2D3W | pdb_00002d3w

Crystal Structure of Escherichia coli SufC, an ATPase compenent of the SUF iron-sulfur cluster assembly machinery


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.293 (Depositor), 0.291 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of Escherichia coli SufC, an ABC-type ATPase component of the SUF iron-sulfur cluster assembly machinery

Kitaoka, S.Wada, K.Hasegawa, Y.Minami, Y.Fukuyama, K.Takahashi, Y.

(2006) FEBS Lett 580: 137-143

  • DOI: https://doi.org/10.1016/j.febslet.2005.11.058
  • Primary Citation Related Structures: 
    2D3W

  • PubMed Abstract: 

    SufC is an ATPase component of the SUF machinery, which is involved in the biosynthesis of Fe-S clusters. To gain insight into the function of this protein, we have determined the crystal structure of Escherichia coli SufC at 2.5A resolution. Despite the similarity of the overall structure with ABC-ATPases (nucleotide-binding domains of ABC transporters), some key differences were observed. Glu171, an invariant residue involved in ATP hydrolysis, is rotated away from the nucleotide-binding pocket to form a SufC-specific salt bridge with Lys152. Due to this salt bridge, D-loop that follows Glu171 is flipped out to the molecular surface, which may sterically inhibit the formation of an active dimer. Thus, the salt bridge may play a critical role in regulating ATPase activity and preventing wasteful ATP hydrolysis. Furthermore, SufC has a unique Q-loop structure on its surface, which may form a binding site for its partner proteins, SufB and/or SufD.


  • Organizational Affiliation
    • Department of Biology, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.

Macromolecule Content 

  • Total Structure Weight: 110.45 kDa 
  • Atom Count: 7,480 
  • Modeled Residue Count: 972 
  • Deposited Residue Count: 992 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable ATP-dependent transporter sufC
A, B, C, D
248Escherichia coliMutation(s): 0 
UniProt
Find proteins for P77499 (Escherichia coli (strain K12))
Explore P77499 
Go to UniProtKB:  P77499
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP77499
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.293 (Depositor), 0.291 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.529α = 90
b = 46.677β = 91.786
c = 149.318γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references