Simanshu Dhirendra K, Satheshkumar P S, Savithri H S, Murthy M R N
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
Biochem Biophys Res Commun. 2003 Nov 7;311(1):193-201. doi: 10.1016/j.bbrc.2003.09.193.
Propionate metabolism in Salmonella typhimurium occurs via 2-methylcitric acid cycle. The last step of this cycle, the cleavage of 2-methylisocitrate to succinate and pyruvate, is catalysed by 2-methylisocitrate lyase (PrpB). Here we report the X-ray crystal structure of the native and the pyruvate/Mg(2+) bound PrpB from S. typhimurium, determined at 2.1 and 2.3A, respectively. The structure closely resembles that of the Escherichia coli enzyme. Unlike the E. coli PrpB, Mg(2+) could not be located in the native Salmonella PrpB. Only in pyruvate bound PrpB structure, Mg(2+) was found coordinated with pyruvate. Binding of pyruvate to PrpB seems to induce movement of the Mg(2+) by 2.5A from its position found in E. coli native PrpB. In both the native enzyme and pyruvate/Mg(2+) bound forms, the active site loop is completely disordered. Examination of the pocket in which pyruvate and glyoxalate bind to 2-methylisocitrate lyase and isocitrate lyase, respectively, reveals plausible rationale for different substrate specificities of these two enzymes. Structural similarities in substrate and metal atom binding site as well as presence of similar residues in the active site suggest possible similarities in the reaction mechanism.
鼠伤寒沙门氏菌中的丙酸代谢通过2-甲基柠檬酸循环进行。该循环的最后一步，即2-甲基异柠檬酸裂解为琥珀酸和丙酮酸，由2-甲基异柠檬酸裂解酶（PrpB）催化。在此，我们报告了鼠伤寒沙门氏菌天然型以及结合丙酮酸/Mg(2+)的PrpB的X射线晶体结构，分辨率分别为2.1 Å和2.3 Å。该结构与大肠杆菌的酶非常相似。与大肠杆菌的PrpB不同，在鼠伤寒沙门氏菌的天然型PrpB中无法定位Mg(2+)。仅在结合丙酮酸的PrpB结构中，发现Mg(2+)与丙酮酸配位。丙酮酸与PrpB的结合似乎使Mg(2+)从其在大肠杆菌天然型PrpB中的位置移动了2.5 Å。在天然酶和结合丙酮酸/Mg(2+)的形式中，活性位点环均完全无序。对丙酮酸和乙醛酸分别结合2-甲基异柠檬酸裂解酶和异柠檬酸裂解酶的口袋进行研究，揭示了这两种酶不同底物特异性的合理原因。底物和金属原子结合位点的结构相似性以及活性位点中相似残基的存在表明反应机制可能存在相似性。
