4N02

Type 2 IDI from S. pneumoniae

Summary for 4N02

• Entry DOI: 10.2210/pdb4n02/pdb
• Descriptor: Isopentenyl-diphosphate delta-isomerase, SULFATE ION, 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, ... (4 entities in total)
• Functional Keywords: tim barrel, isomerase
• Biological source: Streptococcus pneumoniae
• Cellular location: Cytoplasm (By similarity): B2ILS5
• Total number of polymer chains: 1
• Total formula weight: 40664.92

Authors

de Ruyck, J.,Schubert, H.L.,Poulter, C.D. (deposition date: 2013-09-30, release date: 2014-07-02, Last modification date: 2024-02-28)

Primary citation

de Ruyck, J.,Janczak, M.W.,Neti, S.S.,Rothman, S.C.,Schubert, H.L.,Cornish, R.M.,Matagne, A.,Wouters, J.,Poulter, C.D.
Determination of Kinetics and the Crystal Structure of a Novel Type 2 Isopentenyl Diphosphate: Dimethylallyl Diphosphate Isomerase from Streptococcus pneumoniae.
Chembiochem, 15:1452-1458, 2014

PubMed Abstract: Isopentenyl diphosphate isomerase (IDI) is a key enzyme in the isoprenoid biosynthetic pathway and is required for all organisms that synthesize isoprenoid metabolites from mevalonate. Type 1 IDI (IDI-1) is a metalloprotein that is found in eukaryotes, whereas the type 2 isoform (IDI-2) is a flavoenzyme found in bacteria that is completely absent from human. IDI-2 from the pathogenic bacterium Streptococcus pneumoniae was recombinantly expressed in Escherichia coli. Steady-state kinetic studies of the enzyme indicated that FMNH2 (KM =0.3 μM) bound before isopentenyl diphosphate (KM =40 μM) in an ordered binding mechanism. An X-ray crystal structure at 1.4 Å resolution was obtained for the holoenzyme in the closed conformation with a reduced flavin cofactor and two sulfate ions in the active site. These results helped to further approach the enzymatic mechanism of IDI-2 and, thus, open new possibilities for the rational design of antibacterial compounds against sequence-similar and structure-related pathogens such as Enterococcus faecalis or Staphylococcus aureus.

PubMed: 24910111
DOI: 10.1002/cbic.201402046

Experimental method

X-RAY DIFFRACTION (1.4 Å)