Chen Sheng Chia, Shen Chieh Yi, Yen Te Ming, Yu Hui Chia, Chang Ting Hao, Lai Wen Lin, Liaw Shwu Huey
Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan.
Acta Crystallogr D Biol Crystallogr. 2013 Feb;69(Pt 2):227-36. doi: 10.1107/S0907444912044903. Epub 2013 Jan 19.
Eubacterial RibG and yeast Rib2 possess a deaminase domain for pyrimidine deamination in the second and third steps, respectively, of riboflavin biosynthesis. These enzymes are specific for ribose and ribitol, respectively. Here, the crystal structure of Bacillus subtilis RibG in complex with a deaminase product is reported at 2.56 Å resolution. Two loops move towards the product on substrate binding, resulting in interactions with the ribosyl and phosphate groups and significant conformational changes. The product carbonyl moiety is bent out of the pyrimidine ring to coordinate to the catalytic zinc ion. Such distortions in the bound substrate and product may play an essential role in enzyme catalysis. The yeast Rib2 structure was modelled and a mutational analysis was carried out in order to understand the mechanism of substrate recognition in these two enzymes. Detailed structural comparisons revealed that the two consecutive carbonyl backbones that occur prior to the PCXXC signature constitute a binding hole for the target amino group of the substrate. This amino-binding hole is essential in B. subtilis RibG and is also conserved in the RNA/DNA-editing deaminases.
真细菌的RibG和酵母的Rib2分别在核黄素生物合成的第二步和第三步中具有用于嘧啶脱氨的脱氨酶结构域。这些酶分别对核糖和核醇具有特异性。在此，报道了枯草芽孢杆菌RibG与脱氨酶产物复合物的晶体结构，分辨率为2.56 Å。两个环在底物结合时向产物移动，导致与核糖基和磷酸基团相互作用并发生显著的构象变化。产物羰基部分从嘧啶环中弯曲出来以与催化锌离子配位。结合的底物和产物中的这种扭曲可能在酶催化中起重要作用。对酵母Rib2结构进行了建模并进行了突变分析，以了解这两种酶中底物识别的机制。详细的结构比较表明，在PCXXC特征之前出现的两个连续羰基主链构成了底物目标氨基的结合孔。这个氨基结合孔在枯草芽孢杆菌RibG中是必不可少的，并且在RNA/DNA编辑脱氨酶中也保守。
