9XWU

Crystal structure of E.coli CDP-diacylglycerol pyrophosphatase (Cdh) complexed with AMP

Summary for 9XWU

• Entry DOI: 10.2210/pdb9xwu/pdb
• Descriptor: CDP-diacylglycerol pyrophosphatase, ADENOSINE MONOPHOSPHATE (3 entities in total)
• Functional Keywords: cdp-diacylglycerol, phosphatidic acid, bitopic membrane protein, cdp-dag hydrolase, bacterial phospholipid metabolism, amp bound structure, inhibitor bound, hydrolase
• Biological source: Escherichia coli K-12
• Total number of polymer chains: 2
• Total formula weight: 59549.88

Authors

Kim, J.,Salsabila, S.D. (deposition date: 2025-11-28, release date: 2026-04-15, Last modification date: 2026-04-22)

Primary citation

Salsabila, S.D.,Bae, S.,Kim, J.
Structural mechanism of membrane-associated cytidine diphosphate diacylglycerol diphosphatase in Escherichia coli.
Int.J.Biol.Macromol., 359:151839-151839, 2026

PubMed Abstract: Cytidine diphosphate diacylglycerol (CDP-DAG) diphosphatase (Cdh) regulates phospholipid biosynthesis by hydrolyzing CDP-DAG into cytidine monophosphate (CMP) and phosphatidic acid (PA), thereby maintaining the steady-state cellular levels of these key metabolic intermediates. Although CDP-DAG serves as a universal branch point in phospholipid metabolism across all three domains of life, Cdh is found predominantly in prokaryotes and, to a lesser extent, in eukaryotes. In Escherichia coli, Cdh is a membrane-associated enzyme belonging to the histidine-triad (HIT)-like hydrolase family and functions independently of metal ions. Here, we report two X-ray crystal structures of E. coli Cdh in complex with a reaction product, CMP, and an inhibitor, AMP, revealing the molecular basis of nucleotide recognition and substrate binding. Integrating structural and biochemical analyses, we identify a pair of conserved histidine residues, His-140 and His-142, as key catalytic determinants. Furthermore, we demonstrate that Cdh adopts a bitopic membrane topology, in which an N-terminal transmembrane helix spans the lipid bilayer and serves as the primary membrane anchor, positioning the catalytic domain at the membrane interface. Together, these findings establish Cdh as a monomeric, membrane-embedded HIT-like hydrolase and provide mechanistic insight into CDP-DAG turnover at the membrane-cytosol interface.

PubMed: 41946407
DOI: 10.1016/j.ijbiomac.2026.151839

Experimental method

X-RAY DIFFRACTION (2.002 Å)