1IWP

Glycerol Dehydratase-cyanocobalamin Complex of Klebsiella pneumoniae

Summary for 1IWP

• Entry DOI: 10.2210/pdb1iwp/pdb
• Related: 1dio 1eex 1egm
• Descriptor: Glycerol Dehydratase Alpha subunit, Glycerol Dehydratase Beta subunit, Glycerol Dehydratase Gamma subunit, ... (7 entities in total)
• Functional Keywords: b12, glycerol dehydratase, klebsiella pneumoniae, cobalamin, radical catalysis, lyase
• Biological source: Klebsiella pneumoniae; More
• Total number of polymer chains: 6
• Total formula weight: 199347.91

Authors

Yamanishi, M.,Yunoki, M.,Tobimatsu, T.,Toraya, T. (deposition date: 2002-05-28, release date: 2002-10-02, Last modification date: 2023-10-25)

Primary citation

Yamanishi, M.,Yunoki, M.,Tobimatsu, T.,Sato, H.,Matsui, J.,Dokiya, A.,Iuchi, Y.,Oe, K.,Suto, K.,Shibata, N.,Morimoto, Y.,Yasuoka, N.,Toraya, T.
The crystal structure of coenzyme B12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol.
Eur.J.Biochem., 269:4484-4494, 2002

PubMed Abstract: Recombinant glycerol dehydratase of Klebsiella pneumoniae was purified to homogeneity. The subunit composition of the enzyme was most probably alpha 2 beta 2 gamma 2. When (R)- and (S)-propane-1,2-diols were used independently as substrates, the rate with the (R)-enantiomer was 2.5 times faster than that with the (S)-isomer. In contrast to diol dehydratase, an isofunctional enzyme, the affinity of the enzyme for the (S)-isomer was essentially the same or only slightly higher than that for the (R)-isomer (Km(R)/Km(S) = 1.5). The crystal structure of glycerol dehydratase in complex with cyanocobalamin and propane-1,2-diol was determined at 2.1 A resolution. The enzyme exists as a dimer of the alpha beta gamma heterotrimer. Cobalamin is bound at the interface between the alpha and beta subunits in the so-called 'base-on' mode with 5,6-dimethylbenzimidazole of the nucleotide moiety coordinating to the cobalt atom. The electron density of the cyano group was almost unobservable, suggesting that the cyanocobalamin was reduced to cob(II)alamin by X-ray irradiation. The active site is in a (beta/alpha)8 barrel that was formed by a central region of the alpha subunit. The substrate propane-1,2-diol and essential cofactor K+ are bound inside the (beta/alpha)8 barrel above the corrin ring of cobalamin. K+ is hepta-coordinated by the two hydroxyls of the substrate and five oxygen atoms from the active-site residues. These structural features are quite similar to those of diol dehydratase. A closer contact between the alpha and beta subunits in glycerol dehydratase may be reminiscent of the higher affinity of the enzyme for adenosylcobalamin than that of diol dehydratase. Although racemic propane-1,2-diol was used for crystallization, the substrate bound to glycerol dehydratase was assigned to the (R)-isomer. This is in clear contrast to diol dehydratase and accounts for the difference between the two enzymes in the susceptibility of suicide inactivation by glycerol.

PubMed: 12230560
DOI: 10.1046/j.1432-1033.2002.03151.x

Experimental method

X-RAY DIFFRACTION (2.1 Å)