3UWM

Ec_IspH in complex with 4-oxobutyl diphosphate (1302)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

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This is version 1.2 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: https://doi.org/10.1038/ncomms2052
  • Primary Citation of Related Structures:  
    3URK, 3UTC, 3UTD, 3UV3, 3UV6, 3UV7, 3UWM

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
A, B
324Escherichia coli K-12Mutation(s): 0 
Gene Names: ispHlytByaaEb0029JW0027
EC: 1.17.1.2
UniProt
Find proteins for P62623 (Escherichia coli (strain K12))
Explore P62623 
Go to UniProtKB:  P62623
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62623
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.66α = 90
b = 80.7β = 90
c = 111.79γ = 90
Software Package:
Software NamePurpose
RemDAqdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2012-09-19
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description