Titterington James A, Ho Ngoc Anh Thu, Beasley Charles P H, Mann Francis, Baker Edward N, Allison Timothy M, Johnston Jodie M
Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury. Christchurch, New Zealand.
School of Biological Sciences, University of Auckland, Auckland, New Zealand.
Acta Crystallogr F Struct Biol Commun. 2025 May 1;81(Pt 5):193-200. doi: 10.1107/S2053230X25002298. Epub 2025 Apr 1.
We report structures of the Mycobacterium tuberculosis isoprenyl diphosphate synthase Rv2173 in three forms: apo and two substrate-bound forms [isoprenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP)]. The protein possesses a canonical all-α-helical trans-isoprenyl diphosphate synthase fold that is dimeric in each form. There are some differences between the structures: the IPP-bound form shows IPP bound in the DMAPP/allylic substrate-binding site with three divalent metal ions bound around the IPP and the complete C-terminus closing around the active site, while the apo and DMAPP-bound forms are more open, with some of the C-terminal region disordered, supporting suggestions that the C-terminus is important in substrate entry/product exit. In the DMAPP form DMAPP occupies the expected allylic substrate site, but only two metal ions are associated with the binding, with the DMAPP diphosphates adopting a slightly different binding pose compared with IPP in the same site, and the third metal-binding site is unoccupied. In no case is the IPP binding site occupied by IPP. There has been some uncertainty regarding product length for Rv2173, with variable lengths being reported. In the structures reported here, the `capping' residue at the bottom of the binding cavity is tryptophan and comparison with other IPP synthases suggests that the structure of Rv2173 is most consistent with a C-C final product size.
我们报道了结核分枝杆菌异戊二烯基二磷酸合酶Rv2173的三种形式的结构：无底物形式以及两种底物结合形式[异戊二烯基二磷酸（IPP）和二甲基烯丙基二磷酸（DMAPP）]。该蛋白质具有典型的全α螺旋反式异戊二烯基二磷酸合酶折叠结构，每种形式均为二聚体。这些结构之间存在一些差异：IPP结合形式显示IPP结合在DMAPP/烯丙基底物结合位点，三个二价金属离子围绕IPP结合，完整的C末端围绕活性位点闭合，而无底物形式和DMAPP结合形式则更为开放，C末端区域的一些部分无序，这支持了C末端在底物进入/产物排出中起重要作用的观点。在DMAPP形式中，DMAPP占据预期的烯丙基底物位点，但只有两个金属离子与结合相关，与同一位点的IPP相比，DMAPP二磷酸采取略有不同的结合姿势，并且第三个金属结合位点未被占据。在任何情况下，IPP结合位点都未被IPP占据。关于Rv2173的产物长度存在一些不确定性，报道的长度各不相同。在此报道的结构中，结合腔底部的“封端”残基是色氨酸，与其他IPP合酶的比较表明，Rv2173的结构与C-C最终产物大小最为一致。
