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Crystal structure of Schizosaccharomyces pombe riboflavin kinase reveals a novel ATP and riboflavin-binding fold.

Bauer S, Kemter K, Bacher A, Huber R, Fischer M, Steinbacher S
J Mol Biol 326 1463-73 (2003)
Related entries: 1n05, 1n06, 1n07

Cited: 32 times
EuropePMC logo PMID: 12595258

Abstract

The essential redox cofactors riboflavin monophosphate (FMN) and flavin adenine dinucleotide (FAD) are synthesised from their precursor, riboflavin, in sequential reactions by the metal-dependent riboflavin kinase and FAD synthetase. Here, we describe the 1.6A crystal structure of the Schizosaccharomyces pombe riboflavin kinase. The enzyme represents a novel family of phosphoryl transferring enzymes. It is a monomer comprising a central beta-barrel clasped on one side by two C-terminal helices that display an L-like shape. The opposite side of the beta-barrel serves as a platform for substrate binding as demonstrated by complexes with ADP and FMN. Formation of the ATP-binding site requires significant rearrangements in a short alpha-helix as compared to the substrate free form. The diphosphate moiety of ADP is covered by the glycine-rich flap I formed from parts of this alpha-helix. In contrast, no significant changes are observed upon binding of riboflavin. The ribityl side-chain might be covered by a rather flexible flap II. The unusual metal-binding site involves, in addition to the ADP phosphates, only the strictly conserved Thr45. This may explain the preference for zinc observed in vitro.

Articles - 1n08 mentioned but not cited (5)

  1. Reciprocal carbonyl-carbonyl interactions in small molecules and proteins. Rahim A, Saha P, Jha KK, Sukumar N, Sarma BK. Nat Commun 8 78 (2017)
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Reviews citing this publication (5)

  1. Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers. Abbas CA, Sibirny AA. Microbiol Mol Biol Rev 75 321-360 (2011)
  2. Biosynthesis of flavocoenzymes. Fischer M, Bacher A. Nat Prod Rep 22 324-350 (2005)
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  5. Production of riboflavin and related cofactors by biotechnological processes. Liu S, Hu W, Wang Z, Chen T. Microb Cell Fact 19 31 (2020)

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  1. The biological inorganic chemistry of zinc ions. Krężel A, Maret W. Arch Biochem Biophys 611 3-19 (2016)
  2. A comprehensive update of the sequence and structure classification of kinases. Cheek S, Ginalski K, Zhang H, Grishin NV. BMC Struct Biol 5 6 (2005)
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  4. Over-expression in Escherichia coli and characterization of two recombinant isoforms of human FAD synthetase. Brizio C, Galluccio M, Wait R, Torchetti EM, Bafunno V, Accardi R, Gianazza E, Indiveri C, Barile M. Biochem Biophys Res Commun 344 1008-1016 (2006)
  5. The occurrence of riboflavin kinase and FAD synthetase ensures FAD synthesis in tobacco mitochondria and maintenance of cellular redox status. Giancaspero TA, Locato V, de Pinto MC, De Gara L, Barile M. FEBS J 276 219-231 (2009)
  6. Over-expression in Escherichia coli, purification and characterization of isoform 2 of human FAD synthetase. Galluccio M, Brizio C, Torchetti EM, Ferranti P, Gianazza E, Indiveri C, Barile M. Protein Expr Purif 52 175-181 (2007)
  7. Crystal structure of flavin binding to FAD synthetase of Thermotoga maritima. Wang W, Kim R, Yokota H, Kim SH. Proteins 58 246-248 (2005)
  8. 4SCOPmap: automated assignment of protein structures to evolutionary superfamilies. Cheek S, Qi Y, Krishna SS, Kinch LN, Grishin NV. BMC Bioinformatics 5 197 (2004)
  9. Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism. Steinbacher S, Schiffmann S, Richter G, Huber R, Bacher A, Fischer M. J Biol Chem 278 42256-42265 (2003)
  10. Structural insights into the synthesis of FMN in prokaryotic organisms. Herguedas B, Lans I, Sebastián M, Hermoso JA, Martínez-Júlvez M, Medina M. Acta Crystallogr D Biol Crystallogr 71 2526-2542 (2015)
  11. A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels. Ammelburg M, Hartmann MD, Djuranovic S, Alva V, Koretke KK, Martin J, Sauer G, Truffault V, Zeth K, Lupas AN, Coles M. Structure 15 1577-1590 (2007)
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  13. Key residues at the riboflavin kinase catalytic site of the bifunctional riboflavin kinase/FMN adenylyltransferase from Corynebacterium ammoniagenes. Serrano A, Frago S, Herguedas B, Martínez-Júlvez M, Velázquez-Campoy A, Medina M. Cell Biochem Biophys 65 57-68 (2013)
  14. The puzzle of ligand binding to Corynebacterium ammoniagenes FAD synthetase. Frago S, Velázquez-Campoy A, Medina M. J Biol Chem 284 6610-6619 (2009)
  15. A set of engineered Escherichia coli expression strains for selective isotope and reactivity labeling of amino acid side chains and flavin cofactors. Mehlhorn J, Steinocher H, Beck S, Kennis JT, Hegemann P, Mathes T. PLoS One 8 e79006 (2013)
  16. 13C Isotopologue editing of FMN bound to phototropin domains. Eisenreich W, Joshi M, Illarionov B, Richter G, Römisch-Margl W, Müller F, Bacher A, Fischer M. FEBS J 274 5876-5890 (2007)
  17. The Flavoproteome of the Model Plant Arabidopsis thaliana. Schall P, Marutschke L, Grimm B. Int J Mol Sci 21 E5371 (2020)
  18. Effects of nicotinamide and riboflavin on the biodesulfurization activity of dibenzothiophene by Rhodococcus erythropolis USTB-03. Yan H, Sun X, Xu Q, Ma Z, Xiao C, Jun N. J Environ Sci (China) 20 613-618 (2008)
  19. Screening a fragment cocktail library using ultrafiltration. Shibata S, Zhang Z, Korotkov KV, Delarosa J, Napuli A, Kelley AM, Mueller N, Ross J, Zucker FH, Buckner FS, Merritt EA, Verlinde CL, Van Voorhis WC, Hol WG, Fan E. Anal Bioanal Chem 401 1585-1591 (2011)
  20. Specific Features for the Competent Binding of Substrates at the FMN Adenylyltransferase Site of FAD Synthase from Corynebacterium ammoniagenes. Arilla-Luna S, Serrano A, Medina M. Int J Mol Sci 20 E5083 (2019)
  21. Introducing an Artificial Deazaflavin Cofactor in Escherichia coli and Saccharomyces cerevisiae. Lee M, Drenth J, Trajkovic M, de Jong RM, Fraaije MW. ACS Synth Biol 11 938-952 (2022)
  22. Subcellular Localization of Fad1p in Saccharomyces cerevisiae: A Choice at Post-Transcriptional Level? Bruni F, Giancaspero TA, Oreb M, Tolomeo M, Leone P, Boles E, Roberti M, Caselle M, Barile M. Life (Basel) 11 967 (2021)


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