1XTM

Crystal structure of the double mutant Y88H-P104H of a SOD-like protein from Bacillus subtilis.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

From an Inactive Prokaryotic SOD Homologue to an Active Protein through Site-Directed Mutagenesis.

Banci, L.Benvenuti, M.Bertini, I.Cabelli, D.E.Calderone, V.Fantoni, A.Mangani, S.Migliardi, M.Viezzoli, M.S.

(2005) J Am Chem Soc 127: 13287-13292

  • DOI: https://doi.org/10.1021/ja052790o
  • Primary Citation of Related Structures:  
    1XTL, 1XTM

  • PubMed Abstract: 

    It is known that several prokaryotic protein sequences, characterized by high homology with the eukaryotic Cu,ZnSODs, lack some of the metal ligands. In the present work, we have stepwise reintroduced the two missing copper ligands in the SOD-like protein of Bacillus subtilis, through site-directed mutagenesis. The mutant with three out of the four His that bind copper is not active, whereas the fully reconstituted mutant displays an activity of about 10% that of human Cu,ZnSOD. The mutated proteins have been characterized in solution and in the solid state. In solution, the proteins experience conformational disorder, which is believed to be partly responsible for the decreased enzymatic activity and sheds light on the tendency of several human SOD mutants to introduce mobility in the protein frame. In the crystal, on the contrary, the protein has a well-defined conformation, giving rise to dimers through the coordination of an exogenous zinc ion. The catalytic properties of the double mutant, which might be regarded as a step in an artificial evolution from a nonactive SOD to a fully functioning enzyme, are discussed on the basis of the structural and dynamical properties.


  • Organizational Affiliation

    Department of Chemistry and Centro Risonanze Magnetiche, University of Florence, 50019 Sesto Fiorentino, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical superoxide dismutase-like protein yojMA [auth B],
B [auth A]
175Bacillus subtilisMutation(s): 2 
UniProt
Find proteins for O31851 (Bacillus subtilis (strain 168))
Explore O31851 
Go to UniProtKB:  O31851
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO31851
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.462α = 90
b = 104.35β = 90
c = 58.756γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary