3b05

Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with reduced FMN and IPP at 2.2A resolution.Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with reduced FMN and IPP at 2.2A resolution.

Structural highlights 3b05 is a 4 chain structure with sequence from Sulfolobus shibatae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: , , Related: 3b03, 3b04, 3b06 Gene: fni, idi (Sulfolobus shibatae) Activity: Isopentenyl-diphosphate Delta-isomerase, with EC number 5.3.3.2 Resources: FirstGlance, OCA, RCSB, PDBsum Function [IDI2_SULSH] Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP) (By similarity). Publication Abstract from PubMed Evidence for an unusual catalysis of protonation/deprotonation by a reduced flavin mononucleotide cofactor is presented for type-2 isopentenyl diphosphate isomerase (IDI-2), which catalyzes isomerization of the two fundamental building blocks of isoprenoid biosynthesis, isopentenyl diphosphate and dimethylallyl diphosphate. The covalent adducts formed between irreversible mechanism-based inhibitors, 3-methylene-4-penten-1-yl diphosphate or 3-oxiranyl-3-buten-1-yl diphosphate, and the flavin cofactor were investigated by X-ray crystallography and UV-visible spectroscopy. Both the crystal structures of IDI-2 binding the flavin-inhibitor adduct and the UV-visible spectra of the adducts indicate that the covalent bond is formed at C4a of flavin rather than at N5, which had been proposed previously. In addition, the high-resolution crystal structures of IDI-2-substrate complexes and the kinetic studies of new mutants confirmed that only the flavin cofactor can catalyze protonation of the substrates and suggest that N5 of flavin is most likely to be involved in proton transfer. These data provide support for a mechanism where the reduced flavin cofactor acts as a general acid/base catalyst and helps stabilize the carbocationic intermediate formed by protonation. Covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors.,Nagai T, Unno H, Janczak MW, Yoshimura T, Poulter CD, Hemmi H Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20461-6. Epub 2011 Dec 7. PMID:22158896 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Isopentenyl-diphosphate delta-isomerase

spinqualitylabelsall models 3b05, resolution 2.20Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image