3UTD

Ec_IspH in complex with 4-oxopentyl diphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of acetylene hydratase activity of the iron-sulphur protein IspH.

Span, I.Wang, K.Wang, W.Zhang, Y.Bacher, A.Eisenreich, W.Li, K.Schulz, C.Oldfield, E.Groll, M.

(2012) Nat Commun 3: 1042-1042

  • DOI: 10.1038/ncomms2052
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The final step of the methylerythritol phosphate isoprenoid biosynthesis pathway is catalysed by the iron-sulphur enzyme IspH, producing the universal precursors of terpenes: isopentenyl diphosphate and dimethylallyl diphosphate. Here we report an un ...

    The final step of the methylerythritol phosphate isoprenoid biosynthesis pathway is catalysed by the iron-sulphur enzyme IspH, producing the universal precursors of terpenes: isopentenyl diphosphate and dimethylallyl diphosphate. Here we report an unforeseen reaction discovered during the investigation of the interaction of IspH with acetylene inhibitors by X-ray crystallography, Mößbauer, and nuclear magnetic resonance spectroscopy. In addition to its role as a 2H(+)/2e(-) reductase, IspH can hydrate acetylenes to aldehydes and ketones via anti-Markovnikov/Markovnikov addition. The reactions only occur with the oxidised protein and proceed via η(1)-O-enolate intermediates. One of these is characterized crystallographically and contains a C4 ligand oxygen bound to the unique, fourth iron in the 4Fe-4S cluster: this intermediate subsequently hydrolyzes to produce an aldehyde product. This unexpected side to IspH reactivity is of interest in the context of the mechanism of action of other acetylene hydratases, as well as in the design of antiinfectives targeting IspH.


    Organizational Affiliation

    Department of Chemistry, Center for Integrated Protein Science, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
A, B
324Escherichia coli (strain K12)Mutation(s): 0 
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
F3S
Query on F3S

Download SDF File 
Download CCD File 
A, B
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
0CJ
Query on 0CJ

Download SDF File 
Download CCD File 
A, B
4-oxopentyl trihydrogen diphosphate
C5 H12 O8 P2
KREMOGYKSOVBKI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.146 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.110α = 90.00
b = 80.390β = 90.00
c = 111.240γ = 90.00
Software Package:
Software NamePurpose
RemDAqdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
ACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2012-09-19
    Type: Database references