Isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) represent the two central intermediates in the biosynthesis of isoprenoids. The recently discovered deoxyxylulose 5-phosphate pathway generates a mixture of IPP and DMAPP in its final step by reductive dehydroxylation of 1-hydroxy-2-methyl-2-butenyl 4-diphosphate. This conversion is catalyzed by IspH protein comprising a central iron-sulfur cluster as electron transfer cofactor in the active site. The five crystal structures of IspH in complex with substrate, converted substrate, products and PP i reported in this article provide unique insights into the mechanism of this enzyme. While IspH protein crystallizes with substrate bound to a [4Fe-4S] cluster, crystals of IspH in complex with IPP, DMAPP or inorganic pyrophosphate feature [3Fe-4S] clusters. The IspH:substrate complex reveals a hairpin conformation of the ligand with the C(1) hydroxyl group coordinated to the unique site in a [4Fe-4S] cluster of aconitase type. The resulting alkoxide complex is coupled to a hydrogen-bonding network, which serves as proton reservoir via a Thr167 proton relay. Prolonged x-ray irradiation leads to cleavage of the C(1)-O bond (initiated by reducing photo electrons). The data suggest a reaction mechanism involving a combination of Lewis-acid activation and proton coupled electron transfer. The resulting allyl radical intermediate can acquire a second electron via the iron-sulfur cluster. The reaction may be terminated by the transfer of a proton from the β-phosphate of the substrate to C(1) (affording DMAPP) or C(3) (affording IPP).iron-sulfur protein | LytB protein | nonmevalonate pathway | terpene biosynthesis | isoprenoid biosynthesis
Eukaryotes and most prokaryotes require isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) as biosynthetic precursors of terpenes. Whereas animals generate these essential metabolites via the mevalonate pathway, [1] many human pathogens including Plasmodium falciparum and Mycobacterium tuberculosis are known to use the more recently identified non-mevalonate pathway, which is a potential target for drug development.[2-4] The final step of this pathway is catalyzed by IspH protein, which generates a mixture of IPP and DMAPP by reductive dehydration of 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate (HMBPP, Figure 1 a). [5][6][7][8][9][10][11] Recently, Rekittke et al. described the first X-ray structure of IspH protein from the hyperthermophilic eubacterium Aquifex aeolicus in its open state.[12] Herein, we report the crystal structure of the IspH protein from Escherichia coli [11] in its closed conformation, which serves as basis for a detailed discussion of the catalytic pathway.Recombinant E. coli IspH protein (comprising an Nterminal His 6 fusion tag) was purified and crystallized under anaerobic conditions. Its structure was determined to a resolution of 1.8 by single-wavelength anomalous diffraction methods. Three iron sites per protein unit were localized in the anomalous difference Patterson map and were used for phasing. Successive rounds of model building and refinement afforded a well-defined electron density for the entire IspH molecule except for the N-terminal His 6 tag and five Cterminal amino acid residues (R free = 23.8 %, Supporting Information, Table S2). The root mean square (r.m.s.) deviation between the C a positions of the two protein molecules in the asymmetric unit is less than 0.3 . The folding pattern of the monomeric protein involves three structurally similar domains, D1 to D3, which are related by pseudo-C 3 symmetry but are devoid of detectable sequence similarity (Figure 1 b and Supporting Information, Figure S1). Relative to domain D1, domains D2 and D3 appear rotated by angles of approximately 1008 and 1408, respectively. Each domain starts with a conserved cysteine residue that protrudes into a cavity at the center of the protein where it coordinates one respective iron atom of a [3Fe-4S] cluster. The cluster appears to be tilted relative to the pseudotrigonal axis of the apoprotein by about 208. The trigonal symmetric [3Fe-4S] cluster is located in a hydrophobic pocket of the central cavity, which is formed by residues located on D1 (G14 and V15), D2 (P97 and V99), D3 (A199) as well as the C-terminus (F302 and P305), which stabilizes the arrangement of the individual domains. Furthermore, the methylene moiety of C96 in D2 is turned inward generating additional hydrophobic shielding of atom Fe 2 (see Figure 2). Residual electron density located inside the central cavity was identified as inorganic diphosphate (PP i ; see Supporting
The [4Fe-4S] protein IspH in the methylerythritol phosphate isoprenoid biosynthesis pathway is an important anti-infective drug target, but its mechanism of action is still the subject of debate. Here, by using electron paramagnetic resonance (EPR) spectroscopy and 2H, 17O, and 57Fe isotopic labeling, we have characterized and assigned two key reaction intermediates in IspH catalysis. The results are consistent with the bioorganometallic mechanism proposed earlier, and the mechanism is proposed to have similarities to that of ferredoxin: thioredoxin reductase, in that one electron is transferred to the [4Fe-4S]2+ cluster, which then performs a formally two-electron reduction of its substrate, generating an oxidized high potential iron-sulfur protein (HiPIP)-like intermediate. The two paramagnetic reaction intermediates observed correspond to the two intermediates proposed in the bioorganometallic mechanism: the early π-complex in which the substrate’s 3-CH2OH group has rotated away from the reduced iron-sulfur cluster, and the next, η3-allyl complex formed after dehydroxylation. No free radical intermediates are observed, and the two paramagnetic intermediates observed do not fit in a Birch reduction-like or ferraoxetane mechanism. Additionally, we show by using EPR spectroscopy and X-ray crystallography that two substrate analogs (4 and 5) follow the same reaction mechanism.
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