1IB5

X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT W83Y


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Single mutations at the subunit interface modulate copper reactivity in Photobacterium leiognathi Cu,Zn superoxide dismutase.

Stroppolo, M.E.Pesce, A.D'Orazio, M.O'Neill, P.Bordo, D.Rosano, C.Milani, M.Battistoni, A.Bolognesi, M.Desideri, A.

(2001) J Mol Biol 308: 555-563

  • DOI: https://doi.org/10.1006/jmbi.2001.4606
  • Primary Citation of Related Structures:  
    1IB5, 1IBB, 1IBD, 1IBF, 1IBH

  • PubMed Abstract: 

    The functional properties and X-ray structures of five mutant forms of Photobacterium leiognathi Cu,Zn superoxide dismutase carrying single mutations at residues located at the dimer association interface have been investigated. When compared to the wild-type enzyme, the three-dimensional structures of the mutants show structural perturbations limited to the proximity of the mutation sites and substantial identity of active site geometry. Nonetheless, the catalytic rates of all mutants, measured at neutral pH and low ionic strength by pulse radiolysis, are higher than that of the wild-type protein. Such enzymatic activity increase is paralleled by enhanced active site accessibility to external chelating agents, which, in the mutated enzyme, remove more readily the active site copper ion. It is concluded that mutations at the prokaryotic Cu,Zn superoxide dismutase subunit interface can transduce dynamical perturbation to the active site region, promoting substrate active site accessibility. Such long-range intramolecular communication effects have not been extensively described before within the Cu,Zn superoxide dismutase homology family.


  • Organizational Affiliation

    Department of Biology and INFM, University of Rome "Tor Vergata", Rome, Via della Ricerca Scientifica, 00133, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CU,ZN SUPEROXIDE DISMUTASE151Photobacterium leiognathi subsp. leiognathiMutation(s): 1 
EC: 1.15.1.1
UniProt
Find proteins for P00446 (Photobacterium leiognathi)
Explore P00446 
Go to UniProtKB:  P00446
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00446
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.336α = 90
b = 87.336β = 90
c = 98.223γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary