4S3B

IspG in complex with Intermediate II

Summary for 4S3B

• Entry DOI: 10.2210/pdb4s3b/pdb
• Related: 2Y0F 3NOY 4G9P 4S38 4S39 4S3A 4S3C 4S3D 4S3E 4S3F
• Descriptor: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, (3S)-1,3-dihydroxy-4-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-2-methylbut-2-ylium, carbokation intermediate, IRON/SULFUR CLUSTER, ... (4 entities in total)
• Functional Keywords: methylerythritol-phosphate pathway, terpene biosynthesis, iron-sulfur enzymes, reaction mechanisms, drug development, oxidoreductase
• Biological source: Thermus thermophilus HB8
• Total number of polymer chains: 1
• Total formula weight: 44908.76

Authors

Quitterer, F.,Frank, A.,Wang, K.,Rao, G.,O'Dowd, B.,Li, J.,Guerra, F.,Abdel-Azeim, S.,Bacher, A.,Eppinger, J.,Oldfield, E.,Groll, M. (deposition date: 2015-01-26, release date: 2015-04-29, Last modification date: 2023-12-06)

Primary citation

Quitterer, F.,Frank, A.,Wang, K.,Rao, G.,O'Dowd, B.,Li, J.,Guerra, F.,Abdel-Azeim, S.,Bacher, A.,Eppinger, J.,Oldfield, E.,Groll, M.
Atomic-Resolution Structures of Discrete Stages on the Reaction Coordinate of the [Fe4S4] Enzyme IspG (GcpE).
J.Mol.Biol., 427:2220-2228, 2015

PubMed Abstract: IspG is the penultimate enzyme in non-mevalonate biosynthesis of the universal terpene building blocks isopentenyl diphosphate and dimethylallyl diphosphate. Its mechanism of action has been the subject of numerous studies but remained unresolved due to difficulties in identifying distinct reaction intermediates. Using a moderate reducing agent and an epoxide substrate analogue, we were now able to trap and crystallographically characterize various stages in the IspG-catalyzed conversion of 2-C-methyl-D-erythritol-2,4-cyclo-diphosphate into (E)-1-hydroxy-2-methylbut-2-enyl-4-diphosphate. In addition, the enzyme's structure was determined in complex with several inhibitors. These results, combined with recent electron paramagnetic resonance data, allowed us to deduce a detailed and complete IspG catalytic mechanism, which describes all stages from initial ring opening to formation of (E)-1-hydroxy-2-methylbut-2-enyl-4-diphosphate via discrete radical and carbanion intermediates. The data presented in this article provide a guide for the design of selective drugs against many prokaryotic and eukaryotic pathogens to which the non-mevalonate pathway is essential for survival and virulence.

PubMed: 25868383
DOI: 10.1016/j.jmb.2015.04.002

Experimental method

X-RAY DIFFRACTION (1.8 Å)