3CE1

Crystal Structure of the Cu/Zn Superoxide Dismutase from Cryptococcus liquefaciens Strain N6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

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This is version 1.3 of the entry. See complete history


Literature

Structure of Cu/Zn superoxide dismutase from the heavy-metal-tolerant yeast Cryptococcus liquefaciens strain N6.

Teh, A.H.Kanamasa, S.Kajiwara, S.Kumasaka, T.

(2008) Biochem Biophys Res Commun 374: 475-478

  • DOI: https://doi.org/10.1016/j.bbrc.2008.07.046
  • Primary Citation of Related Structures:  
    3CE1

  • PubMed Abstract: 

    The deep-sea yeast Cryptococcus liquefaciens strain N6 shows high tolerance towards heavy metals, and can grow in the presence of high concentrations of copper ions. Enzymatic analysis indicated that copper ions induced the Cu/Zn superoxide dismutase activity of strain N6 (Cl-SOD1). In this study, the 1.2A resolution crystal structure of Cl-SOD1 has revealed several significant residue substitutions compared to the other Cu/Zn SODs. In the electrostatic loop, notably, His135 and Pro136 replace the well-conserved linear residues, while Thr133 substitutes a highly conserved glycine. The electrostatic loop has been shown to be involved in the copper uptake process, and these substitutions have caused an inward dragging of the turn region of the loop. As the introduction of proline and abolishment of glycine decrease loop flexibility, this structural reorganization may have helped stabilize the loop conformation, possibly resulting in more efficient copper uptake and a more stabilized copper-bound form.


  • Organizational Affiliation

    Japan Synchrotron Radiation Research Institute (SPring-8/JASRI), Research & Utilization Division, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]168Naganishia liquefaciensMutation(s): 0 
Gene Names: C-SOD1
EC: 1.15.1.1
UniProt
Find proteins for A0ZPR9 (Naganishia liquefaciens)
Explore A0ZPR9 
Go to UniProtKB:  A0ZPR9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ZPR9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.854α = 90
b = 111.768β = 90
c = 70.456γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description