Crystal Structure of IscA with the [2Fe-2S] cluster

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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The Asymmetric IscA Homodimer with an Exposed [2Fe-2S] Cluster Suggests the Structural Basis of the Fe-S Cluster Biosynthetic Scaffold.

Morimoto, K.Yamashita, E.Kondou, Y.Lee, S.J.Arisaka, F.Tsukihara, T.Nakai, M.

(2006) J Mol Biol 360: 117-132

  • DOI: https://doi.org/10.1016/j.jmb.2006.04.067
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    It has been shown that the so-called scaffold proteins are vital in Fe-S cluster biosynthesis by providing an intermediate site for the assembly of Fe-S clusters. However, since no structural information on such scaffold proteins with bound Fe-S cluster intermediates is available, the structural basis of the core of Fe-S cluster biosynthesis remains poorly understood. Here we report the first Fe-S cluster-bound crystal structure of a scaffold protein, IscA, from Thermosynechococcus elongatus, which carries three strictly conserved cysteine residues. Surprisingly, one partially exposed [2Fe-2S] cluster is coordinated by two conformationally distinct IscA protomers, termed alpha and beta, with asymmetric cysteinyl ligation by Cys37, Cys101, Cys103 from alpha and Cys103 from beta. In the crystal, two alphabeta dimers form an unusual domain-swapped tetramer via central domains of beta protomers. Together with additional biochemical data supporting its physiologically relevant configuration, we propose that the unique asymmetric Fe-S cluster coordination and the resulting distinct conformational stabilities of the two IscA protomers are central to the function of IscA-type Fe-S cluster biosynthetic scaffold.

  • Organizational Affiliation

    Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
112Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: tll0464
Find proteins for Q8DLM0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DLM0 
Go to UniProtKB:  Q8DLM0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DLM0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.472α = 90
b = 102.788β = 90
c = 137.032γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance