with substrate PAP bound, and a product-bound complex with AMP, phosphate, and three Mg(2+) ions bound. Comparison of these structures together with homologues of the superfamily has provided insight into substrate specificity, metal coordination, and catalytic mechanism.
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Affiliation(s)
- Anna I Erickson
- Department of Chemistry, ‡Department of Molecular and Cellular Biology, and §Graduate Program in Biochemistry and Molecular, Cellular and Developmental Biology, University of California , One Shields Avenue, Davis, California 95616, United States
| | - Reta D Sarsam
- Department of Chemistry, ‡Department of Molecular and Cellular Biology, and §Graduate Program in Biochemistry and Molecular, Cellular and Developmental Biology, University of California , One Shields Avenue, Davis, California 95616, United States
| | - Andrew J Fisher
- Department of Chemistry, ‡Department of Molecular and Cellular Biology, and §Graduate Program in Biochemistry and Molecular, Cellular and Developmental Biology, University of California , One Shields Avenue, Davis, California 95616, United States
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11
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Dutta A, Bhattacharyya S, Dutta D, Das AK. Structural elucidation of the binding site and mode of inhibition of Li+and Mg2+in inositol monophosphatase. FEBS J 2014; 281:5309-24. [PMID: 25263816 DOI: 10.1111/febs.13070] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/16/2014] [Accepted: 09/23/2014] [Indexed: 01/20/2023]
Affiliation(s)
- Anirudha Dutta
- Department of Biotechnology; Indian Institute of Technology Kharagpur; Kharagpur West Bengal India
| | - Sudipta Bhattacharyya
- Department of Biotechnology; Indian Institute of Technology Kharagpur; Kharagpur West Bengal India
| | - Debajyoti Dutta
- Department of Biotechnology; Indian Institute of Technology Kharagpur; Kharagpur West Bengal India
| | - Amit Kumar Das
- Department of Biotechnology; Indian Institute of Technology Kharagpur; Kharagpur West Bengal India
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12
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Yeast 3',5'-bisphosphate nucleotidase: an affinity tag for protein purification. Protein Expr Purif 2014; 97:81-7. [PMID: 24613729 DOI: 10.1016/j.pep.2014.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 02/23/2014] [Accepted: 02/25/2014] [Indexed: 11/22/2022]
Abstract
Affinity chromatography is one of the most popular methods for protein purification. Each tag method has its advantages and disadvantages, and combination of different tags and developing of new tags had been proposed and performed. Yeast 3',5'-bisphosphate nucleotidase, also known as HAL2, hydrolyzes 3'-phosphoadenosine 5'-phosphate (PAP) with submicromolar Km, which indicated the tight interactions between HAL2 and PAP. In order to explore the feasibility of HAL2 as a protein purification affinity tag, HAL2 was further characterized with PAP as substrate. Results demonstrated that KmPAP and kcatPAP were ∼0.3μM and ∼11s(-)(1), respectively. Kd for PAP was 0.008μM in the presence of Ca(2+). pH was also found to affect interactions between HAL2 and PAP, with tightest binding (Kd∼8nM) at pH 7.5 and 8. The purification protocol was rationally designed based on nanomolar affinity to PAP agarose in the presence of Ca(2+), which could satisfy the metal requirement for PAP binding, prevent hydrolysis of immobilized PAP and could be chelated by ethylene glycol tetraacetic acid (EGTA) for elution. A series of expression vectors were further constructed and Escherichia coli adenosine 5'-phosphosulfate kinase (APSK) was prokaryotically expressed, purified and characterized. Ready to use expression vector with eight commonly used restriction enzyme recognition sites in multiple cloning site was subsequently constructed. By comparing with current popular tags, HAL2 was found to be an efficient and economical tag for prokaryotic protein expression and purification.
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13
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Lu S, Huang W, Li X, Huang Z, Liu X, Chen Y, Shi T, Zhang J. Insights into the role of magnesium triad in myo-inositol monophosphatase: metal mechanism, substrate binding, and lithium therapy. J Chem Inf Model 2012; 52:2398-409. [PMID: 22889135 DOI: 10.1021/ci300172r] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
myo-Inositol monophosphatase (IMPase) plays a pivotal role in the intracellular phosphatidylinositol cell signaling pathway. It has attracted considerable attention as a putative therapeutic target for lithium therapy in the treatment of bipolar disorder. A trio of activated cofactor Mg²⁺ ions is required for inositol monophosphate hydrolysis by IMPase. In the present study, computational studies, including two-layered ONIOM-based quantum mechanics/mechanical mechanics (QM/MM) calculations, molecular modeling, and molecular dynamics (MD) simulations, were performed to ascertain the role of the Mg²⁺ triad in the IMPase active site. The QM/MM calculations show that the structural identity of the nucleophilic water molecule W1 shared by Mg²⁺-1 and Mg²⁺-3, activated by Thr95/Asp47 dyad, is a hydroxide ion. Moreover, Mg²⁺-3 needs to be conjugated with Mg²⁺-1 in the binding site to create the activated nucleophilic hydroxide ion in accordance with the three-metal ion catalytic mechanism. The MD simulation of the IMPase-substrate-Mg²⁺ complex shows that the three Mg²⁺ ions promote substrate binding and help fix the phosphate moiety of the substrate for nucleophilic attack by the hydroxide ion. When Mg²⁺-2 is displaced with Li⁺, the MD simulations of the postreaction complex indicate that the conformation of the catalytic loop (residues 33 to 44) is disrupted and water molecule W2 does not coordinate with Li⁺. This disruption traps the inorganic phosphate and inositolate in the active site, which lead to IMPase inhibition. By contrast, in the native Mg²⁺ system, the W2 ligated by Mg²⁺-2 and Asp200 aids in protonation of the leaving inositolate moiety.
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Affiliation(s)
- Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiaotong University, School of Medicine, Shanghai 200025, China
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Dudev T, Lim C. Competition between Li+ and Mg2+ in Metalloproteins. Implications for Lithium Therapy. J Am Chem Soc 2011; 133:9506-15. [DOI: 10.1021/ja201985s] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Todor Dudev
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
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15
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Gutka HJ, Rukseree K, Wheeler PR, Franzblau SG, Movahedzadeh F. glpX gene of Mycobacterium tuberculosis: heterologous expression, purification, and enzymatic characterization of the encoded fructose 1,6-bisphosphatase II. Appl Biochem Biotechnol 2011; 164:1376-89. [PMID: 21451980 DOI: 10.1007/s12010-011-9219-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 03/01/2011] [Indexed: 12/22/2022]
Abstract
The glpX gene (Rv1099c) of Mycobacterium tuberculosis (Mtb) encodes Fructose 1,6-bisphosphatase II (FBPase II; EC 3.1.3.11); a key gluconeogenic enzyme. Mtb possesses glpX homologue as the major known FBPase. This study explored the expression, purification and enzymatic characterization of functionally active FBPase II from Mtb. The glpX gene was cloned, expressed and purified using a two step purification strategy including affinity and size exclusion chromatography. The specific activity of Mtb FBPase II is 1.3 U/mg. The enzyme is oligomeric, followed Michaelis-Menten kinetics with an apparent km = 44 μM. Enzyme activity is dependent on bivalent metal ions and is inhibited by lithium and inorganic phosphate. The pH optimum and thermostability of the enzyme have been determined. The robust expression, purification and assay protocols ensure sufficient production of this protein for structural biology and screening of inhibitors against this enzyme.
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Affiliation(s)
- Hiten J Gutka
- Institute for Tuberculosis Research (M/C 964), College of Pharmacy, Room 412, University of Illinois at Chicago, 833 S. Wood St, Chicago, IL 60612-7231, USA
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16
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Kuznetsova E, Xu L, Singer A, Brown G, Dong A, Flick R, Cui H, Cuff M, Joachimiak A, Savchenko A, Yakunin AF. Structure and activity of the metal-independent fructose-1,6-bisphosphatase YK23 from Saccharomyces cerevisiae. J Biol Chem 2010; 285:21049-59. [PMID: 20427268 DOI: 10.1074/jbc.m110.118315] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fructose-1,6-bisphosphatase (FBPase), a key enzyme of gluconeogenesis and photosynthetic CO(2) fixation, catalyzes the hydrolysis of fructose 1,6-bisphosphate (FBP) to produce fructose 6-phosphate, an important precursor in various biosynthetic pathways. All known FBPases are metal-dependent enzymes, which are classified into five different classes based on their amino acid sequences. Eukaryotes are known to contain only the type-I FBPases, whereas all five types exist in various combinations in prokaryotes. Here we demonstrate that the uncharacterized protein YK23 from Saccharomyces cerevisiae efficiently hydrolyzes FBP in a metal-independent reaction. YK23 is a member of the histidine phosphatase (phosphoglyceromutase) superfamily with homologues found in all organisms. The crystal structure of the YK23 apo-form was solved at 1.75-A resolution and revealed the core domain with the alpha/beta/alpha-fold covered by two small cap domains. Two liganded structures of this protein show the presence of two phosphate molecules (an inhibitor) or FBP (a substrate) bound to the active site. FBP is bound in its linear, open conformation with the cleavable C1-phosphate positioned deep in the active site. Alanine replacement mutagenesis of YK23 identified six conserved residues absolutely required for activity and suggested that His(13) and Glu(99) are the primary catalytic residues. Thus, YK23 represents the first family of metal-independent FBPases and a second FBPase family in eukaryotes.
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Affiliation(s)
- Ekaterina Kuznetsova
- Banting and Best Department of Medical Research, Centre for Structural Proteomics in Toronto, University of Toronto, Toronto, Ontario M5G 1L6, Canada
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17
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Abstract
Clinicians have long used lithium to treat manic depression. They have also observed that lithium causes granulocytosis and lymphopenia while it enhances immunological activities of monocytes and lymphocytes. In fact, clinicians have long used lithium to treat granulocytopenia resulting from radiation and chemotherapy, to boost immunoglobulins after vaccination, and to enhance natural killer activity. Recent studies revealed a mechanism that ties together these disparate effects of lithium. Lithium acts through multiple pathways to inhibit glycogen synthetase kinase-3beta (GSK3 beta). This enzyme phosphorylates and inhibits nuclear factors that turn on cell growth and protection programs, including the nuclear factor of activated T cells (NFAT) and WNT/beta-catenin. In animals, lithium upregulates neurotrophins, including brain-derived neurotrophic factor (BDNF), nerve growth factor, neurotrophin-3 (NT3), as well as receptors to these growth factors in brain. Lithium also stimulates proliferation of stem cells, including bone marrow and neural stem cells in the subventricular zone, striatum, and forebrain. The stimulation of endogenous neural stem cells may explain why lithium increases brain cell density and volume in patients with bipolar disorders. Lithium also increases brain concentrations of the neuronal markers n-acetyl-aspartate and myoinositol. Lithium also remarkably protects neurons against glutamate, seizures, and apoptosis due to a wide variety of neurotoxins. The effective dose range for lithium is 0.6-1.0 mM in serum and >1.5 mM may be toxic. Serum lithium levels of 1.5-2.0 mM may have mild and reversible toxic effects on kidney, liver, heart, and glands. Serum levels of >2 mM may be associated with neurological symptoms, including cerebellar dysfunction. Prolonged lithium intoxication >2 mM can cause permanent brain damage. Lithium has low mutagenic and carcinogenic risk. Lithium is still the most effective therapy for depression. It "cures" a third of the patients with manic depression, improves the lives of about a third, and is ineffective in about a third. Recent studies suggest that some anticonvulsants (i.e., valproate, carbamapazine, and lamotrigene) may be useful in patients that do not respond to lithium. Lithium has been reported to be beneficial in animal models of brain injury, stroke, Alzheimer's, Huntington's, and Parkinson's diseases, amyotrophic lateral sclerosis (ALS), spinal cord injury, and other conditions. Clinical trials assessing the effects of lithium are under way. A recent clinical trial suggests that lithium stops the progression of ALS.
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Affiliation(s)
- Wise Young
- W. M. Keck Center for Collaborative Neuroscience, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA.
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18
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Brown G, Singer A, Lunin VV, Proudfoot M, Skarina T, Flick R, Kochinyan S, Sanishvili R, Joachimiak A, Edwards AM, Savchenko A, Yakunin AF. Structural and biochemical characterization of the type II fructose-1,6-bisphosphatase GlpX from Escherichia coli. J Biol Chem 2009; 284:3784-92. [PMID: 19073594 PMCID: PMC2635049 DOI: 10.1074/jbc.m808186200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2008] [Revised: 12/08/2008] [Indexed: 11/06/2022] Open
Abstract
Gluconeogenesis is an important metabolic pathway, which produces glucose from noncarbohydrate precursors such as organic acids, fatty acids, amino acids, or glycerol. Fructose-1,6-bisphosphatase, a key enzyme of gluconeogenesis, is found in all organisms, and five different classes of these enzymes have been identified. Here we demonstrate that Escherichia coli has two class II fructose-1,6-bisphosphatases, GlpX and YggF, which show different catalytic properties. We present the first crystal structure of a class II fructose-1,6-bisphosphatase (GlpX) determined in a free state and in the complex with a substrate (fructose 1,6-bisphosphate) or inhibitor (phosphate). The crystal structure of the ligand-free GlpX revealed a compact, globular shape with two alpha/beta-sandwich domains. The core fold of GlpX is structurally similar to that of Li+-sensitive phosphatases implying that they have a common evolutionary origin and catalytic mechanism. The structure of the GlpX complex with fructose 1,6-bisphosphate revealed that the active site is located between two domains and accommodates several conserved residues coordinating two metal ions and the substrate. The third metal ion is bound to phosphate 6 of the substrate. Inorganic phosphate strongly inhibited activity of both GlpX and YggF, and the crystal structure of the GlpX complex with phosphate demonstrated that the inhibitor molecule binds to the active site. Alanine replacement mutagenesis of GlpX identified 12 conserved residues important for activity and suggested that Thr(90) is the primary catalytic residue. Our data provide insight into the molecular mechanisms of the substrate specificity and catalysis of GlpX and other class II fructose-1,6-bisphosphatases.
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Affiliation(s)
- Greg Brown
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
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19
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Brucet M, Querol-Audí J, Bertlik K, Lloberas J, Fita I, Celada A. Structural and biochemical studies of TREX1 inhibition by metals. Identification of a new active histidine conserved in DEDDh exonucleases. Protein Sci 2008; 17:2059-69. [PMID: 18780819 DOI: 10.1110/ps.036426.108] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
TREX1 is the major exonuclease in mammalian cells, exhibiting the highest level of activity with a 3'-->5' activity. This exonuclease is responsible in humans for Aicardi-Goutières syndrome and for an autosomal dominant retinal vasculopathy with cerebral leukodystrophy. In addition, this enzyme is associated with systemic lupus erythematosus. TREX1 belongs to the exonuclease DEDDh family, whose members display low levels of sequence identity, while possessing a common fold and active site organization. For these exonucleases, a catalytic mechanism has been proposed that involves two divalent metal ions bound to the DEDD motif. Here we studied the interaction of TREX1 with the monovalent cations lithium and sodium. We demonstrate that these metals inhibit the exonucleolytic activity of TREX1, as measured by the classical gel method, as well as by a new technique developed for monitoring the real-time exonuclease reaction. The X-ray structures of the enzyme in complex with these two cations and with a nucleotide, a product of the exonuclease reaction, were determined at 2.1 A and 2.3 A, respectively. A comparison with the structures of the active complexes (in the presence of magnesium or manganese) explains that the inhibition mechanism is caused by the noncatalytic metals competing with distinct affinities for the two metal-binding sites and inducing subtle rearrangements in active centers. Our analysis also reveals that a histidine residue (His124), highly conserved in the DEDDh family, is involved in the activity of TREX1, as confirmed by mutational studies. Our results shed further light on the mechanism of activity of the DEDEh family of exonucleases.
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Affiliation(s)
- Marina Brucet
- Macrophage Biology Group, Institute for Research in Biomedicine and University of Barcelona, Barcelona Science Park, 08028 Barcelona, Spain
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20
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Hatzios SK, Iavarone AT, Bertozzi CR. Rv2131c from Mycobacterium tuberculosis is a CysQ 3'-phosphoadenosine-5'-phosphatase. Biochemistry 2008; 47:5823-31. [PMID: 18454554 PMCID: PMC2711008 DOI: 10.1021/bi702453s] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
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Mycobacterium tuberculosis (Mtb) produces a number of sulfur-containing metabolites that contribute to its pathogenesis and ability to survive in the host. These metabolites are products of the sulfate assimilation pathway. CysQ, a 3′-phosphoadenosine-5′-phosphatase, is considered an important regulator of this pathway in plants, yeast, and other bacteria. By controlling the pools of 3′-phosphoadenosine 5′-phosphate (PAP) and 3′-phosphoadenosine 5′-phosphosulfate (PAPS), CysQ has the potential to modulate flux in the biosynthesis of essential sulfur-containing metabolites. Bioinformatic analysis of the Mtb genome suggests the presence of a CysQ homologue encoded by the gene Rv2131c. However, a recent biochemical study assigned the protein’s function as a class IV fructose-1,6-bisphosphatase. In the present study, we expressed Rv2131c heterologously and found that the protein dephosphorylates PAP in a magnesium-dependent manner, with optimal activity observed between pH 8.5 and pH 9.5 using 0.5 mM MgCl2. A sensitive electrospray ionization mass spectrometry-based assay was used to extract the kinetic parameters for PAP, revealing a Km (8.1 ± 3.1 μM) and kcat (5.4 ± 1.1 s−1) comparable to those reported for other CysQ enzymes. The second-order rate constant for PAP was determined to be over 3 orders of magnitude greater than those determined for myo-inositol 1-phosphate (IMP) and fructose 1,6-bisphosphate (FBP), previously considered to be the primary substrates of this enzyme. Moreover, the ability of the Rv2131c-encoded enzyme to dephosphorylate PAP and PAPS in vivo was confirmed by functional complementation of an Escherichia coli ΔcysQ mutant. Taken together, these studies indicate that Rv2131c encodes a CysQ enzyme that may play a role in mycobacterial sulfur metabolism.
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Affiliation(s)
- Stavroula K Hatzios
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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21
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Creation of salt-insensitive 3′(2′),5′-bisphosphate nucleotidase by modeling and mutagenesis approach. Arch Biochem Biophys 2008; 469:174-83. [DOI: 10.1016/j.abb.2007.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Revised: 10/17/2007] [Accepted: 10/19/2007] [Indexed: 01/11/2023]
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22
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Imming P, Sinning C, Meyer A. Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov 2006; 5:821-34. [PMID: 17016423 DOI: 10.1038/nrd2132] [Citation(s) in RCA: 484] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
What is a drug target? And how many such targets are there? Here, we consider the nature of drug targets, and by classifying known drug substances on the basis of the discussed principles we provide an estimation of the total number of current drug targets.
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Affiliation(s)
- Peter Imming
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle, Germany.
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23
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Zhang JY, Zou J, Bao Q, Chen WL, Wang L, Yang H, Zhang CC. A lithium-sensitive and sodium-tolerant 3'-phosphoadenosine-5'-phosphatase encoded by halA from the cyanobacterium Arthrospira platensis is closely related to its counterparts from yeasts and plants. Appl Environ Microbiol 2006; 72:245-51. [PMID: 16391050 PMCID: PMC1352299 DOI: 10.1128/aem.72.1.245-251.2006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3'-Phosphoadenosine-5'-phosphatase (PAPase) is required for the removal of toxic 3'-phosphoadenosine-5'-phosphate (PAP) produced during sulfur assimilation in various eukaryotic organisms. This enzyme is a well-known target of lithium and sodium toxicity and has been used for the production of salt-resistant transgenic plants. In addition, PAPase has also been proposed as a target in the treatment of manic-depressive patients. One gene, halA, which could encode a protein closely related to the PAPases of yeasts and plants, was identified from the cyanobacterium Arthrospira (Spirulina) platensis. Phylogenic analysis indicated that proteins related to PAPases from several cyanobacteria were found in different clades, suggesting multiple origins of PAPases in cyanobacteria. The HalA polypeptide from A. platensis was overproduced in Escherichia coli and used for the characterization of its biochemical properties. HalA was dependent on Mg2+ for its activity and could use PAP or 3'-phosphoadenosine-5'-phosphosulfate as a substrate. HalA is sensitive to Li+ (50% inhibitory concentration [IC50] = 3.6 mM) but only slightly sensitive to Na+ (IC50 = 600 mM). The salt sensitivity of HalA was thus different from that of most of its eukaryotic counterparts, which are much more sensitive to both Li+ and Na+, but was comparable to the PAPase AtAHL (Hal2p-like protein) from Arabidopsis thaliana. The properties of HalA could help us to understand the structure-function relationship underlying the salt sensitivity of PAPases. The expression of halA improved the Li+ tolerance of E. coli, suggesting that the sulfur-assimilating pathway is a likely target of salt toxicity in bacteria as well.
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Affiliation(s)
- Ju-Yuan Zhang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
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24
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Pérez-Arellano I, Rubio V, Cervera J. Dissection of Escherichia coli glutamate 5-kinase: functional impact of the deletion of the PUA domain. FEBS Lett 2005; 579:6903-8. [PMID: 16337196 DOI: 10.1016/j.febslet.2005.11.037] [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] [Received: 08/22/2005] [Revised: 11/15/2005] [Accepted: 11/15/2005] [Indexed: 11/30/2022]
Abstract
Glutamate 5-kinase (G5K) catalyzes the controlling first step of the synthesis of the osmoprotective amino acid proline, which feed-back inhibits G5K. Microbial G5K generally consists of one amino acid kinase (AAK) and one PUA (named after pseudo uridine synthases and archaeosine-specific transglycosylases) domain. To investigate the role of the PUA domain, we have deleted it from Escherichia coli G5K. We show that wild-type G5K requires free Mg for activity, it is tetrameric, and it aggregates to higher forms in a proline-dependent way. G5K lacking the PUA domain remains tetrameric, active, and proline-inhibitable, but the Mg requirement and the proline-triggered aggregation are greatly diminished and abolished, respectively, and more proline is needed for inhibition. We propose that the PUA domain modulates the function of the AAK domain, opening the way to potential PUA domain-mediated regulation of G5K; and that this domain moves, exposing new surfaces upon proline binding.
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Affiliation(s)
- Isabel Pérez-Arellano
- Centro de Investigación Príncipe Felipe, Avda. Autopista del Saler, 16, Valencia 46013, Spain
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25
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Marco-Marín C, Gil-Ortiz F, Rubio V. The crystal structure of Pyrococcus furiosus UMP kinase provides insight into catalysis and regulation in microbial pyrimidine nucleotide biosynthesis. J Mol Biol 2005; 352:438-54. [PMID: 16095620 DOI: 10.1016/j.jmb.2005.07.045] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2005] [Revised: 07/12/2005] [Accepted: 07/14/2005] [Indexed: 11/21/2022]
Abstract
UMP kinase (UMPK), the enzyme responsible for microbial UMP phosphorylation, plays a key role in pyrimidine nucleotide biosynthesis, regulating this process via feed-back control and via gene repression of carbamoyl phosphate synthetase (the first enzyme of the pyrimidine biosynthesis pathway). We present crystal structures of Pyrococcus furiosus UMPK, free or complexed with AMPPNP or AMPPNP and UMP, at 2.4 A, 3 A and 2.55 A resolution, respectively, providing a true snapshot of the catalytically competent bisubstrate complex. The structure proves that UMPK does not resemble other nucleoside monophosphate kinases, including the UMP/CMP kinase found in animals, and thus UMPK may be a potential antimicrobial target. This enzyme has a homohexameric architecture centred around a hollow nucleus, and is organized as a trimer of dimers. The UMPK polypeptide exhibits the amino acid kinase family (AAKF) fold that has been reported in carbamate kinase and acetylglutamate kinase. Comparison with acetylglutamate kinase reveals that the substrates bind within each subunit at equivalent, adequately adapted sites. The UMPK structure contains two bound Mg ions, of which one helps stabilize the transition state, thus having the same catalytic role as one lysine residue found in acetylglutamate kinase, which is missing from P.furiosus UMPK. Relative to carbamate kinase and acetylglutamate kinase, UMPK presents a radically different dimer architecture, lacking the characteristic 16-stranded beta-sheet backbone that was considered a signature of AAKF enzymes. Its hexameric architecture, also a novel trait, results from equatorial contacts between the A and B subunits of adjacent dimers combined with polar contacts between A or B subunits, and may be required for the UMPK regulatory functions, such as gene regulation, proposed here to be mediated by hexamer-hexamer interactions with the DNA-binding protein PepA.
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Affiliation(s)
- Clara Marco-Marín
- Instituto de Biomedicina de Valencia (IBV-CSIC), Jaume Roig 11,Valencia 46010, Spain
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26
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Fonseca CP, Montezinho LP, Nabais C, Tomé AR, Freitas H, Geraldes CFGC, Castro MMCA. Effects of Li+ transport and intracellular binding on Li+/Mg2+ competition in bovine chromaffin cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2004; 1691:79-90. [PMID: 15110989 DOI: 10.1016/j.bbamcr.2003.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2003] [Revised: 12/16/2003] [Accepted: 12/17/2003] [Indexed: 11/18/2022]
Abstract
Li(+) transport, intracellular immobilisation and Li(+)/Mg(2+) competition were studied in Li(+)-loaded bovine chromaffin cells. Li(+) influx rate constants, k(i), obtained by atomic absorption (AA) spectrophotometry, in control (without and with ouabain) and depolarising (without and with nitrendipine) conditions, showed that L-type voltage-sensitive Ca(2+) channels have an important role in Li(+) uptake under depolarising conditions. The Li(+) influx apparent rate constant, k(iapp), determined under control conditions by (7)Li NMR spectroscopy with the cells immobilised and perfused, was much lower than the AA-determined value for the cells in suspension. Loading of cell suspensions with 15 mmol l(-1) LiCl led, within 90 min, to a AA-measured total intracellular Li(+) concentration, [Li(+)](iT)=11.39+/-0.56 mmol (l cells)(-1), very close to the steady state value. The intracellular Li(+) T(1)/T(2) ratio of (7)Li NMR relaxation times of the Li(+)-loaded cells reflected a high degree of Li(+) immobilisation in bovine chromaffin cells, similar to neuroblastoma, but larger than for lymphoblastoma and erythrocyte cells. A 52% increase in the intracellular free Mg(2+) concentration, Delta[Mg(2+)](f)=0.27+/-0.05 mmol (l cells)(-1) was measured for chromaffin cells loaded with the Mg(2+)-specific fluorescent probe furaptra, after 90-min loading with 15 mmol l(-1) LiCl, using fluorescence spectroscopy, indicating significant displacement of Mg(2+) by Li(+) from its intracellular binding sites. Comparison with other cell types showed that the extent of intracellular Li(+)/Mg(2+) competition at the same Li(+) loading level depends on intracellular Li(+) transport and immobilisation in a cell-specific manner, being maximal for neuroblastoma cells.
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Affiliation(s)
- C P Fonseca
- Department of Biochemistry and Centre for Neuroscience of Coimbra, University of Coimbra, P.O. Box 3126, 3001-401 Coimbra, Portugal
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27
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Gutteridge A, Thornton J. Conformational change in substrate binding, catalysis and product release: an open and shut case? FEBS Lett 2004; 567:67-73. [PMID: 15165895 DOI: 10.1016/j.febslet.2004.03.067] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2004] [Revised: 03/01/2004] [Accepted: 03/07/2004] [Indexed: 11/18/2022]
Abstract
The role of conformational change in substrate binding, catalysis and product release is reviewed for 11 enzymes, for which crystal structures are available for the apo, substrate- and product-bound states. The extent of global conformational changes is measured, and the movements of the functional regions involved in catalysis and ligand binding are compared to the rest of the structure. We find that most of these enzymes undergo relatively small amounts of conformational change and particularly small changes in catalytic residue geometry, usually less than 1 A. In some enzymes there is significant movement of the binding residues, usually on surface loops.
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Affiliation(s)
- Alex Gutteridge
- EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
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28
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Lovell SC, Davis IW, Arendall WB, de Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins 2003; 50:437-50. [PMID: 12557186 DOI: 10.1002/prot.10286] [Citation(s) in RCA: 3649] [Impact Index Per Article: 173.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Geometrical validation around the Calpha is described, with a new Cbeta measure and updated Ramachandran plot. Deviation of the observed Cbeta atom from ideal position provides a single measure encapsulating the major structure-validation information contained in bond angle distortions. Cbeta deviation is sensitive to incompatibilities between sidechain and backbone caused by misfit conformations or inappropriate refinement restraints. A new phi,psi plot using density-dependent smoothing for 81,234 non-Gly, non-Pro, and non-prePro residues with B < 30 from 500 high-resolution proteins shows sharp boundaries at critical edges and clear delineation between large empty areas and regions that are allowed but disfavored. One such region is the gamma-turn conformation near +75 degrees,-60 degrees, counted as forbidden by common structure-validation programs; however, it occurs in well-ordered parts of good structures, it is overrepresented near functional sites, and strain is partly compensated by the gamma-turn H-bond. Favored and allowed phi,psi regions are also defined for Pro, pre-Pro, and Gly (important because Gly phi,psi angles are more permissive but less accurately determined). Details of these accurate empirical distributions are poorly predicted by previous theoretical calculations, including a region left of alpha-helix, which rates as favorable in energy yet rarely occurs. A proposed factor explaining this discrepancy is that crowding of the two-peptide NHs permits donating only a single H-bond. New calculations by Hu et al. [Proteins 2002 (this issue)] for Ala and Gly dipeptides, using mixed quantum mechanics and molecular mechanics, fit our nonrepetitive data in excellent detail. To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (http://www-cryst.bioc.cam.ac.uk/rampage).
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Affiliation(s)
- Simon C Lovell
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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29
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