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Walter P, Mechaly A, Bous J, Haouz A, England P, Lai‐Kee‐Him J, Ancelin A, Hoos S, Baron B, Trapani S, Bron P, Labesse G, Munier‐Lehmann H. Structural basis for the allosteric inhibition of UMP kinase from Gram‐positive bacteria, a promising antibacterial target. FEBS J 2022; 289:4869-4887. [DOI: 10.1111/febs.16393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/18/2022] [Accepted: 02/09/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Patrick Walter
- Unité de Chimie et Biocatalyse Département de Biologie Structurale et Chimie Institut Pasteur CNRS UMR3523 Paris France
| | - Ariel Mechaly
- Plate‐Forme de Cristallographie C2RT Institut Pasteur CNRS UMR3528 Paris France
| | - Julien Bous
- Centre de Biologie Structurale (CBS) Univ Montpellier INSERM CNRS Montpellier France
| | - Ahmed Haouz
- Plate‐Forme de Cristallographie C2RT Institut Pasteur CNRS UMR3528 Paris France
| | - Patrick England
- Plate‐Forme de Biophysique Moléculaire C2RT Institut Pasteur CNRS UMR3528 Paris France
| | - Joséphine Lai‐Kee‐Him
- Centre de Biologie Structurale (CBS) Univ Montpellier INSERM CNRS Montpellier France
| | - Aurélie Ancelin
- Centre de Biologie Structurale (CBS) Univ Montpellier INSERM CNRS Montpellier France
| | - Sylviane Hoos
- Plate‐Forme de Biophysique Moléculaire C2RT Institut Pasteur CNRS UMR3528 Paris France
| | - Bruno Baron
- Plate‐Forme de Biophysique Moléculaire C2RT Institut Pasteur CNRS UMR3528 Paris France
| | - Stefano Trapani
- Centre de Biologie Structurale (CBS) Univ Montpellier INSERM CNRS Montpellier France
| | - Patrick Bron
- Centre de Biologie Structurale (CBS) Univ Montpellier INSERM CNRS Montpellier France
| | - Gilles Labesse
- Centre de Biologie Structurale (CBS) Univ Montpellier INSERM CNRS Montpellier France
| | - Hélène Munier‐Lehmann
- Unité de Chimie et Biocatalyse Département de Biologie Structurale et Chimie Institut Pasteur CNRS UMR3523 Paris France
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Chemo-enzymatic synthesis of 13C- and 19F-labeled uridine-5′-triphosphate for RNA NMR probing. MONATSHEFTE FUR CHEMIE 2021. [DOI: 10.1007/s00706-021-02757-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Qi Y, Wang H, Chen X, Wei G, Tao S, Fan M. Altered Metabolic Strategies: Elaborate Mechanisms Adopted by Oenococcus oeni in Response to Acid Stress. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2906-2918. [PMID: 33587641 DOI: 10.1021/acs.jafc.0c07599] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Oenococcus oeni plays a key role in inducing malolactic fermentation in wine. Acid stress is often encountered under wine conditions. However, the lack of systematic studies of acid resistance mechanisms limits the downstream fermentation applications. In this study, the acid responses of O. oeni were investigated by combining transcriptome, metabolome, and genome-scale metabolic modeling approaches. Metabolite profiling highlighted the decreased abundance of nucleotides under acid stress. The gene-metabolite bipartite network showed negative correlations between nucleotides and genes involved in ribosome assembly, translation, and post-translational processes, suggesting that stringent response could be activated under acid stress. Genome-scale metabolic modeling revealed marked flux rerouting, including reallocation of pyruvate, attenuation of glycolysis, utilization of carbon sources other than glucose, and enhancement of nucleotide salvage and the arginine deiminase pathway. This study provided novel insights into the acid responses of O. oeni, which will be useful for designing strategies to address acid stress in wine malolactic fermentation.
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Affiliation(s)
- Yiman Qi
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hao Wang
- College of Life Sciences and State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiangdan Chen
- College of Life Sciences and State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gehong Wei
- College of Life Sciences and State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shiheng Tao
- College of Life Sciences and State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingtao Fan
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
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Poppe J, Brünle S, Hail R, Wiesemann K, Schneider K, Ermler U. The Molybdenum Storage Protein: A soluble ATP hydrolysis-dependent molybdate pump. FEBS J 2018; 285:4602-4616. [PMID: 30367742 DOI: 10.1111/febs.14684] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/11/2018] [Accepted: 10/23/2018] [Indexed: 12/30/2022]
Abstract
A continuous FeMo cofactor supply for nitrogenase maturation is ensured in Azotobacter vinelandii by developing a cage-like molybdenum storage protein (MoSto) capable to store ca. 120 molybdate molecules ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msubsup><mml:mtext>MoO</mml:mtext> <mml:mrow><mml:mn>4</mml:mn></mml:mrow> <mml:mrow><mml:mn>2</mml:mn> <mml:mo>-</mml:mo></mml:mrow> </mml:msubsup> </mml:math> ) as discrete polyoxometalate (POM) clusters. To gain mechanistic insight into this process, MoSto was characterized by Mo and ATP/ADP content, structural, and kinetic analysis. We defined three functionally relevant states specified by the presence of both ATP/ADP and POM clusters (MoStofunct ), of only ATP/ADP (MoStobasal ) and of neither ATP/ADP nor POM clusters (MoStozero ), respectively. POM clusters are only produced when ATP is hydrolyzed to ADP and phosphate. Vmax was ca. 13 μmolphosphate ·min-1 ·mg-1 and Km for molybdate and ATP/Mg2+ in the low micromolar range. ATP hydrolysis presumably proceeds at subunit α, inferred from a highly occupied α-ATP/Mg2+ and a weaker occupied β-ATP/no Mg2+ -binding site found in the MoStofunct structure. Several findings indicate that POM cluster storage is separated into a rapid ATP hydrolysis-dependent molybdate transport across the protein cage wall and a slow molybdate assembly induced by combined auto-catalytic and protein-driven processes. The cage interior, the location of the POM cluster depot, is locked in all three states and thus not rapidly accessible for molybdate from the outside. Based on Vmax , the entire Mo storage process should be completed in less than 10 s but requires, according to the molybdate content analysis, ca. 15 min. Long-time incubation of MoStobasal with nonphysiological high molybdate amounts implicates an equilibrium in and outside the cage and POM cluster self-formation without ATP hydrolysis. DATABASES: The crystal structures MoSto in the MoSto-F6, MoSto-F7, MoStobasal , MoStozero , and MoSto-F1vitro states were deposited to PDB under the accession numbers PDB 6GU5, 6GUJ, 6GWB, 6GWV, and 6GX4.
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Affiliation(s)
- Juliane Poppe
- Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany
| | - Steffen Brünle
- Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany
| | - Ron Hail
- Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany.,Biochemie I, Fakultät für Chemie, Universität Bielefeld, Bielefeld, Germany
| | - Katharina Wiesemann
- Abteilung molelukare Biowissensschaften, Molekulare Zellbiologie der Pflanzen, Goethe Universität, Frankfurt am Main, Germany
| | - Klaus Schneider
- Biochemie I, Fakultät für Chemie, Universität Bielefeld, Bielefeld, Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany
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Abstract
The development and application of a highly versatile suite of tools for mycobacterial genetics, coupled with widespread use of "omics" approaches to elucidate the structure, function, and regulation of mycobacterial proteins, has led to spectacular advances in our understanding of the metabolism and physiology of mycobacteria. In this article, we provide an update on nucleotide metabolism and DNA replication in mycobacteria, highlighting key findings from the past 10 to 15 years. In the first section, we focus on nucleotide metabolism, ranging from the biosynthesis, salvage, and interconversion of purine and pyrimidine ribonucleotides to the formation of deoxyribonucleotides. The second part of the article is devoted to DNA replication, with a focus on replication initiation and elongation, as well as DNA unwinding. We provide an overview of replication fidelity and mutation rates in mycobacteria and summarize evidence suggesting that DNA replication occurs during states of low metabolic activity, and conclude by suggesting directions for future research to address key outstanding questions. Although this article focuses primarily on observations from Mycobacterium tuberculosis, it is interspersed, where appropriate, with insights from, and comparisons with, other mycobacterial species as well as better characterized bacterial models such as Escherichia coli. Finally, a common theme underlying almost all studies of mycobacterial metabolism is the potential to identify and validate functions or pathways that can be exploited for tuberculosis drug discovery. In this context, we have specifically highlighted those processes in mycobacterial DNA replication that might satisfy this critical requirement.
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New biocatalysts for one pot multistep enzymatic synthesis of pyrimidine nucleoside diphosphates from readily available reagents. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2014.12.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Alexandre T, Rayna B, Munier-Lehmann H. Two classes of bacterial IMPDHs according to their quaternary structures and catalytic properties. PLoS One 2015; 10:e0116578. [PMID: 25706619 PMCID: PMC4338043 DOI: 10.1371/journal.pone.0116578] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/10/2014] [Indexed: 11/19/2022] Open
Abstract
Inosine-5'-monophosphate dehydrogenase (IMPDH) occupies a key position in purine nucleotide metabolism. In this study, we have performed the biochemical and physico-chemical characterization of eight bacterial IMPDHs, among which six were totally unexplored. This study led to a classification of bacterial IMPDHs according to the regulation of their catalytic properties and their quaternary structures. Class I IMPDHs are cooperative enzymes for IMP, which are activated by MgATP and are octameric in all tested conditions. On the other hand, class II IMPDHs behave as Michaelis-Menten enzymes for both substrates and are tetramers in their apo state or in the presence of IMP, which are shifted to octamers in the presence of NAD or MgATP. Our work provides new insights into the IMPDH functional regulation and a model for the quaternary structure modulation is proposed.
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Affiliation(s)
- Thomas Alexandre
- Institut Pasteur, Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, 28 rue du Dr Roux, F-75015, Paris, France
- Centre Nationale de la Recherche Scientifique, Unité Mixte de Recherche 3523, F-75015, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, F-75205, Paris, France
| | - Bertrand Rayna
- Institut Pasteur, Proteopole, Plateforme de biophysique des macromolecules et de leurs interactions, 25 rue du Dr Roux, F-75015, Paris, France
- Centre Nationale de la Recherche Scientifique, Unité Mixte de Recherche 3528, F-75015, Paris, France
| | - Hélène Munier-Lehmann
- Institut Pasteur, Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, 28 rue du Dr Roux, F-75015, Paris, France
- Centre Nationale de la Recherche Scientifique, Unité Mixte de Recherche 3523, F-75015, Paris, France
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Uridine monophosphate kinase as potential target for tuberculosis: From target to lead identification. Interdiscip Sci 2014; 5:296-311. [DOI: 10.1007/s12539-013-0180-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 03/08/2013] [Accepted: 03/12/2013] [Indexed: 12/31/2022]
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Chu CH, Liu MH, Chen PC, Lin MH, Li YC, Hsiao CD, Sun YJ. Structures of Helicobacter pylori uridylate kinase: insight into release of the product UDP. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:773-83. [PMID: 22751662 DOI: 10.1107/s0907444912011407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 03/15/2012] [Indexed: 11/10/2022]
Abstract
Uridylate kinase (UMPK; EC 2.7.4.22) transfers the γ-phosphate of ATP to UMP, forming UDP. It is allosterically regulated by GTP. Structures of Helicobacter pylori UMPK (HpUMPK) complexed with GTP (HpUMPK-GTP) and with UDP (HpUMPK-UDP) were determined at 1.8 and 2.5 Å resolution, respectively. As expected, HpUMPK-GTP forms a hexamer with six GTP molecules at its centre. Interactions between HpUMPK and GTP are made by the β3 strand of the sheet, loop β3α4 and the α4 helix. In HpUMPK-UDP, the hexameric symmetry typical of UMPKs is absent. Only four of the HpUMPK molecules bind UDP; the other two HpUMPK molecules are in the UDP-free state. The asymmetric hexamer of HpUMPK-UDP, which has an exposed dimer interface, may assist in UDP release. Furthermore, the flexibility of the α2 helix, which interacts with UDP, is found to increase when UDP is absent in HpUMPK-UDP. In HpUMPK-GTP, the α2 helix is too flexible to be observed. This suggests that GTP binding may affect the conformation of the α2 helix, thereby promoting UDP release.
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Affiliation(s)
- Chen-Hsi Chu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
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Hari Prasad O, Nanda Kumar Y, Reddy OVS, Chaudhary A, Sarma PVGK. Cloning, Expression, Purification and Characterization of UMP Kinase from Staphylococcus aureus. Protein J 2012; 31:345-52. [DOI: 10.1007/s10930-012-9410-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Marcos E, Crehuet R, Bahar I. Changes in dynamics upon oligomerization regulate substrate binding and allostery in amino acid kinase family members. PLoS Comput Biol 2011; 7:e1002201. [PMID: 21980279 PMCID: PMC3182869 DOI: 10.1371/journal.pcbi.1002201] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 08/04/2011] [Indexed: 11/25/2022] Open
Abstract
Oligomerization is a functional requirement for many proteins. The interfacial interactions and the overall packing geometry of the individual monomers are viewed as important determinants of the thermodynamic stability and allosteric regulation of oligomers. The present study focuses on the role of the interfacial interactions and overall contact topology in the dynamic features acquired in the oligomeric state. To this aim, the collective dynamics of enzymes belonging to the amino acid kinase family both in dimeric and hexameric forms are examined by means of an elastic network model, and the softest collective motions (i.e., lowest frequency or global modes of motions) favored by the overall architecture are analyzed. Notably, the lowest-frequency modes accessible to the individual subunits in the absence of multimerization are conserved to a large extent in the oligomer, suggesting that the oligomer takes advantage of the intrinsic dynamics of the individual monomers. At the same time, oligomerization stiffens the interfacial regions of the monomers and confers new cooperative modes that exploit the rigid-body translational and rotational degrees of freedom of the intact monomers. The present study sheds light on the mechanism of cooperative inhibition of hexameric N-acetyl-L-glutamate kinase by arginine and on the allosteric regulation of UMP kinases. It also highlights the significance of the particular quaternary design in selectively determining the oligomer dynamics congruent with required ligand-binding and allosteric activities. Protein function requires a three-dimensional structure with specific dynamic features for catalytic and binding events, and, in many cases, the structure results from the assembly of more than one polypeptide chain (also called monomer or subunit) to form an oligomer or multimer. Proteins such as hemoglobin or chaperonin GroEL are oligomers formed by 2 and 14 subunits, respectively, whereas virus capsids are multimers composed of hundreds of monomers. In these cases, the architecture of the interface between the subunits and the overall assembly geometry are essential in determining the functional motions that these sophisticated structures are able to perform under physiological conditions. Here we present results from our computational study of the large-amplitude motions of dimeric and hexameric proteins that belong to the Amino Acid Kinase family. Our study reveals that the monomers in these oligomeric proteins are arranged in such a way that the oligomer inherits the intrinsic dynamic features of its components. The packing geometry additionally confers the ability to perform highly cooperative conformational changes that involve all monomers and enable the biological activity of the multimer. The study highlights the significance of the quaternary design in favoring the oligomer dynamics that enables ligand-binding and allosteric regulation functions.
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Affiliation(s)
- Enrique Marcos
- Department of Biological Chemistry and Molecular Modelling, IQAC-CSIC, Barcelona, Spain
| | - Ramon Crehuet
- Department of Biological Chemistry and Molecular Modelling, IQAC-CSIC, Barcelona, Spain
- * E-mail: (RC) (RC); (IB) (IB)
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (RC) (RC); (IB) (IB)
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