1PZS

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

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: 10.1074/jbc.M404699200

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Superoxide dismutase [Cu-Zn]
A
208Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: sodC
EC: 1.15.1.1
Find proteins for P9WGE9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGE9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU
Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.150 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.040α = 90.00
b = 58.420β = 126.99
c = 51.390γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
MAR345data collection
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description
  • Version 1.4: 2018-01-31
    Type: Experimental preparation