Exploration of archaeal nucleotide sugar epimerases unveils a new and highly promiscuous GDP-Gal4E subgroup
Tài liệu tham khảo
Allard, 2001, Epimerases: Structure, function and mechanism, Cell. Mol. Life Sci., 58, 1650, 10.1007/PL00000803
Bang, 2009, Functional analysis of mutations in UDP-galactose-4-epimerase (GALE) associated with galactosemia in Korean patients using mammalian GALE-null cells, FEBS J., 276, 1952, 10.1111/j.1742-4658.2009.06922.x
Beerens, 2022, GDP-Mannose 3,5-Epimerase: A View on Structure, Mechanism, and Industrial Potential, Front. Mol. Biosci., 8, 1, 10.3389/fmolb.2021.784142
Beerens, 2015, UDP-hexose 4-epimerases: a view on structure, mechanism and substrate specificity, Carbohydr. Res., 414, 8, 10.1016/j.carres.2015.06.006
Beerens, 2013, Characterization and mutational analysis of the UDP-Glc (NAc) 4-epimerase from Marinithermus hydrothermalis, Appl. Microbiol. Biotechnol., 97, 7733, 10.1007/s00253-012-4635-6
Bloom, 2006, Protein stability promotes evolvability, Proc. Natl. Acad. Sci. U. S. A., 103, 5869, 10.1073/pnas.0510098103
Chen, 1999, Cloning, expression and characterization of a UDP-galactose 4-epimerase from Escherichia coli, Biotechnol. Lett., 21, 1131, 10.1023/A:1005678225031
Chung, 2012, Characterization of UDP-glucose 4-epimerase from Pyrococcus horikoshii: Regeneration of UDP to produce UDP-galactose using two-enzyme system with trehalose, Bioresour. Technol., 110, 423, 10.1016/j.biortech.2012.01.046
Da Costa, 2021, Structure-function relationships in NDP-sugar active SDR enzymes: Fingerprints for functional annotation and enzyme engineering, Biotechnol. Adv., 48, 10.1016/j.biotechadv.2021.107705
Daenzer, 2012, UDP-Galactose 4′-epimerase activities toward UDP-Gal and UDP-GalNAc play different roles in the development of Drosophila melanogaster, PLoS Genet., 8, e1002721, 10.1371/journal.pgen.1002721
Demendi, 2005, Towards a better understanding of the substrate specificity of the UDP-N-acetylglucosamine C4 epimerase WbpP, Biochem. J., 389, 173, 10.1042/BJ20050263
Eichler, 2013, Extreme sweetness: Protein glycosylation in archaea, Nat. Rev. Microbiol., 11, 151, 10.1038/nrmicro2957
Friedman, 2012, The Molecular Dynamics of Trypanosoma brucei UDP-Galactose 4′-Epimerase: A Drug Target for African Sleeping Sickness, Chem. Biol. Drug Des., 80, 173, 10.1111/j.1747-0285.2012.01392.x
Fushinobu, 2021, Molecular evolution and functional divergence of UDP-hexose 4-epimerases, Curr. Opin. Chem. Biol., 61, 53, 10.1016/j.cbpa.2020.09.007
Gevaert, 2019, Characterization of the First Bacterial and Thermostable GDP-Mannose 3,5-Epimerase, Int. J. Mol. Sci., 20, 3530, 10.3390/ijms20143530
Gevaert, 2020, GDP-altrose as novel product of GDP-mannose 3,5-epimerase: Revisiting its reaction mechanism, Int. J. Biol. Macromol., 165, 1862, 10.1016/j.ijbiomac.2020.10.067
Guindon, 2010, New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0, Syst. Biol., 59, 307, 10.1093/sysbio/syq010
Hoffmeister, 2000, The NDP-sugar co-substrate concentration and the enzyme expression level influence the substrate specificity of glycosyltransferases: cloning and characterization of deoxysugar biosynthetic genes of the urdamycin biosynthetic gene cluster, Chem. Biol., 7, 821, 10.1016/S1074-5521(00)00029-6
Holden, 2003, Structure and Function of Enzymes of the Leloir Pathway for Galactose Metabolism, J. Biol. Chem., 278, 43885, 10.1074/jbc.R300025200
Huson, 2012, Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks, Syst. Biol., 61, 1061, 10.1093/sysbio/sys062
Ishiyama, 2004, Crystal structure of WbpP, a genuine UDP-N-acetylglucosamine 4-epimerase from Pseudomonas aeruginosa: Substrate specificity in UDP-hexose 4-epimerases, J. Biol. Chem., 279, 22635, 10.1074/jbc.M401642200
Kuipers, 2010, 3DM: Systematic analysis of heterogeneous superfamily data to discover protein functionalities, Proteins Struct. Funct. Bioinforma., 78, 2101
Liu, 2011, Functional expression of L-fucokinase/guanosine 5′-diphosphate-L-fucose pyrophosphorylase from Bacteroides fragilis in Saccharomyces cerevisiae for the production of nucleotide sugars from exogenous monosaccharides, Glycobiology, 21, 1228, 10.1093/glycob/cwr057
Mirdita, M., Ovchinnikov, S., Steinegger, M., 2021. ColabFold - Making protein folding accessible to all. bioRxiv 2021.08.15.456425. https://doi.org/10.1101/2021.08.15.456425.
Nam, 2019, Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum, Sci. Rep., 9, 11081, 10.1038/s41598-019-47591-w
Niou, 2009, Role of galE on biofilm formation by Thermus spp, Biochem. Biophys. Res. Commun., 390, 313, 10.1016/j.bbrc.2009.09.120
Ohashi, 2017, Effective Synthesis of Guanosine 5’-Diphospho-β-L-galactose using Bacterial L-Fucokinase/Guanosine 5’-diphosphate-L-fucose Pyrophosphorylase, Adv. Synth. Catal., 359, 4227, 10.1002/adsc.201700901
Pacinelli, 2002, Relationship of Yersinia pseudotuberculosis O antigens IA, IIA, and IVB: The IIA gene cluster was derived from that of IVB, Infect. Immun., 70, 3271, 10.1128/IAI.70.6.3271-3276.2002
Rapp, 2020, Expanding the Enzyme Repertoire for Sugar Nucleotide Epimerization: The CDP-Tyvelose 2-Epimerase from Thermodesulfatator atlanticus for Glucose/Mannose Interconversion, Appl. Environ. Microbiol., 87, 10.1128/AEM.02131-20
Sakuraba, 2011, Crystal structure of UDP-galactose 4-epimerase from the hyperthermophilic archaeon Pyrobaculum calidifontis, Arch. Biochem. Biophys., 512, 126, 10.1016/j.abb.2011.05.013
Sato, 2011, Novel metabolic pathways in Archaea, Curr. Opin. Microbiol., 14, 307, 10.1016/j.mib.2011.04.014
Shin, 2015, The structural basis of substrate promiscuity in UDP-hexose 4-epimerase from the hyperthermophilic Eubacterium Thermotoga maritima, Arch. Biochem. Biophys., 585, 39, 10.1016/j.abb.2015.08.025
Sievers, 2018, Clustal Omega for making accurate alignments of many protein sequences, Protein Sci., 27, 135, 10.1002/pro.3290
Szklarczyk, 2019, STRING v11: Protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets, Nucleic Acids Res., 47, D607, 10.1093/nar/gky1131
Tanner, 2002, Understanding nature’s strategies for enzyme-catalyzed racemization and epimerization, Acc. Chem. Res., 35, 237, 10.1021/ar000056y
Thoden, 1996, Molecular structure of the NADH/UDP-glucose abortive complex of UDP-galactose 4-epimerase from Escherichia coli: Implications for the catalytic mechanism, Biochemistry, 35, 5137, 10.1021/bi9601114
Thoden, 2000, Crystallographic evidence for Tyr 157 functioning as the active site base in human UDP-galactose 4-epimerase, Biochemistry, 39, 5691, 10.1021/bi000215l
Tokuriki, 2009, Protein Dynamism and Evolvability, Science, 324, 203, 10.1126/science.1169375
Van Overtveldt, 2020, Determinants of the Nucleotide Specificity in the Carbohydrate Epimerase Family 1, Biotechnol. J., 15, 1, 10.1002/biot.202000132
Van Overtveldt, 2015, A structural classification of carbohydrate epimerases: From mechanistic insights to practical applications, Biotechnol. Adv., 33, 1814, 10.1016/j.biotechadv.2015.10.010
Verhees, C.H., Kengen, S.W., Tuininga, J.E., Schut, G.J., Adams, M.W., Vos, D., W.m, Oost, V. Der, J, 2003. The unique features of glycolytic pathways. Archaea. Biochem J 375, 231–246. https://doi.org/10.1042/BJ20021472.
Wolucka, 2001, Partial purification and identification of GDP-mannose 3″,5″-epimerase of Arabidopsis thaliana, a key enzyme of the plant vitamin C pathway, Proc. Natl. Acad. Sci. U. S. A., 98, 14843, 10.1073/pnas.011578198
Zhu, 2018, KfoA, the UDP-glucose-4-epimerase of Escherichia coli strain O5:K4:H4, shows preference for acetylated substrates, Appl. Microbiol. Biotechnol., 102, 751, 10.1007/s00253-017-8639-0
