Crystal Structure of a Cu-Zn Superoxide Dismutase from Mycobacterium tuberculosis at 1.63 resolution

Experimental Data Snapshot

  • Resolution: 1.63 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

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Unique Features of the sodC-encoded Superoxide Dismutase from Mycobacterium tuberculosis, a Fully Functional Copper-containing Enzyme Lacking Zinc in the Active Site.

Spagnolo, L.Toro, I.D'Orazio, M.O'Neill, P.Pedersen, J.Z.Carugo, O.Rotilio, G.Battistoni, A.Djinovic-Carugo, K.

(2004) J Biol Chem 279: 33447-33455

  • DOI: https://doi.org/10.1074/jbc.M404699200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The sodC-encoded Mycobacterium tuberculosis superoxide dismutase (SOD) shows high sequence homology to other members of the copper/zinc-containing SOD family. Its three-dimensional structure is reported here, solved by x-ray crystallography at 1.63-A resolution. Metal analyses of the recombinant protein indicate that the native form of the enzyme lacks the zinc ion, which has a very important structural and functional role in all other known enzymes of this class. The absence of zinc within the active site is due to significant rearrangements in the zinc subloop, including deletion or mutation of the metal ligands His115 and His123. Nonetheless, the enzyme has a catalytic rate close to the diffusion limit; and unlike all other copper/zinc-containing SODs devoid of zinc, the geometry of the copper site is pH-independent. The protein shows a novel dimer interface characterized by a long and rigid loop, which confers structural stability to the enzyme. As the survival of bacterial pathogens within their host critically depends on their ability to recruit zinc in highly competitive environments, we propose that the observed structural rearrangements are required to build up a zinc-independent but fully active and stable copper-containing SOD.

  • Organizational Affiliation

    Structural Biology Laboratory, ELETTRA, Sincrotrone Trieste, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]208Mycobacterium tuberculosisMutation(s): 0 
Gene Names: SODC OR RV0432 OR MT0447 OR MTCY22G10.29
Find proteins for P9WGE9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGE9 
Go to UniProtKB:  P9WGE9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WGE9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CU

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.63 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.04α = 90
b = 58.42β = 126.99
c = 51.39γ = 90
Software Package:
Software NamePurpose
MAR345data collection
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation
  • Version 1.5: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description