1YAI

X-RAY STRUCTURE OF A BACTERIAL COPPER,ZINC SUPEROXIDE DISMUTASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.149 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Novel dimeric interface and electrostatic recognition in bacterial Cu,Zn superoxide dismutase.

Bourne, Y.Redford, S.M.Steinman, H.M.Lepock, J.R.Tainer, J.A.Getzoff, E.D.

(1996) Proc Natl Acad Sci U S A 93: 12774-12779

  • DOI: 10.1073/pnas.93.23.12774
  • Primary Citation of Related Structures:  
    1YAI

  • PubMed Abstract: 
  • Eukaryotic Cu,Zn superoxide dismutases (CuZnSODs) are antioxidant enzymes remarkable for their unusually stable beta-barrel fold and dimer assembly, diffusion-limited catalysis, and electrostatic guidance of their free radical substrate. Point mutations of CuZnSOD cause the fatal human neurodegenerative disease amyotrophic lateral sclerosis ...

    Eukaryotic Cu,Zn superoxide dismutases (CuZnSODs) are antioxidant enzymes remarkable for their unusually stable beta-barrel fold and dimer assembly, diffusion-limited catalysis, and electrostatic guidance of their free radical substrate. Point mutations of CuZnSOD cause the fatal human neurodegenerative disease amyotrophic lateral sclerosis. We determined and analyzed the first crystallographic structure (to our knowledge) for CuZnSOD from a prokaryote, Photobacterium leiognathi, a luminescent symbiont of Leiognathid fish. This structure, exemplifying prokaryotic CuZnSODs, shares the active-site ligand geometry and the topology of the Greek key beta-barrel common to the eukaryotic CuZnSODs. However, the beta-barrel elements recruited to form the dimer interface, the strategy used to forge the channel for electrostatic recognition of superoxide radical, and the connectivity of the intrasubunit disulfide bond in P. leiognathi CuZnSOD are discrete and strikingly dissimilar from those highly conserved in eukaryotic CuZnSODs. This new CuZnSOD structure broadens our understanding of structural features necessary and sufficient for CuZnSOD activity, highlights a hitherto unrecognized adaptability of the Greek key beta-barrel building block in evolution, and reveals that prokaryotic and eukaryotic enzymes diverged from one primordial CuZnSOD and then converged to distinct dimeric enzymes with electrostatic substrate guidance.


    Related Citations: 
    • Crystallographic Characterization of a Cu,Zn Superoxide Dismutase from Photobacterium Leiognathi
      Redford, S.M., Mcree, D.E., Getzoff, E.D., Steinman, H.M., Tainer, J.A.
      (1990) J Mol Biol 212: 449

    Organizational Affiliation

    Scripps Research Institute, La Jolla, CA 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COPPER, ZINC SUPEROXIDE DISMUTASEA, B, C151Photobacterium leiognathi subsp. leiognathiMutation(s): 0 
Gene Names: PHSOD
EC: 1.15.1.1
UniProt
Find proteins for P00446 (Photobacterium leiognathi)
Explore P00446 
Go to UniProtKB:  P00446
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.149 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.7α = 90
b = 87β = 90.6
c = 43.5γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
AMoREphasing
TNTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-08-20
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance