2zrx | pdb_00002zrx

Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with FMN and DMAPP.

spinqualitylabelsall models 2zrx, resolution 3.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2zrx 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: DMA, FMN, MG Related: 2zru, 2zrv, 2zrw, 2zry, 2zrz Gene: fni, idi (Sulfolobus shibatae) Activity: Isopentenyl-diphosphate Delta-isomerase, with EC number 5.3.3.2 Resources: FirstGlance, OCA, RCSB, PDBsum Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed Using FMN and a reducing agent such as NAD(P)H, type 2 isopentenyl-diphosphate isomerase catalyzes isomerization between isopentenyl diphosphate and dimethylallyl diphosphate, both of which are elemental units for the biosynthesis of highly diverse isoprenoid compounds. Although the flavin cofactor is expected to be integrally involved in catalysis, its exact role remains controversial. Here we report the crystal structures of the substrate-free and complex forms of type 2 isopentenyl-diphosphate isomerase from the thermoacidophilic archaeon Sulfolobus shibatae, not only in the oxidized state but also in the reduced state. Based on the active-site structures of the reduced FMN-substrate-enzyme ternary complexes, which are in the active state, and on the data from site-directed mutagenesis at highly conserved charged or polar amino acid residues around the active site, we demonstrate that only reduced FMN, not amino acid residues, can catalyze proton addition/elimination required for the isomerase reaction. This discovery is the first evidence for this long suspected, but previously unobserved, role of flavins just as a general acid-base catalyst without playing any redox roles, and thereby expands the known functions of these versatile coenzymes. New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase.,Unno H, Yamashita S, Ikeda Y, Sekiguchi SY, Yoshida N, Yoshimura T, Kusunoki M, Nakayama T, Nishino T, Hemmi H J Biol Chem. 2009 Apr 3;284(14):9160-7. Epub 2009 Jan 21. PMID:19158086 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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