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The first crystal structure of L-threonine dehydrogenase.

Ishikawa K, Higashi N, Nakamura T, Matsuura T, Nakagawa A
J Mol Biol 366 857-67 (2007)
Cited: 22 times
EuropePMC logo PMID: 17188300

Abstract

L-threonine dehydrogenase (TDH) is an enzyme that catalyzes the oxidation of L-threonine to 2-amino-3-ketobutyrate. We solved the first crystal structure of a medium chain L-threonine dehydrogenase from a hyperthermophilic archaeon, Pyrococcus horikoshii (PhTDH), by the single wavelength anomalous diffraction method using a selenomethionine-substituted enzyme. This recombinant PhTDH is a homo-tetramer in solution. Three monomers of PhTDHs were located in the crystallographic asymmetric unit, however, the crystal structure exhibits a homo-tetramer structure with crystallographic and non-crystallographic 222 symmetry in the cell. Despite the low level of sequence identity to a medium-chain NAD(H)-dependent alcohol dehydrogenase (ADH) and the different substrate specificity, the overall folds of the PhTDH monomer and tetramer are similar to those of the other ADH. Each subunit is composed of two domains: a nicotinamide cofactor (NAD(H))-binding domain and a catalytic domain. The NAD(H)-binding domain contains the alpha/beta Rossmann fold motif, characteristic of the NAD(H)-binding protein. One molecule of PhTDH contains one zinc ion playing a structural role. This metal ion exhibits coordination with four cysteine ligands and some of the ligands are conserved throughout the structural zinc-containing ADHs and TDHs. However, the catalytic zinc ion that is coordinated at the bottom of the cleft in the case of ADH was not observed in the crystal of PhTDH. There is a significant difference in the orientation of the catalytic domain relative to the coenzyme-binding domain that results in a larger interdomain cleft.

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  2. Targeted killing of a mammalian cell based upon its specialized metabolic state. Alexander PB, Wang J, McKnight SL. Proc. Natl. Acad. Sci. U.S.A. 108 15828-15833 (2011)
  3. Characterization of a zinc-containing alcohol dehydrogenase with stereoselectivity from the hyperthermophilic archaeon Thermococcus guaymasensis. Ying X, Ma K. J. Bacteriol. 193 3009-3019 (2011)
  4. Structure and function of the l-threonine dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis. Bowyer A, Mikolajek H, Stuart JW, Wood SP, Jamil F, Rashid N, Akhtar M, Cooper JB. J. Struct. Biol. 168 294-304 (2009)
  5. Highly thermostable L-threonine dehydrogenase from the hyperthermophilic archaeon Thermococcus kodakaraensis. Bashir Q, Rashid N, Jamil F, Imanaka T, Akhtar M. J. Biochem. 146 95-102 (2009)
  6. Crystal structure of UDP-galactose 4-epimerase-like L-threonine dehydrogenase belonging to the intermediate short-chain dehydrogenase-reductase superfamily. Yoneda K, Sakuraba H, Muraoka I, Oikawa T, Ohshima T. FEBS J. 277 5124-5132 (2010)
  7. Crystal structure and biochemical properties of the D-arabinose dehydrogenase from Sulfolobus solfataricus. Brouns SJ, Turnbull AP, Willemen HL, Akerboom J, van der Oost J. J. Mol. Biol. 371 1249-1260 (2007)
  8. Investigating a catalytic mechanism of hyperthermophilic L-threonine dehydrogenase from Pyrococcus horikoshii. Higashi N, Tanimoto K, Nishioka M, Ishikawa K, Taya M. J. Biochem. 144 77-85 (2008)
  9. Chirality measures for vectors, matrices, operators and functions. Dryzun C, Avnir D. Chemphyschem 12 197-205 (2011)
  10. Crystal structure of binary and ternary complexes of archaeal UDP-galactose 4-epimerase-like L-threonine dehydrogenase from Thermoplasma volcanium. Yoneda K, Sakuraba H, Araki T, Ohshima T. J. Biol. Chem. 287 12966-12974 (2012)
  11. Binding of NAD+ and L-threonine induces stepwise structural and flexibility changes in Cupriavidus necator L-threonine dehydrogenase. Nakano S, Okazaki S, Tokiwa H, Asano Y. J. Biol. Chem. 289 10445-10454 (2014)
  12. Enantioselective oxidation of galactitol 1-phosphate by galactitol-1-phosphate 5-dehydrogenase from Escherichia coli. Benavente R, Esteban-Torres M, Kohring GW, Cortés-Cabrera Á, Sánchez-Murcia PA, Gago F, Acebrón I, de las Rivas B, Muñoz R, Mancheño JM. Acta Crystallogr. D Biol. Crystallogr. 71 1540-1554 (2015)
  13. Crystallization and preliminary X-ray diffraction analysis of L-threonine dehydrogenase (TDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis. Bowyer A, Mikolajek H, Wright JN, Coker A, Erskine PT, Cooper JB, Bashir Q, Rashid N, Jamil F, Akhtar M. Acta Crystallogr Sect F Struct Biol Cryst Commun 64 828-830 (2008)
  14. Structural insights on mouse L-threonine dehydrogenase: A regulatory role of Arg180 in catalysis. He C, Huang X, Liu Y, Li F, Yang Y, Tao H, Han C, Zhao C, Xiao Y, Shi Y. J. Struct. Biol. 192 510-518 (2015)
  15. Crystal structure of thermostable acetaldehyde dehydrogenase from the hyperthermophilic archaeon Sulfolobus tokodaii. Mine S, Nakabayashi M, Ishikawa K. Acta Crystallogr F Struct Biol Commun 79 159-165 (2023)
  16. Molecular evolutionary insight of structural zinc atom in yeast xylitol dehydrogenases and its application in bioethanol production by lignocellulosic biomass. Yoshiwara K, Watanabe S, Watanabe Y. Sci Rep 13 1920 (2023)
  17. Structure and function of L-threonine-3-dehydrogenase from the parasitic protozoan Trypanosoma brucei revealed by X-ray crystallography and geometric simulations. Adjogatse E, Erskine P, Wells SA, Kelly JM, Wilden JD, Chan AWE, Selwood D, Coker A, Wood S, Cooper JB. Acta Crystallogr D Struct Biol 74 861-876 (2018)
  18. The X-ray structure of L-threonine dehydrogenase from the common hospital pathogen Clostridium difficile. Adjogatse E, Bennett J, Guo J, Erskine PT, Wood SP, Wren BW, Cooper JB. Acta Crystallogr F Struct Biol Commun 77 269-274 (2021)


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