5DDV

Crystal structure of IspD from Bacillus subtilis at 2.30 Angstroms resolution, crystal form II

Summary for 5DDV

• Entry DOI: 10.2210/pdb5ddv/pdb
• Related: 5DDT
• Descriptor: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (2 entities in total)
• Functional Keywords: transferase
• Biological source: Bacillus subtilis (strain 168)
• Total number of polymer chains: 1
• Total formula weight: 25879.46

Authors

Jin, Y.,Liu, Z.C.,Wang, G.G. (deposition date: 2015-08-25, release date: 2016-08-31, Last modification date: 2023-11-08)

Primary citation

Jin, Y.,Liu, Z.,Li, Y.,Liu, W.,Tao, Y.,Wang, G.
A structural and functional study on the 2-C-methyl-d-erythritol-4-phosphate cytidyltransferase (IspD) from Bacillus subtilis.
Sci Rep, 6:36379-36379, 2016

PubMed Abstract: 2-C-Methyl-D-erythritol-4-phosphate cytidyltransferase (IspD) is an essential enzyme in the mevalonate-independent pathway of isoprenoid biosynthesis. This enzyme catalyzes 2-C-Methyl-d-erythritol 4-phosphate (MEP) and cytosine triphosphate (CTP) to 4-diphosphocytidyl-2-C-methyl-d-erythritol (CDPME) and inorganic pyrophosphate (PPi). Bacillus subtilis was a kind of excellent isoprene producer. However, the studies on the key enzymes of MEP pathway in B. subtilis were still absent. In this work, the crystal structures of IspD and IspD complexed with CTP from B.subtilis were determined. For the first time, the intact P-loop was observed in the apo structure of IspD enzyme. Structural comparisons revealed that the concerted movements of the P-loop and loops close to the active site were essential in the reaction catalyzed by IspD. Meanwhile, kinetic analysis showed that the CTP hydrolytic activity of IspD from B.subtilis was over two times higher than that from Escherichia coli. These results will be useful for future target-based screening of potential inhibitors and the metabolic engineering for isoprenoid biosynthesis.

PubMed: 27821871
DOI: 10.1038/srep36379

Experimental method

X-RAY DIFFRACTION (2.3 Å)