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Updated: Jun 4, 2026
Modeling Ligands into Maps Derived from Electron Cryomicroscopy
Published on: July 19, 2024
Crystal structure of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE) from Mycobacterium tuberculosis
Shan Shan1, Xuehui Chen, Ting Liu
1Structural Biology Laboratory, Tsinghua University, Beijing, China.
Abstract:
Isoprenoid precursors, which are a large group of natural products and play key roles in many biological pathways, can only be biosynthesized by the 2-C-methyl-d-erythritol 4-phosphate pathway in Mycobacterium tuberculosis. The 4-diphosphocytidyl-2-C-methyl-d-erythritol kinase (IspE), which is an essential enzyme in the isoprenoid precursor biosynthesis pathway, catalyzes ATP-dependent phosphorylation of 4-diphosphocytidyl-2-C-methyl-d-erythritol (CDP-ME) to 4-diphosphocytidyl-2C-methyl-d-erythritol-2-phosphate and plays a crucial role in M. tuberculosis survival. Therefore, IspE is characterized as an attractive and potential target for antimicrobial drug discovery. However, no experimental structure of M. tuberculosis IspE has been reported, which has hindered our understanding of its structural details and mechanism of action. Here, we report the expression and purification of fully active full-length M. tuberculosis IspE and solve the high-resolution crystal structures of IspE alone and in complex with either the substrate CDP-ME or nonhydrolyzable ATP analog or ADP. The structures present a characteristic galactose/homoserine/mevalonate/phosphomevalonate kinase superfamily α/β-fold with a catalytic center located in a cleft between 2 domains and display clear substrate and ATP binding pockets. Our results also indicate distinct differences in ligand binding of M. tuberculosis IspE with other reported IspEs. Combined with the results of mutagenesis and enzymatic studies, our results provide useful information on the structural basis of IspE for future anti-M. tuberculosis drug discovery targeting this kinase.
Insights
Researchers determined the crystal structures of Mycobacterium tuberculosis IspE, an essential enzyme for survival. This provides crucial insights into its mechanism and potential as a target for new tuberculosis drugs.
Area of Science:
- Biochemistry
- Structural Biology
- Drug Discovery
Background:
- Isoprenoid precursors are vital natural products biosynthesized via the 2-C-methyl-d-erythritol 4-phosphate pathway in Mycobacterium tuberculosis.
- The enzyme 4-diphosphocytidyl-2-C-methyl-d-erythritol kinase (IspE) is essential for M. tuberculosis survival, catalyzing a key phosphorylation step in isoprenoid biosynthesis.
Purpose of the Study:
- To elucidate the structural details and mechanism of action of M. tuberculosis IspE.
- To provide a structural basis for the development of novel anti-tuberculosis drugs targeting IspE.
Main Methods:
- Expression and purification of active full-length M. tuberculosis IspE.
- Solving high-resolution crystal structures of IspE alone and in complex with CDP-ME, ATP analog, or ADP.
- Mutagenesis and enzymatic studies.
Main Results:
- The crystal structures reveal a characteristic α/β-fold with a catalytic center in a cleft, displaying distinct substrate and ATP binding pockets.
- Ligand binding in M. tuberculosis IspE shows differences compared to other reported IspEs.
- Mutagenesis and enzymatic data provide functional insights into the catalytic mechanism.
Conclusions:
- The determined structures offer valuable information on the structural basis of M. tuberculosis IspE.
- These findings are crucial for future anti-tuberculosis drug discovery efforts targeting this essential kinase.
