2ZU0

Crystal structure of SufC-SufD complex involved in the iron-sulfur cluster biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular dynamism of Fe-S cluster biosynthesis implicated by the structure of SufC(2)-SufD(2) complex

Wada, K.Sumi, N.Nagai, R.Iwasaki, K.Sato, T.Suzuki, K.Hasegawa, Y.Kitaoka, S.Minami, Y.Outten, F.W.Takahashi, Y.Fukuyama, K.

(2009) J.Mol.Biol. 387: 245-258

  • DOI: 10.1016/j.jmb.2009.01.054

  • PubMed Abstract: 
  • Maturation of iron-sulfur (Fe-S) proteins is achieved by the SUF machinery in a wide number of eubacteria and archaea, as well as eukaryotic chloroplasts. This machinery is encoded in Escherichia coli by the sufABCDSE operon, where three Suf componen ...

    Maturation of iron-sulfur (Fe-S) proteins is achieved by the SUF machinery in a wide number of eubacteria and archaea, as well as eukaryotic chloroplasts. This machinery is encoded in Escherichia coli by the sufABCDSE operon, where three Suf components, SufB, SufC, and SufD, form a complex and appear to provide an intermediary site for the Fe-S cluster assembly. Here, we report the quaternary structure of the SufC(2)-SufD(2) complex in which SufC is bound to the C-terminal domain of SufD. Comparison with the monomeric structure of SufC revealed conformational change of the active-site residues: SufC becomes competent for ATP binding and hydrolysis upon association with SufD. The two SufC subunits were spatially separated in the SufC(2)-SufD(2) complex, whereas cross-linking experiments in solution have indicated that two SufC molecules associate with each other in the presence of Mg(2+) and ATP. Such dimer formation of SufC may lead to a gross structural change of the SufC(2)-SufD(2) complex. Furthermore, genetic analysis of SufD revealed an essential histidine residue buried inside the dimer interface, suggesting that conformational change may expose this crucial residue. These findings, together with biochemical characterization of the SufB-SufC-SufD complex, have led us to propose a model for the Fe-S cluster biosynthesis in the complex.


    Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein sufD
A, B
423Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: sufD (ynhC)
Find proteins for P77689 (Escherichia coli (strain K12))
Go to UniProtKB:  P77689
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Probable ATP-dependent transporter sufC
C, D
267Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: sufC (ynhD)
Find proteins for P77499 (Escherichia coli (strain K12))
Go to UniProtKB:  P77499
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download SDF File 
Download CCD File 
C
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 96.110α = 90.00
b = 106.150β = 90.00
c = 171.670γ = 90.00
Software Package:
Software NamePurpose
BSSdata collection
CNSrefinement
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-10-11 
  • Released Date: 2009-03-10 
  • Deposition Author(s): Wada, K.

Revision History 

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance