3B05

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

Summary for 3B05

• Entry DOI: 10.2210/pdb3b05/pdb
• Related: 3B03 3B04 3B06
• Descriptor: Isopentenyl-diphosphate delta-isomerase, 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL, 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: type 2, idi, fmn, isopentenyl diphosphate isomerase, ipp, isomerase
• Biological source: Sulfolobus shibatae
• Cellular location: Cytoplasm (By similarity): P61615
• Total number of polymer chains: 4
• Total formula weight: 164818.29

Authors

Unno, H.,Nagai, T.,Hemmi, H. (deposition date: 2011-06-03, release date: 2011-11-02, Last modification date: 2024-03-13)

Primary citation

Nagai, T.,Unno, H.,Janczak, M.W.,Yoshimura, T.,Poulter, C.D.,Hemmi, H.
Covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors.
Proc.Natl.Acad.Sci.USA, 108:20461-20466, 2011

PubMed Abstract: 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.

PubMed: 22158896
DOI: 10.1073/pnas.1115749108

Experimental method

X-RAY DIFFRACTION (2.2 Å)