嗜酸氧化亚铁硫杆菌的核糖-5-磷酸异构酶的同源建模研究

Homology Modeling of RpiA from Acidithiobacillus ferrooxidans

采用同源建模技术和分子动力学模拟方法,构建了嗜酸氧化亚铁硫杆菌Acidithiobacillus ferrooxidans(A.f)的核糖-5-磷酸异构酶(rpiA)基因编码的蛋白质三维分子结构模型。将结构模型进行绑定位点搜索并与底物核糖-5-磷酸(R5P)进行柔性分子对接,结果显示,R5P被招募到A.ferrooxidans的RpiA的活性位点并随后被激活;残基Asp81,Thr31,Lys121,Ser30,Glu103,Asp84,Lys94,Asp118,Lys7,Gly97,Gly29,Gly95,Thr28和H2O对底物绑定或催化起重要作用,其中,Gly97,Gly29,Gly95和Thr28是新识别的残基,它们在其他生物体的RpiA中相当保守但未被发现。

A three-dimensional protein molecular structure,which was encoded by the gene Ribose-5-phosphate isomerase A（RpiA） from Acidithiobacillus ferrooxidans,was constructed by the homology-modeling technique and molecular-dynamics simulation.The obtained structure was applied to search binding sites and carry out flexible docking with the substrate ribose-5-phosphate（R5P）.The results showed that the substrate R5P can be effectively recruited into the active pocket and be activated immediately;the residues of Asp81,Thr31,Lys121,Ser30,Glu103,Asp84,Lys94,Asp118,Lys7,Gly97,Gly29,Gly95,Thr28 and H2O play a critical role in the binding or catalysis of R5P.Among the above residues,Gly97,Gly29,Gly95,Thr28 are fitly conserved in RpiA from all kinds of sources but have not been detected before.