Crystal structures of nonoxidative zinc-dependent 2,6-dihydroxybenzoate (gamma-resorcylate) decarboxylase from Rhizobium sp. strain MTP-10005.
Reversible 2,6-dihydroxybenzoate decarboxylase from Rhizobium sp. strain MTP-10005 belongs to a nonoxidative decarboxylase family. We have determined the structures of the following three forms of the enzyme: the native form, the complex with the true substrate (2,6-dihydroxybenzoate), and the complex with 2,3-dihydroxybenzaldehyde at 1.7-, 1.9-, and 1.7-A resolution, respectively. The enzyme exists as a tetramer, and the subunit consists of one (alphabeta)8 triose-phosphate isomerase-barrel domain with three functional linkers and one C-terminal tail. The native enzyme possesses one Zn2+ ion liganded by Glu8, His10, His164, Asp287, and a water molecule at the active site center, although the enzyme has been reported to require no cofactor for its catalysis. The substrate carboxylate takes the place of the water molecule and is coordinated to the Zn2+ ion. The 2-hydroxy group of the substrate is hydrogen-bonded to Asp287, which forms a triad together with His218 and Glu221 and is assumed to be the catalytic base. On the basis of the geometrical consideration, substrate specificity is uncovered, and the catalytic mechanism is proposed for the novel Zn2+-dependent decarboxylation.
Goto
Masaru
M
Department of Biochemistry, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan.
Hayashi
Hideyuki
H
Miyahara
Ikuko
I
Hirotsu
Ken
K
Yoshida
Masahiro
M
Oikawa
Tadao
T
D001547:Benzaldehydes / Q000378:metabolism; D001665:Binding Sites; D002262:Carboxy-Lyases / Q000737:chemistry* / Q000378:metabolism; D002396:Catechols / Q000378:metabolism; D003460:Crystallization; D018360:Crystallography, X-Ray; D062385:Hydroxybenzoates / Q000378:metabolism; D008958:Models, Molecular; D010084:Oxidation-Reduction; D011487:Protein Conformation; D012231:Rhizobium / Q000201:enzymology*; D013379:Substrate Specificity; D015032:Zinc / Q000378:metabolism*
D001547:Benzaldehydes; D002396:Catechols; D062385:Hydroxybenzoates; C067077:2,3-dihydroxybenzaldehyde; C488807:2,6-dihydroxybenzoate decarboxylase; D002262:Carboxy-Lyases; D015032:Zinc; C412605:gamma-resorcylic acid