Sugimoto Keisuke, Senda Miki, Kasai Daisuke, Fukuda Masao, Masai Eiji, Senda Toshiya
Department of Materials Chemistry, Asahikawa National College of Technology, Asahikawa, Hokkaido, Japan.
Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan.
PLoS One. 2014 Mar 21;9(3):e92249. doi: 10.1371/journal.pone.0092249. eCollection 2014.
DesB, which is derived from Sphingobium sp. SYK-6, is a type II extradiol dioxygenase that catalyzes a ring opening reaction of gallate. While typical extradiol dioxygenases show broad substrate specificity, DesB has strict substrate specificity for gallate. The substrate specificity of DesB seems to be required for the efficient growth of S. sp. SYK-6 using lignin-derived aromatic compounds. Since direct coordination of hydroxyl groups of the substrate to the non-heme iron in the active site is a critical step for the catalytic reaction of the extradiol dioxygenases, the mechanism of the substrate recognition and coordination of DesB was analyzed by biochemical and crystallographic methods. Our study demonstrated that the direct coordination between the non-heme iron and hydroxyl groups of the substrate requires a large shift of the Fe (II) ion in the active site. Mutational analysis revealed that His124 and His192 in the active site are essential to the catalytic reaction of DesB. His124, which interacts with OH (4) of the bound gallate, seems to contribute to proper positioning of the substrate in the active site. His192, which is located close to OH (3) of the gallate, is likely to serve as the catalytic base. Glu377' interacts with OH (5) of the gallate and seems to play a critical role in the substrate specificity. Our biochemical and structural study showed the substrate recognition and catalytic mechanisms of DesB.
DesB源自鞘氨醇单胞菌属（Sphingobium sp.）SYK-6，是一种II型间苯二酚双加氧酶，可催化没食子酸盐的开环反应。虽然典型的间苯二酚双加氧酶具有广泛的底物特异性，但DesB对没食子酸盐具有严格的底物特异性。DesB的底物特异性似乎是鞘氨醇单胞菌属SYK-6利用木质素衍生的芳香族化合物高效生长所必需的。由于底物羟基与活性位点中非血红素铁的直接配位是间苯二酚双加氧酶催化反应的关键步骤，因此通过生化和晶体学方法分析了DesB的底物识别和配位机制。我们的研究表明，非血红素铁与底物羟基之间的直接配位需要活性位点中Fe（II）离子的大幅移动。突变分析表明，活性位点中的His124和His192对DesB的催化反应至关重要。与结合的没食子酸盐的OH（4）相互作用的His124似乎有助于底物在活性位点中的正确定位。靠近没食子酸盐OH（3）的His192可能作为催化碱。Glu377'与没食子酸盐的OH（5）相互作用，似乎在底物特异性中起关键作用。我们的生化和结构研究揭示了DesB的底物识别和催化机制。
