Crystal structure of Indolepyruvate decarboxylase from Enterobacter cloacae

Experimental Data Snapshot

  • Resolution: 2.65 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

Starting Model: experimental
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Crystal structure of thiamindiphosphate-dependent indolepyruvate decarboxylase from Enterobacter cloacae, an enzyme involved in the biosynthesis of the plant hormone indole-3-acetic acid

Schutz, A.Sandalova, T.Ricagno, S.Hubner, G.Konig, S.Schneider, G.

(2003) Eur J Biochem 270: 2312-2321

  • DOI: https://doi.org/10.1046/j.1432-1033.2003.03601.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The thiamin diphosphate-dependent enzyme indolepyruvate decarboxylase catalyses the formation of indoleacetaldehyde from indolepyruvate, one step in the indolepyruvate pathway of biosynthesis of the plant hormone indole-3-acetic acid. The crystal structure of this enzyme from Enterobacter cloacae has been determined at 2.65 A resolution and refined to a crystallographic R-factor of 20.5% (Rfree 23.6%). The subunit of indolepyruvate decarboxylase contains three domains of open alpha/beta topology, which are similar in structure to that of pyruvate decarboxylase. The tetramer has pseudo 222 symmetry and can be described as a dimer of dimers. It resembles the tetramer of pyruvate decarboxylase from Zymomonas mobilis, but with a relative difference of 20 degrees in the angle between the two dimers. Active site residues are highly conserved in indolepyruvate/pyruvate decarboxylase, suggesting that the interactions with the cofactor thiamin diphosphate and the catalytic mechanisms are very similar. The substrate binding site in indolepyruvate decarboxylase contains a large hydrophobic pocket which can accommodate the bulky indole moiety of the substrate. In pyruvate decarboxylases this pocket is smaller in size and allows discrimination of larger vs. smaller substrates. In most pyruvate decarboxylases, restriction of cavity size is due to replacement of residues at three positions by large, hydrophobic amino acids such as tyrosine or tryptophan.

  • Organizational Affiliation

    Institute of Biochemistry, Department of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Germany.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Indole-3-pyruvate decarboxylase
A, B, C, D
552Enterobacter cloacaeMutation(s): 0 
Gene Names: IPDC
Find proteins for P23234 (Enterobacter cloacae)
Explore P23234 
Go to UniProtKB:  P23234
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23234
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.65 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.2α = 90
b = 151.62β = 90
c = 107.55γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-03
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description