Structure Determination of Bacillus subtilis RibG in Complex with its Substrates

• Main Authors: Yu-Hsin Lin, 林俞昕
• Other Authors: Shwu-Huey Liaw
• Format: Others
• Language: zh-TW
• Published: 2006
• Online Access: http://ndltd.ncl.edu.tw/handle/75763969110479126443

碩士 === 國立陽明大學 === 醫學生物技術研究所 === 94 === Bacterial RibG contains an N-terminal deaminase domain and a C-terminal reductase domain involved in the second and third steps in the riboflavin biosynthesis, and hence it is an attractive candidate for development of antimicrobial drug. Here we have solved the complex structure of Bacillus subtilis RibG with its substrate, 5-amino-6-ribosylamino-2,4(1H,3H)- pyrimidinedione 5’-phosphate, at 2.56-Å resolution. Analytic ultracentrifugation experiments demonstrated that BsRibG exists as a tetramer in solution as well as in crystal form, where the enzyme forms a tetrameric ring-like structure. The deaminase domain belongs to the cytidine deaminase superfamily. A structure based sequence alignment of a variety of nucleotide deaminases reveals not only the unique signatures in each family member for gene annotation but also putative substrate-interacting residues for RNA-editing deaminases. The strong structural conservation between the reductase domain and the pharmaceutically important dihydrofolate reductase suggests that these two reductases involved in the riboflavin and folate biosyntheses have evolved from a single ancestral gene. The complex structure exhibits that the O-2 atom of the pyrimidine ring interacts with Lys151 Nζ, the NH-3 and O-4 with Thr172 Oγ1, the NH2 with Ser167Oγ and O4 with amide group of Ile170. Asp199 makes close contacts with the C2’-OH and C3’-OH groups of the ribose. Arg183, Arg206 and Leu203 form hydrogen bonds with the phosphate group. These detailed enzyme-substrate interactions may provide useful information for rational drug design.