Crystallographic analysis of TarI and TarJ, a cytidylyltransferase and reductase pair for CDP-ribitol synthesis in Staphylococcus aureus wall teichoic acid biogenesis
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Afonine, 2012, Towards automated crystallographic structure refinement with phenix.refine, Acta Crystallogr. D. Biol. Crystallogr., 68, 352, 10.1107/S0907444912001308
Atilano, 2010, Teichoic acids are temporal and spatial regulators of peptidoglycan cross-linking in Staphylococcus aureus, Proc. Natl. Acad. Sci. U. S. A., 107, 18991, 10.1073/pnas.1004304107
Baatarkhuu, 2018, Synthesis and Kinetic evaluation of an azido analogue of methylerythritol phosphate: a Novel Inhibitor of E. coli YgbP/IspD, Sci. Rep., 8, 17892, 10.1038/s41598-018-35586-y
Badurina, 2003, CTP:glycerol 3-phosphate cytidylyltransferase (TarD) from Staphylococcus aureus catalyzes the cytidylyl transfer via an ordered Bi-Bi reaction mechanism with micromolar K(m) values, Biochim. Biophys. Acta, 1646, 196, 10.1016/S1570-9639(03)00019-0
Baker, 2009, Active site dynamics in the zinc-dependent medium chain alcohol dehydrogenase superfamily, Proc. Natl. Acad. Sci., 106, 779, 10.1073/pnas.0807529106
Baker, 1992, Structural consequences of sequence patterns in the fingerprint region of the nucleotide binding fold. Implications for nucleotide specificity, J. Mol. Biol., 228, 662, 10.1016/0022-2836(92)90848-E
Baur, 2009, Synthesis of CDP-activated ribitol for teichoic acid precursors in Streptococcus pneumoniae, J. Bacteriol., 191, 1200, 10.1128/JB.01120-08
Benavente, 2015, Enantioselective oxidation of galactitol 1-phosphate by galactitol-1-phosphate 5-dehydrogenase from Escherichia coli, Acta Crystallogr. Sect. D Biol. Crystallogr., 71, 1540, 10.1107/S1399004715009281
Brown, 2016, Antibacterial drug discovery in the resistance era, Nature, 529, 336, 10.1038/nature17042
Campbell, 2011, Synthetic lethal compound combinations reveal a fundamental connection between wall teichoic acid and peptidoglycan biosyntheses in Staphylococcus aureus, ACS Chem. Biol., 6, 106, 10.1021/cb100269f
Caveney, 2018, Enzyme structures of the bacterial peptidoglycan and wall teichoic acid biogenesis pathways, Curr. Opin. Struct. Biol., 53, 45, 10.1016/j.sbi.2018.05.002
Celniker, 2013, ConSurf: Using evolutionary data to raise testable hypotheses about protein function, Isr. J. Chem., 53, 199, 10.1002/ijch.201200096
Chen, 2012, Expression, purification, crystallization and preliminary X-ray analysis of ribitol-5-phosphate cytidylyltransferase from Bacillus subtilis., Acta Crystallogr. Sect. F. Struct. Biol. Cryst. Commun., 68, 1195, 10.1107/S1744309112035142
D’Elia, M.A, Millar, K.E., Bhavsar, A.P., Tomljenovic, A.M., Hutter, B., Schaab, C., Moreno-Hagelsieb, G., Brown, E.D., 2009. Probing teichoic acid genetics with bioactive molecules reveals new interactions among diverse processes in bacterial cell wall biogenesis. Chem. Biol. 16, 548–56. https://doi.org/10.1016/j.chembiol.2009.04.009.
D’Elia, M.A, Pereira, M.P., Chung, Y.S., Zhao, W., Chau, A., Kenney, T.J., Sulavik, M.C., Black, T. a, Brown, E.D., 2006. Lesions in teichoic acid biosynthesis in Staphylococcus aureus lead to a lethal gain of function in the otherwise dispensable pathway. J. Bacteriol. 188, 4183–9. https://doi.org/10.1128/JB.00197-06.
De Vries, 2010, The HADDOCK web server for data-driven biomolecular docking, Nat. Protoc., 5, 883, 10.1038/nprot.2010.32
Denapaite, 2012, Biosynthesis of teichoic acids in Streptococcus pneumoniae and closely related species: lessons from genomes, Microb. Drug Resist., 18, 344, 10.1089/mdr.2012.0026
Eklund, 1982, Binding of substrate in a ternary complex of horse liver alcohol dehydrogenase, J. Biol. Chem., 257, 14349, 10.1016/S0021-9258(19)45387-8
Eklund, 2008, Medium- and short-chain dehydrogenase/reductase gene and protein families: Three-dimensional structures of MDR alcohol dehydrogenases, Cell. Mol. Life Sci., 65, 3907, 10.1007/s00018-008-8589-x
Eklund, 1981, Structure of a triclinic ternary complex of horse liver alcohol dehydrogenase at 2.9 Å resolution, J. Mol. Biol., 146, 561, 10.1016/0022-2836(81)90047-4
Elander, 2003, Industrial production of beta-lactam antibiotics, Appl. Microbiol. Biotechnol., 61, 385, 10.1007/s00253-003-1274-y
Emsley, 2010, Features and development of Coot, Acta Crystallogr. D. Biol. Crystallogr., 66, 486, 10.1107/S0907444910007493
Farha, M.A, Leung, A., Sewell, E.W., D’Elia, M. a, Allison, S.E., Ejim, L., Pereira, P.M., Pinho, M.G., Wright, G.D., Brown, E.D., 2013. Inhibition of WTA synthesis blocks the cooperative action of PBPs and sensitizes MRSA to β-lactams. ACS Chem. Biol. 8, 226–33. https://doi.org/10.1021/cb300413m.
Fong, D.H., Yim, V.C.-N., D’Elia, M. a, Brown, E.D., Berghuis, A.M., 2006. Crystal structure of CTP:glycerol-3-phosphate cytidylyltransferase from Staphylococcus aureus: examination of structural basis for kinetic mechanism. Biochim. Biophys. Acta 1764, 63–9. https://doi.org/10.1016/j.bbapap.2005.10.015.
Formstone, 2008, Localization and Interactions of Teichoic Acid Synthetic Enzymes in Bacillus subtilis, J. Bacteriol., 190, 1812, 10.1128/JB.01394-07
Grochulski, 2011, Beamline 08ID-1, the prime beamline of the Canadian macromolecular crystallography facility, J. Synchrotron Radiat., 18, 681, 10.1107/S0909049511019431
Jin, 2016, A structural and functional study on the 2-C-methyl-d-erythritol-4-phosphate cytidyltransferase (IspD) from Bacillus subtilis, Sci. Rep., 6, 1, 10.1038/srep36379
Kawai, 2011, A widespread family of bacterial cell wall assembly proteins, EMBO J., 30, 4931, 10.1038/emboj.2011.358
Kojima, 1983, Structure of linkage region between ribitol teichoic acid and peptidoglycan in cell walls of Staphylococcus aureus H, J. Biol. Chem., 258, 9043, 10.1016/S0021-9258(17)44628-X
Kunfermann, 2014, Pseudilins: Halogenated, allosteric inhibitors of the non-mevalonate pathway enzyme IspD, Angew. Chemie - Int. Ed., 53, 2235, 10.1002/anie.201309557
Lange, 2000, Isoprenoid biosynthesis: The evolution of two ancient and distinct pathways across genomes, Proc. Natl. Acad. Sci., 97, 13172, 10.1073/pnas.240454797
Laskowski, 2011, LigPlot+: multiple ligand-protein interaction diagrams for drug discovery, J. Chem. Inf. Model., 51, 2778, 10.1021/ci200227u
Lazarevic, 1995, The tagGH operon of Bacillus subtilis 168 encodes a two-component ABC transporter involved in the metabolism of two wall teichoic acids, Mol. Microbiol., 16, 345, 10.1111/j.1365-2958.1995.tb02306.x
McCoy, 2007, Phaser crystallographic software, J. Appl. Crystallogr., 40, 658, 10.1107/S0021889807021206
Meredith, 2008, Late-stage polyribitol phosphate wall teichoic acid biosynthesis in Staphylococcus aureus, J. Bacteriol., 190, 3046, 10.1128/JB.01880-07
Merkley, 2014, Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine-lysine distances, Protein Sci., 23, 747, 10.1002/pro.2458
Pauly, 2003, X-ray crystallographic and kinetic studies of human sorbitol dehydrogenase, Structure, 11, 1071, 10.1016/S0969-2126(03)00167-9
Pereira, 2004, Bifunctional catalysis by CDP-ribitol synthase: convergent recruitment of reductase and cytidylyltransferase activities in Haemophilus influenzae and Staphylococcus aureus, Biochemistry, 43, 11802, 10.1021/bi048866v
Pereira, 2008, Duplication of teichoic acid biosynthetic genes in Staphylococcus aureus leads to functionally redundant poly(ribitol phosphate) polymerases, J. Bacteriol., 190, 5642, 10.1128/JB.00526-08
Petrotchenko, 2014, DXMSMS match program for automated analysis of LC-MS/MS data obtained using isotopically coded CID-cleavable cross-linking reagents, Curr. Protoc. Bioinforma., 48, 8.18.1-19, 10.1002/0471250953.bi0818s48
Pettersen, 2004, UCSF Chimera–a visualization system for exploratory research and analysis, J. Comput. Chem., 25, 1605, 10.1002/jcc.20084
Price, 2016, Molecular Mechanism of Action of Antimalarial Benzoisothiazolones: Species-Selective Inhibitors of the Plasmodium spp. MEP Pathway enzyme, IspD. Sci. Rep., 6, 1
Qian, 2006, Genomic characterization of ribitol teichoic acid synthesis in Staphylococcus aureus: genes, genomic organization and gene duplication, BMC Genomics, 7, 74, 10.1186/1471-2164-7-74
Richard, S.B., Bowman, M.E., Kwiatkowski, W., Kang, I., Chow, C., Lillo, a M., Cane, D.E., Noel, J.P., 2001. Structure of 4-diphosphocytidyl-2-C- methylerythritol synthetase involved in mevalonate- independent isoprenoid biosynthesis. Nat. Struct. Biol. 8, 641–648. https://doi.org/10.1038/89691.
Richard, 2004, Kinetic analysis of Escherichia coli 2-C-methyl-D-erythritol-4-phosphate cytidyltransferase, wild type and mutants, reveals roles of active site amino acids, Biochemistry, 43, 12189, 10.1021/bi0487241
Riemersma, 2015, Human ISPD Is a Cytidyltransferase Required for Dystroglycan O-Mannosylation, Chem. Biol., 22, 1643, 10.1016/j.chembiol.2015.10.014
Riveros-Rosas, 2003, Diversity, taxonomy and evolution of medium-chain dehydrogenase/reductase superfamily, Eur. J. Biochem., 270, 3309, 10.1046/j.1432-1033.2003.03704.x
Robert, 2014, Deciphering key features in protein structures with the new ENDscript server, Nucleic Acids Res., 42, W320, 10.1093/nar/gku316
Salentin, 2015, PLIP: fully automated protein–ligand interaction profiler, Nucleic Acids Res., 43, W443, 10.1093/nar/gkv315
Schlag, 2010, Role of staphylococcal wall teichoic acid in targeting the major autolysin Atl, Mol. Microbiol., 75, 864, 10.1111/j.1365-2958.2009.07007.x
Schwab, 2017, Mechanism of allosteric inhibition of the enzyme IspD by three different classes of ligands, ACS Chem. Biol., 12, 2132, 10.1021/acschembio.7b00004
Shevchenko, 2007, In-gel digestion for mass spectrometric characterization of proteins and proteomes, Nat. Protoc., 1, 2856, 10.1038/nprot.2006.468
The PyMOL Molecular Graphics System, 2019. Version 2.3 Schrödinger, LLC.
Vedadi, M., Niesen, F.H., Allali-Hassani, A., Fedorov, O.Y., Finerty, P.J., Wasney, G.A, Yeung, R., Arrowsmith, C., Ball, L.J., Berglund, H., Hui, R., Marsden, B.D., Nordlund, P., Sundstrom, M., Weigelt, J., Edwards, A.M., 2006. Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination. Proc. Natl. Acad. Sci. U. S. A. 103, 15835–40. https://doi.org/10.1073/pnas.0605224103.
Weidenmaier, 2005, Lack of wall teichoic acids in Staphylococcus aureus leads to reduced interactions with endothelial cells and to attenuated virulence in a rabbit model of endocarditis, J. Infect. Dis., 191, 1771, 10.1086/429692
Weissgerber, 2017, Data visualization, bar naked: A free tool for creating interactive graphics, J. Biol. Chem., 292, 20592, 10.1074/jbc.RA117.000147
Winn, 2011, Overview of the CCP4 suite and current developments, Acta Crystallogr. Sect. D Biol. Crystallogr., 67, 235, 10.1107/S0907444910045749
Witschel, 2011, Inhibitors of the herbicidal target IspD: Allosteric site binding, Angew. Chemie - Int. Ed., 50, 7931, 10.1002/anie.201102281
Wungsintaweekul, J., 2001. Enzymes of the Alternative Terpenoid Pathway in Escherichia coli.
Xia, 2010, The wall teichoic acid and lipoteichoic acid polymers of Staphylococcus aureus, Int. J. Med. Microbiol., 300, 148, 10.1016/j.ijmm.2009.10.001
Zalacain, 2003, A global approach to identify novel broad-spectrum antibacterial targets among proteins of unknown function, J. Mol. Microbiol. Biotechnol., 6, 109
Zolli, 2001, Reduction precedes cytidylyl transfer without substrate channeling in distinct active sites of the bifunctional CDP-ribitol synthase from Haemophilus influenzae, Biochemistry, 40, 5041, 10.1021/bi002745n