Structure of the 2-Methylisocitrate Lyase (PrpB) from Escherichia coli

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.218 

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Crystal structure of 2-methylisocitrate lyase (PrpB) from Escherichia coli and modelling of its ligand bound active centre.

Grimm, C.Evers, A.Brock, M.Maerker, C.Klebe, G.Buckel, W.Reuter, K.

(2003) J Mol Biol 328: 609-621

  • DOI: https://doi.org/10.1016/s0022-2836(03)00358-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Following acetate, propionate is the second most abundant low molecular mass carbon compound found in soil. Many microorganisms, including most, if not all fungi, as well as several aerobic bacteria, such as Escherichia coli and Salmonella enterica oxidize propionate via the methylcitrate cycle. The enzyme 2-methylisocitrate lyase (PrpB) from Escherichia coli catalysing the last step of this cycle, the cleavage of 2-methylisocitrate to pyruvate and succinate, was crystallised and its structure determined to a resolution of 1.9A. The enzyme, which strictly depends on Mg(2+) for catalysis, belongs to the isocitrate lyase protein family. A common feature of members of this enzyme family is the movement of a so-called "active site loop" from an open into a closed conformation upon substrate binding thus shielding the reactants from the surrounding solvent. Since in the presented structure, PrpB contains, apart from a Mg(2+), no ligand, the active site loop is found in an open conformation. This conformation, however, differs significantly from the open conformation present in the so far known structures of ligand-free isocitrate lyases. A possible impact of this observation with respect to the different responses of isocitrate lyases and PrpB upon treatment with the common inhibitor 3-bromopyruvate is discussed. Based on the structure of ligand-bound isocitrate lyase from Mycobacterium tuberculosis a model of the substrate-bound PrpB enzyme in its closed conformation was created which provides hints towards the substrate specificity of this enzyme.

  • Organizational Affiliation

    Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-methylisocitrate lyase
A, B
295Escherichia coliMutation(s): 0 
Find proteins for P77541 (Escherichia coli (strain K12))
Explore P77541 
Go to UniProtKB:  P77541
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP77541
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.218 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.895α = 90
b = 82.895β = 90
c = 166.25γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-29
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations