Biosynthesis of Isoprenoids: Crystal Structure of the [4Fe–4S] Cluster Protein IspG

• Published in: Journal of molecular biology Vol. 404; no. 4; pp. 600 - 610
• Main Authors: Lee, Matthias, Gräwert, Tobias, Quitterer, Felix, Rohdich, Felix, Eppinger, Jörg, Eisenreich, Wolfgang, Bacher, Adelbert, Groll, Michael
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 10.12.2010
• Subjects: Bacteria - enzymology; Bacteria - metabolism; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Crystallography, X-Ray; GcpE protein; Hemiterpenes - metabolism; iron–sulfur protein; methylerythritol phosphate pathway; Models, Molecular; non-mevalonate pathway; Organophosphorus Compounds - metabolism; Protein Multimerization; Protein Structure, Quaternary; Protein Subunits - chemistry; terpene biosynthesis; Terpenes - metabolism; N domain; RCSB; C domain; IPP; iron–sulfur protein; non-mevalonate pathway; MAD; GcpE protein; methylerythritol phosphate pathway; terpene biosynthesis; DMAPP; SLS; NCS
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2010.09.050

IspG protein serves as the penultimate enzyme of the recently discovered non-mevalonate pathway for the biosynthesis of the universal isoprenoid precursors, isopentenyl diphosphate and dimethylallyl diphosphate. The enzyme catalyzes the reductive ring opening of 2 C-methyl- d-erythritol 2,4-cyclodiphosphate, which affords 1-hydroxy-2-methyl-2-( E)-butenyl 4-diphosphate. The protein was crystallized under anaerobic conditions, and its three-dimensional structure was determined to a resolution of 2.7 Å. Each subunit of the c 2 symmetric homodimer folds into two domains connected by a short linker sequence. The N-terminal domain (N domain) is an eight-stranded β barrel that belongs to the large TIM-barrel superfamily. The C-terminal domain (C domain) consists of a β sheet that is flanked on both sides by helices. One glutamate and three cysteine residues of the C domain coordinate a [4Fe–4S] cluster. Homodimer formation involves an extended contact area (about 1100 Å 2) between helices 8 and 9 of each respective β barrel. Moreover, each C domain contacts the N domain of the partner subunit, but the interface regions are small (about 430 Å 2). We propose that the enzyme substrate binds to the positively charged surface area at the C-terminal pole of the β barrel. The C domain carrying the iron–sulfur cluster could then move over to form a closed conformation where the substrate is sandwiched between the N domain and the C domain. This article completes the set of three-dimensional structures of the non-mevalonate pathway enzymes, which are of specific interest as potential targets for tuberculostatic and antimalarial drugs. [Display omitted] ► [4Fe–4S] protein IspG (GcpE) of Aquifex aeolicus is a c 2 symmetric functional dimer. ► IspG catalytic domain comprises a TIM-barrel fold with positively charged patch. ► Reduction of negatively charged substrate by FeS cluster upon proposed domain flip. ► [4Fe–4S] cluster coordinated by glutamate and three cysteines in C-terminal domain.