1GX1

Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase

Summary for 1GX1

• Entry DOI: 10.2210/pdb1gx1/pdb
• Related: 1JY8
• Descriptor: 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE, ZINC ION, CYTIDINE-5'-DIPHOSPHATE, ... (6 entities in total)
• Functional Keywords: synthase, isoprenoid, lyase, isoprene biosynthesis
• Biological source: ESCHERICHIA COLI
• Total number of polymer chains: 3
• Total formula weight: 53378.32

Authors

Kemp, L.E.,Bond, C.S.,Hunter, W.N. (deposition date: 2002-03-26, release date: 2002-04-03, Last modification date: 2018-02-28)

Primary citation

Kemp, L.E.,Bond, C.S.,Hunter, W.N.
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.USA, 99:6591-, 2002

PubMed Abstract: 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.

PubMed: 11997478
DOI: 10.1073/PNAS.102679799

Experimental method

X-RAY DIFFRACTION (1.8 Å)