2DFV

Hyperthermophilic threonine dehydrogenase from Pyrococcus horikoshii

Summary for 2DFV

• Entry DOI: 10.2210/pdb2dfv/pdb
• Descriptor: Probable L-threonine 3-dehydrogenase, ZINC ION, SULFATE ION, ... (5 entities in total)
• Functional Keywords: threonine dehydrogenase, pyrococcus horikoshii, archaea, alchol dehydrogenase, ph0655, oxidoreductase
• Biological source: Pyrococcus horikoshii
• Cellular location: Cytoplasm (By similarity): O58389
• Total number of polymer chains: 3
• Total formula weight: 116401.89

Authors

Ishikawa, K.,Higashi, N.,Nakamura, T.,Matsuura, T.,Nakagawa, A. (deposition date: 2006-03-03, release date: 2007-01-16, Last modification date: 2024-11-20)

Primary citation

Ishikawa, K.,Higashi, N.,Nakamura, T.,Matsuura, T.,Nakagawa, A.
The first crystal structure of L-threonine dehydrogenase.
J.Mol.Biol., 366:857-867, 2007

PubMed 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.

PubMed: 17188300
DOI: 10.1016/j.jmb.2006.11.060

Experimental method

X-RAY DIFFRACTION (2.05 Å)