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Structural studies of ROK fructokinase YdhR from Bacillus subtilis: insights into substrate binding and fructose specificity.

Nocek B, Stein AJ, Jedrzejczak R, Cuff ME, Li H, Volkart L, Joachimiak A
J Mol Biol 406 325-42 (2011)
Related entries: 1xc3, 3ohr

Cited: 20 times
EuropePMC logo PMID: 21185308

Abstract

The main pathway of bacterial sugar phosphorylation utilizes specific phosphoenolpyruvate phosphotransferase system (PTS) enzymes. In addition to the classic PTS system, a PTS-independent secondary system has been described in which nucleotide-dependent sugar kinases are used for monosaccharide phosphorylation. Fructokinase (FK), which phosphorylates d-fructose with ATP as a cofactor, has been shown to be a member of this secondary system. Bioinformatic analysis has shown that FK is a member of the "ROK" (bacterial Repressors, uncharacterized Open reading frames, and sugar Kinases) sequence family. In this study, we report the crystal structures of ROK FK from Bacillus subtilis (YdhR) (a) apo and in the presence of (b) ADP and (c) ADP/d-fructose. All structures show that YdhR is a homodimer with a monomer composed of two similar α/β domains forming a large cleft between domains that bind ADP and D-fructose. Enzymatic activity assays support YdhR function as an ATP-dependent fructose kinase.

Articles - 3lm9 mentioned but not cited (3)

  1. Structural studies of ROK fructokinase YdhR from Bacillus subtilis: insights into substrate binding and fructose specificity. Nocek B, Stein AJ, Jedrzejczak R, Cuff ME, Li H, Volkart L, Joachimiak A. J Mol Biol 406 325-342 (2011)
  2. The basis for non-canonical ROK family function in the N-acetylmannosamine kinase from the pathogen Staphylococcus aureus. Coombes D, Davies JS, Newton-Vesty MC, Horne CR, Setty TG, Subramanian R, Moir JWB, Friemann R, Panjikar S, Griffin MDW, North RA, Dobson RCJ. J Biol Chem 295 3301-3315 (2020)
  3. Large-scale conformational changes and redistribution of surface negative charge upon sugar binding dictate the fidelity of phosphorylation in Vibrio cholerae fructokinase. Paul R, Chatterjee S, Nath S, Sen U. Sci Rep 8 16925 (2018)


Reviews citing this publication (2)

  1. Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation. Bräsen C, Esser D, Rauch B, Siebers B. Microbiol Mol Biol Rev 78 89-175 (2014)
  2. Plant Fructokinases: Evolutionary, Developmental, and Metabolic Aspects in Sink Tissues. Stein O, Granot D. Front Plant Sci 9 339 (2018)

Articles citing this publication (15)

  1. Bioretrosynthetic construction of a didanosine biosynthetic pathway. Birmingham WR, Starbird CA, Panosian TD, Nannemann DP, Iverson TM, Bachmann BO. Nat Chem Biol 10 392-399 (2014)
  2. Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum. Kazanov MD, Li X, Gelfand MS, Osterman AL, Rodionov DA. Nucleic Acids Res 41 790-803 (2013)
  3. Crystal structures of N-acetylmannosamine kinase provide insights into enzyme activity and inhibition. Martinez J, Nguyen LD, Hinderlich S, Zimmer R, Tauberger E, Reutter W, Saenger W, Fan H, Moniot S. J Biol Chem 287 13656-13665 (2012)
  4. Cross Talk among Transporters of the Phosphoenolpyruvate-Dependent Phosphotransferase System in Bacillus subtilis. Morabbi Heravi K, Altenbuchner J. J Bacteriol 200 e00213-18 (2018)
  5. Structure and Function of N-Acetylmannosamine Kinases from Pathogenic Bacteria. Gangi Setty T, Sarkar A, Coombes D, Dobson RCJ, Subramanian R. ACS Omega 5 30923-30936 (2020)
  6. The dimerization domain in DapE enzymes is required for catalysis. Nocek B, Starus A, Makowska-Grzyska M, Gutierrez B, Sanchez S, Jedrzejczak R, Mack JC, Olsen KW, Joachimiak A, Holz RC. PLoS One 9 e93593 (2014)
  7. Crystal structure of N-acetylmannosamine kinase from Fusobacterium nucleatum. Caing-Carlsson R, Goyal P, Sharma A, Ghosh S, Setty TG, North RA, Friemann R, Ramaswamy S. Acta Crystallogr F Struct Biol Commun 73 356-362 (2017)
  8. Sensor Domain of Histidine Kinase VxrA of Vibrio cholerae- A Hairpin-swapped Dimer and its Conformational Change. Tan K, Teschler JK, Wu R, Jedrzejczak RP, Zhou M, Shuvalova LA, Endres MJ, Welk LF, Kwon K, Anderson WF, Satchell KJF, Yildiz FH, Joachimiak A. J Bacteriol 203 JB.00643-20 (2021)
  9. Characterization of DNA Binding Sites of RokB, a ROK-Family Regulator from Streptomyces coelicolor Reveals the RokB Regulon. Bekiesch P, Forchhammer K, Apel AK. PLoS One 11 e0153249 (2016)
  10. Characterization of a thermotolerant ROK-type mannofructokinase from Streptococcus mitis: application to the synthesis of phosphorylated sugars. Vergne-Vaxelaire C, Mariage A, Petit JL, Fossey-Jouenne A, Guérard-Hélaine C, Darii E, Debard A, Nepert S, Pellouin V, Lemaire M, Zaparucha A, Salanoubat M, de Berardinis V. Appl Microbiol Biotechnol 102 5569-5583 (2018)
  11. Molecular and biochemical characterization of Entamoeba histolytica fructokinase. Matt J, Duchêne M. Parasitol Res 114 1939-1947 (2015)
  12. N-acetylmuramic acid recognition by MurK kinase from the MurNAc auxotrophic oral pathogen Tannerella forsythia. Stasiak AC, Gogler K, Borisova M, Fink P, Mayer C, Stehle T, Zocher G. J Biol Chem 299 105076 (2023)
  13. Predicting drug targets by homology modelling of Pseudomonas aeruginosa proteins of unknown function. Babic N, Kovacic F. PLoS One 16 e0258385 (2021)
  14. The ROK kinase N-acetylglucosamine kinase uses a sequential random enzyme mechanism with successive conformational changes upon each substrate binding. Roy S, Vivoli Vega M, Ames JR, Britten N, Kent A, Evans K, Isupov MN, Harmer NJ, GoVV Consortium. J Biol Chem 299 103033 (2023)
  15. Whole genome sequencing and analysis of selenite-reducing bacteria Bacillus paralicheniformis SR14 in response to different sugar supplements. Wang F, Gong T, Du M, Xiao X, Jiang Z, Hu W, Wang Y, Cheng Y. AMB Express 13 93 (2023)


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