8F8K

The structure of Rv2173 from M. tuberculosis with IPP bound

8F8K の概要

• エントリーDOI: 10.2210/pdb8f8k/pdb
• 分子名称: (2E,6E)-farnesyl diphosphate synthase, GLYCEROL, ACETATE ION, ... (7 entities in total)
• 機能のキーワード: rv2173, m. tuberculosis, isoprenyl diphosphate synthase, ipp (isopentenyl diphosphate) bound, transferase
• 由来する生物種: Mycobacterium tuberculosis
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 42803.76

構造登録者

Johnston, J.M.,Allison, T.M.,Titterington, J.,Beasley, C.P.H. (登録日: 2022-11-22, 公開日: 2023-11-29, 最終更新日: 2025-05-07)

主引用文献

Titterington, J.A.,Ho, N.A.T.,Beasley, C.P.H.,Mann, F.,Baker, E.N.,Allison, T.M.,Johnston, J.M.
Structures of Mycobacterium tuberculosis isoprenyl diphosphate synthase Rv2173 in substrate-bound forms.
Acta Crystallogr.,Sect.F, 81:193-200, 2025

PubMed Abstract: 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.

PubMed: 40166974
DOI: 10.1107/S2053230X25002298

実験手法

X-RAY DIFFRACTION (2.2 Å)