5JO9

Structural characterization of the thermostable Bradyrhizobium japonicum d-sorbitol dehydrogenase

Summary for 5JO9

• Entry DOI: 10.2210/pdb5jo9/pdb
• Descriptor: Ribitol 2-dehydrogenase, PHOSPHATE ION, sorbitol (3 entities in total)
• Functional Keywords: glucitol dehydrogenase, oxidoreductase
• Biological source: Bradyrhizobium japonicum
• Total number of polymer chains: 1
• Total formula weight: 26395.50

Authors

Fredslund, F.,Otten, H.,Navarro Poulsen, J.-C.,Lo Leggio, L. (deposition date: 2016-05-02, release date: 2016-11-09, Last modification date: 2024-01-10)

Primary citation

Fredslund, F.,Otten, H.,Gemperlein, S.,Poulsen, J.C.,Carius, Y.,Kohring, G.W.,Lo Leggio, L.
Structural characterization of the thermostable Bradyrhizobium japonicumD-sorbitol dehydrogenase.
Acta Crystallogr F Struct Biol Commun, 72:846-852, 2016

PubMed Abstract: Bradyrhizobium japonicum sorbitol dehydrogenase is NADH-dependent and is active at elevated temperatures. The best substrate is D-glucitol (a synonym for D-sorbitol), although L-glucitol is also accepted, giving it particular potential in industrial applications. Crystallization led to a hexagonal crystal form, with crystals diffracting to 2.9 Å resolution. In attempts to phase the data, a molecular-replacement solution based upon PDB entry 4nbu (33% identical in sequence to the target) was found. The solution contained one molecule in the asymmetric unit, but a tetramer similar to that found in other short-chain dehydrogenases, including the search model, could be reconstructed by applying crystallographic symmetry operations. The active site contains electron density consistent with D-glucitol and phosphate, but there was not clear evidence for the binding of NADH. In a search for the features that determine the thermostability of the enzyme, the T for the orthologue from Rhodobacter sphaeroides, for which the structure was already known, was also determined, and this enzyme proved to be considerably less thermostable. A continuous β-sheet is formed between two monomers in the tetramer of the B. japonicum enzyme, a feature not generally shared by short-chain dehydrogenases, and which may contribute to thermostability, as may an increased Pro/Gly ratio.

PubMed: 27827356
DOI: 10.1107/S2053230X16016927

Experimental method

X-RAY DIFFRACTION (2.894 Å)