1XTL

Crystal structure of P104H mutant of SOD-like protein from Bacillus subtilis.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1021/ja052790o
  • Primary Citation of Related Structures:  

  • 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 pr ...

    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.


    Related Citations: 
    • A prokaryotic superoxide dismutase paralog lacking two Cu ligands: from largely unstructured in solution to ordered in the crystal.
      Banci, L.,Bertini, I.,Calderone, V.,Cramaro, F.,Del Conte, R.,Fantoni, A.,Mangani, S.,Quattrone, A.,Viezzoli, M.S.
      (2005) Proc.Natl.Acad.Sci.USA 102: 7541


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypothetical superoxide dismutase-like protein yojM
B, A, C, D
175Bacillus subtilis (strain 168)Mutation(s): 1 
Gene Names: yojM
Find proteins for O31851 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O31851
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B, C, D
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.232 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 52.147α = 78.24
b = 56.586β = 89.91
c = 59.118γ = 85.47
Software Package:
Software NamePurpose
MOLREPphasing
CCP4data scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance