3KE8

Crystal structure of IspH:HMBPP-complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Probing the reaction mechanism of IspH protein by x-ray structure analysis.

Grawert, T.Span, I.Eisenreich, W.Rohdich, F.Eppinger, J.Bacher, A.Groll, M.

(2010) Proc.Natl.Acad.Sci.USA 107: 1077-1081

  • DOI: 10.1073/pnas.0913045107
  • Primary Citation of Related Structures:  3KE9, 3KEF, 3KEL, 3KEM

  • PubMed Abstract: 
  • Isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) represent the two central intermediates in the biosynthesis of isoprenoids. The recently discovered deoxyxylulose 5-phosphate pathway generates a mixture of IPP and DMAPP in its fina ...

    Isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) represent the two central intermediates in the biosynthesis of isoprenoids. The recently discovered deoxyxylulose 5-phosphate pathway generates a mixture of IPP and DMAPP in its final step by reductive dehydroxylation of 1-hydroxy-2-methyl-2-butenyl 4-diphosphate. This conversion is catalyzed by IspH protein comprising a central iron-sulfur cluster as electron transfer cofactor in the active site. The five crystal structures of IspH in complex with substrate, converted substrate, products and PP(i) reported in this article provide unique insights into the mechanism of this enzyme. While IspH protein crystallizes with substrate bound to a [4Fe-4S] cluster, crystals of IspH in complex with IPP, DMAPP or inorganic pyrophosphate feature [3Fe-4S] clusters. The IspH:substrate complex reveals a hairpin conformation of the ligand with the C(1) hydroxyl group coordinated to the unique site in a [4Fe-4S] cluster of aconitase type. The resulting alkoxide complex is coupled to a hydrogen-bonding network, which serves as proton reservoir via a Thr167 proton relay. Prolonged x-ray irradiation leads to cleavage of the C(1)-O bond (initiated by reducing photo electrons). The data suggest a reaction mechanism involving a combination of Lewis-acid activation and proton coupled electron transfer. The resulting allyl radical intermediate can acquire a second electron via the iron-sulfur cluster. The reaction may be terminated by the transfer of a proton from the beta-phosphate of the substrate to C(1) (affording DMAPP) or C(3) (affording IPP).


    Organizational Affiliation

    Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, Garching, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
A, B
326Escherichia coli (strain K12)Gene Names: ispH (lytB, yaaE)
EC: 1.17.7.4
Find proteins for P62623 (Escherichia coli (strain K12))
Go to UniProtKB:  P62623
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EIP
Query on EIP

Download SDF File 
Download CCD File 
A, B
4-HYDROXY-3-METHYL BUTYL DIPHOSPHATE
C5 H14 O8 P2
URURINNTPGGDIV-YFKPBYRVSA-N
 Ligand Interaction
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.241 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.890α = 90.00
b = 80.660β = 90.00
c = 111.160γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-12-04
    Type: Database references