Structure of 2C-methyl-D-erythritol 2,4- cyclodiphosphate synthase: an essential enzyme for isoprenoid biosynthesis and target for antimicrobial drug development

Proc Natl Acad Sci U S A. 2002 May 14;99(10):6591-6. doi: 10.1073/pnas.102679799. Epub 2002 May 7.


The crystal structure of the zinc enzyme Escherichia coli 2C-methyl-d-erythritol 2,4-cyclodiphosphate synthase in complex with cytidine 5'-diphosphate and Mn(2+) has been determined to 1.8-A resolution. This enzyme is essential in E. coli and participates in the nonmevalonate pathway of isoprenoid biosynthesis, a critical pathway present in some bacterial and apicomplexans but distinct from that used by mammals. Our analysis reveals a homotrimer, built around a beta prism, carrying three active sites, each of which is formed in a cleft between pairs of subunits. Residues from two subunits recognize and bind the nucleotide in an active site that contains a Zn(2+) with tetrahedral coordination. A Mn(2+), with octahedral geometry, is positioned between the alpha and beta phosphates acting in concert with the Zn(2+) to align and polarize the substrate for catalysis. A high degree of sequence conservation for the enzymes from E. coli, Plasmodium falciparum, and Mycobacterium tuberculosis suggests similarities in secondary structure, subunit fold, quaternary structure, and active sites. Our model will therefore serve as a template to facilitate the structure-based design of potential antimicrobial agents targeting two of the most serious human diseases, tuberculosis and malaria.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Anti-Bacterial Agents*
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Computer Simulation
  • Crystallography, X-Ray
  • Drug Design
  • Erythritol / analogs & derivatives*
  • Erythritol / chemistry
  • Escherichia coli / enzymology*
  • Escherichia coli / genetics
  • Escherichia coli Proteins*
  • Manganese / chemistry
  • Models, Molecular
  • Molecular Sequence Data
  • Phosphorus-Oxygen Lyases*
  • Protein Structure, Tertiary
  • Sequence Homology, Amino Acid
  • Sugar Phosphates / chemistry
  • Terpenes / metabolism*
  • Zinc / chemistry


  • 4-diphosphocytidyl-2C methylerythritol 2-phosphate
  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Escherichia coli Proteins
  • Sugar Phosphates
  • Terpenes
  • Manganese
  • Phosphorus-Oxygen Lyases
  • ISPF protein, E coli
  • Zinc
  • Erythritol

Associated data

  • PDB/1GX1