The crystal structure of coenzyme B12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol.
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.
Yamanishi
Mamoru
M
Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Okayama, Japan.
Yunoki
Michio
M
Tobimatsu
Takamasa
T
Sato
Hideaki
H
Matsui
Junko
J
Dokiya
Ayako
A
Iuchi
Yasuhiro
Y
Oe
Kazunori
K
Suto
Kyoko
K
Shibata
Naoki
N
Morimoto
Yukio
Y
Yasuoka
Noritake
N
Toraya
Tetsuo
T
D001665:Binding Sites; D003038:Cobamides / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D004926:Escherichia coli; D006836:Hydro-Lyases / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D007700:Kinetics; D008958:Models, Molecular; D011188:Potassium / Q000378:metabolism; D011408:Propanediol Dehydratase / Q000737:chemistry; D019946:Propylene Glycol / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics; D013057:Spectrum Analysis; D013379:Substrate Specificity; D014805:Vitamin B 12 / Q000737:chemistry* / Q000378:metabolism
D003038:Cobamides; D011994:Recombinant Proteins; D019946:Propylene Glycol; D006836:Hydro-Lyases; D011408:Propanediol Dehydratase; C020671:glycerol dehydratase; C000913:cobamamide; D014805:Vitamin B 12; D011188:Potassium