Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.376 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.276 

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This is version 1.4 of the entry. See complete history


The crystal structure and active site location of isocitrate lyase from the fungus Aspergillus nidulans.

Britton, K.Langridge, S.Baker, P.J.Weeradechapon, K.Sedelnikova, S.E.De Lucas, J.R.Rice, D.W.Turner, G.

(2000) Structure 8: 349-362

  • DOI: https://doi.org/10.1016/s0969-2126(00)00117-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Isocitrate lyase catalyses the first committed step of the carbon-conserving glyoxylate bypass, the Mg(2+)-dependent reversible cleavage of isocitrate into succinate and glyoxylate. This metabolic pathway is an inviting target for the control of a number of diseases, because the enzymes involved in this cycle have been identified in many pathogens including Mycobacterium leprae and Leishmania. As part of a programme of rational drug design the structure of the tetrameric Aspergillus nidulans isocitrate lyase and its complex with glyoxylate and a divalent cation have been solved to 2.8 A resolution using X-ray diffraction. Each subunit comprises two domains, one of which adopts a folding pattern highly reminiscent of the triose phosphate isomerase (TIM) barrel. A 'knot' between subunits observed in the three-dimensional structure, involving residues towards the C terminus, implies that tetramer assembly involves considerable flexibility in this part of the protein. Difference Fourier analysis together with the pattern of sequence conservation has led to the identification of both the glyoxylate and metal binding sites and implicates the C-terminal end of the TIM barrel as the active site, which is consistent with studies of other enzymes with this fold. Two disordered regions of the polypeptide chain lie close to the active site, one of which includes a critical cysteine residue suggesting that conformational rearrangements are essential for catalysis. Structural similarities between isocitrate lyase and both PEP mutase and enzymes belonging to the enolase superfamily suggest possible relationships in aspects of the mechanism.

  • Organizational Affiliation

    Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield, S10 2TN, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ISOCITRATE LYASE538Aspergillus nidulansMutation(s): 0 
Find proteins for P28298 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore P28298 
Go to UniProtKB:  P28298
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28298
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.376 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.276 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.93α = 90
b = 91.93β = 90
c = 152.77γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling
ROTAVATAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-05-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Advisory, Refinement description
  • Version 1.4: 2024-02-07
    Changes: Advisory, Data collection, Database references