2q2v
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Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas putida
OverviewOverview
D-3-Hydroxybutyrate dehydrogenase from Pseudomonas putida belongs to the, family of short-chain dehydrogenases/reductases. We have determined X-ray, structures of the D-3-hydroxybutyrate dehydrogenase from Pseudomonas, putida, which was recombinantly expressed in Escherichia coli, in three, different crystal forms to resolutions between 1.9 and 2.1 A. The, so-called substrate-binding loop (residues 187-210) was partially, disordered in several subunits, in both the presence and absence of, NAD(+). However, in two subunits, this loop was completely defined in an, open conformation in the apoenzyme and in a closed conformation in the, complex structure with NAD(+). Structural comparisons indicated that the, loop moves as a rigid body by about 46 degrees . However, the two small, alpha-helices (alphaFG1 and alphaFG2) of the loop also re-orientated, slightly during the conformational change. Probably, the interactions of, Val185, Thr187 and Leu189 with the cosubstrate induced the conformational, change. A model of the binding mode of the substrate D-3-hydroxybutyrate, indicated that the loop in the closed conformation, as a result of NAD(+), binding, is positioned competent for catalysis. Gln193 is the only residue, of the substrate-binding loop that interacts directly with the substrate., A translation, libration and screw (TLS) analysis of the rigid body, movement of the loop in the crystal showed significant librational, displacements, describing the coordinated movement of the, substrate-binding loop in the crystal. NAD(+) binding increased the, flexibility of the substrate-binding loop and shifted the equilibrium, between the open and closed forms towards the closed form. The finding, that all NAD(+)-bound subunits are present in the closed form and all, NAD(+)-free subunits in the open form indicates that the loop closure is, induced by cosubstrate binding alone. This mechanism may contribute to the, sequential binding of cosubstrate followed by substrate.
About this StructureAbout this Structure
2Q2V is a Single protein structure of sequence from Pseudomonas putida with as ligand. Active as 3-hydroxybutyrate dehydrogenase, with EC number 1.1.1.30 Full crystallographic information is available from OCA.
ReferenceReference
Cosubstrate-induced dynamics of D-3-hydroxybutyrate dehydrogenase from Pseudomonas putida., Paithankar KS, Feller C, Kuettner EB, Keim A, Grunow M, Strater N, FEBS J. 2007 Nov;274(21):5767-5779. PMID:17958702
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