4N02

Type 2 IDI from S. pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Determination of Kinetics and the Crystal Structure of a Novel Type 2 Isopentenyl Diphosphate: Dimethylallyl Diphosphate Isomerase from Streptococcus pneumoniae.

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.

(2014) Chembiochem 15: 1452-1458

  • DOI: 10.1002/cbic.201402046
  • Primary Citation of Related Structures:  
    4N02

  • 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 eukaryote ...

    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.


    Organizational Affiliation

    Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, Utah 84112 (USA); Department of Chemistry, UNamur, 61 rue de Bruxelles, 5000 Namur (Belgium).



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isopentenyl-diphosphate delta-isomeraseA357Streptococcus pneumoniae CGSP14Mutation(s): 0 
Gene Names: fniSPCG_0379
EC: 5.3.3.2
Find proteins for B2ILS5 (Streptococcus pneumoniae (strain CGSP14))
Explore B2ILS5 
Go to UniProtKB:  B2ILS5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FNR
Query on FNR

Download CCD File 
A
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
C17 H23 N4 O9 P
YTNIXZGTHTVJBW-SCRDCRAPSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.329α = 90
b = 131.329β = 90
c = 59.412γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-07-16
    Changes: Database references