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Crystal structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism.

Suzuki R, Katayama T, Kim BJ, Wakagi T, Shoun H, Ashida H, Yamamoto K, Fushinobu S
J Biol Chem 285 34279-87 (2010)
Related entries: 3ahc, 3ahd, 3ahe, 3ahf, 3ahg, 3ahh, 3ahi

Cited: 31 times
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Abstract

Thiamine diphosphate (ThDP)-dependent enzymes are ubiquitously present in all organisms and catalyze essential reactions in various metabolic pathways. ThDP-dependent phosphoketolase plays key roles in the central metabolism of heterofermentative bacteria and in the pentose catabolism of various microbes. In particular, bifidobacteria, representatives of beneficial commensal bacteria, have an effective glycolytic pathway called bifid shunt in which 2.5 mol of ATP are produced per glucose. Phosphoketolase catalyzes two steps in the bifid shunt because of its dual-substrate specificity; they are phosphorolytic cleavage of fructose 6-phosphate or xylulose 5-phosphate to produce aldose phosphate, acetyl phosphate, and H(2)O. The phosphoketolase reaction is different from other well studied ThDP-dependent enzymes because it involves a dehydration step. Although phosphoketolase was discovered more than 50 years ago, its three-dimensional structure remains unclear. In this study we report the crystal structures of xylulose 5-phosphate/fructose 6-phosphate phosphoketolase from Bifidobacterium breve. The structures of the two intermediates before and after dehydration (α,β-dihydroxyethyl ThDP and 2-acetyl-ThDP) and complex with inorganic phosphate give an insight into the mechanism of each step of the enzymatic reaction.

Articles - 3ahj mentioned but not cited (2)

  1. SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. Dana JM, Gutmanas A, Tyagi N, Qi G, O'Donovan C, Martin M, Velankar S. Nucleic Acids Res 47 D482-D489 (2019)
  2. Crystal structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism. Suzuki R, Katayama T, Kim BJ, Wakagi T, Shoun H, Ashida H, Yamamoto K, Fushinobu S. J Biol Chem 285 34279-34287 (2010)


Reviews citing this publication (3)

  1. CC bond formation using ThDP-dependent lyases. Müller M, Sprenger GA, Pohl M. Curr Opin Chem Biol 17 261-270 (2013)
  2. Sweet siblings with different faces: the mechanisms of FBP and F6P aldolase, transaldolase, transketolase and phosphoketolase revisited in light of recent structural data. Tittmann K. Bioorg Chem 57 263-280 (2014)
  3. Structure and evolution of the bifidobacterial carbohydrate metabolism proteins and enzymes. Fushinobu S, Abou Hachem M. Biochem Soc Trans 49 563-578 (2021)

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  5. Catabolism of glucose and lactose in Bifidobacterium animalis subsp. lactis, studied by 13C Nuclear Magnetic Resonance. González-Rodríguez I, Gaspar P, Sánchez B, Gueimonde M, Margolles A, Neves AR. Appl Environ Microbiol 79 7628-7638 (2013)
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  8. Unexpected tautomeric equilibria of the carbanion-enamine intermediate in pyruvate oxidase highlight unrecognized chemical versatility of thiamin. Meyer D, Neumann P, Koers E, Sjuts H, Lüdtke S, Sheldrick GM, Ficner R, Tittmann K. Proc Natl Acad Sci U S A 109 10867-10872 (2012)
  9. Bifidobacterial α-galactosidase with unique carbohydrate-binding module specifically acts on blood group B antigen. Wakinaka T, Kiyohara M, Kurihara S, Hirata A, Chaiwangsri T, Ohnuma T, Fukamizo T, Katayama T, Ashida H, Yamamoto K. Glycobiology 23 232-240 (2013)
  10. Complete genome sequence and comparative genomic analysis of Mycobacterium massiliense JCM 15300 in the Mycobacterium abscessus group reveal a conserved genomic island MmGI-1 related to putative lipid metabolism. Sekizuka T, Kai M, Nakanaga K, Nakata N, Kazumi Y, Maeda S, Makino M, Hoshino Y, Kuroda M. PLoS One 9 e114848 (2014)
  11. Establishment of an alternative phosphoketolase-dependent pathway for fructose catabolism in Ralstonia eutropha H16. Fleige C, Kroll J, Steinbüchel A. Appl Microbiol Biotechnol 91 769-776 (2011)
  12. Allosteric regulation of Lactobacillus plantarum xylulose 5-phosphate/fructose 6-phosphate phosphoketolase (Xfp). Glenn K, Smith KS. J Bacteriol 197 1157-1163 (2015)
  13. Biochemical and kinetic characterization of xylulose 5-phosphate/fructose 6-phosphate phosphoketolase 2 (Xfp2) from Cryptococcus neoformans. Glenn K, Ingram-Smith C, Smith KS. Eukaryot Cell 13 657-663 (2014)
  14. The pentose phosphate pathway of cellulolytic clostridia relies on 6-phosphofructokinase instead of transaldolase. Koendjbiharie JG, Hon S, Pabst M, Hooftman R, Stevenson DM, Cui J, Amador-Noguez D, Lynd LR, Olson DG, van Kranenburg R. J Biol Chem 295 1867-1878 (2020)
  15. Characterization of three putative xylulose 5-phosphate/fructose 6-phosphate phosphoketolases in the cyanobacterium Anabaena sp. PCC 7120. Moriyama T, Tajima N, Sekine K, Sato N. Biosci Biotechnol Biochem 79 767-774 (2015)
  16. A Theoretical Study of the Benzoylformate Decarboxylase Reaction Mechanism. Planas F, Sheng X, McLeish MJ, Himo F. Front Chem 6 205 (2018)
  17. Effects of probiotics on loperamide-induced constipation in rats. Inatomi T, Honma M. Sci Rep 11 24098 (2021)
  18. Phosphoketolases from Lactococcus lactis, Leuconostoc mesenteroides and Pseudomonas aeruginosa: dissimilar sequences, similar substrates but distinct enzymatic characteristics. Petrareanu G, Balasu MC, Vacaru AM, Munteanu CV, Ionescu AE, Matei I, Szedlacsek SE. Appl Microbiol Biotechnol 98 7855-7867 (2014)
  19. An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria. Lu KJ, Chang CW, Wang CH, Chen FY, Huang IY, Huang PH, Yang CH, Wu HY, Wu WJ, Hsu KC, Ho MC, Tsai MD, Liao JC. Nat Metab 5 1111-1126 (2023)
  20. Comprehensive analysis of metabolites produced by co-cultivation of Bifidobacterium breve MCC1274 with human iPS-derived intestinal epithelial cells. Sen A, Nishimura T, Yoshimoto S, Yoshida K, Gotoh A, Katoh T, Yoneda Y, Hashimoto T, Xiao JZ, Katayama T, Odamaki T. Front Microbiol 14 1155438 (2023)
  21. Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis. Planas F, McLeish MJ, Himo F. Beilstein J Org Chem 15 145-159 (2019)
  22. Constitutive expression of phosphoketolase, a key enzyme for metabolic shift from homo- to heterolactic fermentation in Enterococcus mundtii QU 25. Nabeta K, Watanabe S, Chibazakura T, Zendo T, Sonomoto K, Shimizu-Kadota M, Yoshikawa H. Biosci Microbiota Food Health 38 111-114 (2019)
  23. Construction of an artificial phosphoketolase pathway that efficiently catabolizes multiple carbon sources to acetyl-CoA. Yang Y, Liu Y, Zhao H, Liu D, Zhang J, Cheng J, Yang Q, Chu H, Lu X, Luo M, Sheng X, Zhang YPJ, Jiang H, Ma Y. PLoS Biol 21 e3002285 (2023)
  24. Gut microbiome diversity, variability, and latent community types compared with shifts in body weight during the freshman year of college in dormitory-housed adolescents. Mohr AE, Ahern MM, Sears DD, Bruening M, Whisner CM. Gut Microbes 15 2250482 (2023)
  25. Production of Lacto-N-biose I Using Crude Extracts of Bifidobacterial Cells. Machida S, Saito K, Nishimoto M, Kitaoka M. J Appl Glycosci (1999) 69 15-21 (2022)
  26. Single-Turnover Kinetics Reveal a Distinct Mode of Thiamine Diphosphate-Dependent Catalysis in Vitamin K Biosynthesis. Qin M, Song H, Dai X, Chan CK, Chan W, Guo Z. Chembiochem 19 1514-1522 (2018)


Related citations provided by authors (1)

  1. Overexpression, crystallization and preliminary X-ray analysis of xylulose-5-phosphate/fructose-6-phosphate phosphoketolase from Bifidobacterium breve.. Suzuki R, Kim BJ, Shibata T, Iwamoto Y, Katayama T, Ashida H, Wakagi T, Shoun H, Fushinobu S, Yamamoto K Acta Crystallogr Sect F Struct Biol Cryst Commun 66 941-3 (2010)

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