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Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis.

Käck H, Sandmark J, Gibson KJ, Schneider G, Lindqvist Y
Protein Sci 7 2560-6 (1998)
Cited: 12 times
EuropePMC logo PMID: 9865950

Abstract

The crystal structures of two complexes of dethiobiotin synthetase, enzyme-diaminopelargonic acid-MgADP-AlF3 and enzyme-dethiobiotin-MgADP-Pi, respectively, have been determined to 1.8 A resolution. In dethiobiotin synthetase, AlF3 together with carbamylated diaminopelargonic acid mimics the phosphorylated reaction intermediate rather than the transition state complex for phosphoryl transfer. Observed differences in the binding of substrate, diaminopelargonic acid, and the product, dethiobiotin, suggest considerable displacements of substrate atoms during the ring closure step of the catalytic reaction. In both complexes, two metal ions are observed at the active site, providing evidence for a two-metal mechanism for this enzyme.

Reviews - 1bs1 mentioned but not cited (1)

  1. Comprehensive evaluation of mapping complex traits in wheat using genome-wide association studies. Saini DK, Chopra Y, Singh J, Sandhu KS, Kumar A, Bazzer S, Srivastava P. Mol Breed 42 1 (2022)

Articles - 1bs1 mentioned but not cited (3)

  1. Crystal structure of Escherichia coli cytidine triphosphate synthetase, a nucleotide-regulated glutamine amidotransferase/ATP-dependent amidoligase fusion protein and homologue of anticancer and antiparasitic drug targets. Endrizzi JA, Kim H, Anderson PM, Baldwin EP. Biochemistry 43 6447-6463 (2004)
  2. Mechanisms of product feedback regulation and drug resistance in cytidine triphosphate synthetases from the structure of a CTP-inhibited complex. Endrizzi JA, Kim H, Anderson PM, Baldwin EP. Biochemistry 44 13491-13499 (2005)
  3. Autonomous aggregation suppression by acidic residues explains why chaperones favour basic residues. Houben B, Michiels E, Ramakers M, Konstantoulea K, Louros N, Verniers J, van der Kant R, De Vleeschouwer M, Chicória N, Vanpoucke T, Gallardo R, Schymkowitz J, Rousseau F. EMBO J 39 e102864 (2020)


Reviews citing this publication (1)

  1. Structural enzymology of biotin biosynthesis. Schneider G, Lindqvist Y. FEBS Lett 495 7-11 (2001)

Articles citing this publication (7)

  1. Catalysing new reactions during evolution: economy of residues and mechanism. Bartlett GJ, Borkakoti N, Thornton JM. J Mol Biol 331 829-860 (2003)
  2. When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families. Denessiouk KA, Johnson MS. Proteins 38 310-326 (2000)
  3. Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase . Dey S, Lane JM, Lee RE, Rubin EJ, Sacchettini JC. Biochemistry 49 6746-6760 (2010)
  4. The phosphoryl-transfer mechanism of Escherichia coli phosphoenolpyruvate carboxykinase from the use of AlF(3). Sudom AM, Prasad L, Goldie H, Delbaere LT. J Mol Biol 314 83-92 (2001)
  5. Biochemical and structural characterization of the Arabidopsis bifunctional enzyme dethiobiotin synthetase-diaminopelargonic acid aminotransferase: evidence for substrate channeling in biotin synthesis. Cobessi D, Dumas R, Pautre V, Meinguet C, Ferrer JL, Alban C. Plant Cell 24 1608-1625 (2012)
  6. Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members. Porebski PJ, Klimecka M, Chruszcz M, Nicholls RA, Murzyn K, Cuff ME, Xu X, Cymborowski M, Murshudov GN, Savchenko A, Edwards A, Minor W. FEBS J 279 1093-1105 (2012)
  7. A conserved and seemingly redundant Escherichia coli biotin biosynthesis gene expressed only during anaerobic growth. Song X, Cronan JE. Mol Microbiol 116 1315-1327 (2021)


Related citations provided by authors (2)

  1. Snapshot of a Phosphorylated Substrate Intermediate by Kinetic Crystallography. Kaeck H, Gibson KJ, Schneider G, Lindqvist Y Proc. Natl. Acad. Sci. U.S.A. 95 5495- (1998)
  2. Crystal Structure of an ATP-Dependent Carboxylase, Dethiobiotin Synthetase, at 1.65 A Resolution. Huang W, Lindqvist Y, Schneider G, Gibson KJ, Flint D, Lorimer G Structure 2 407- (1994)

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