2APS

CU/ZN SUPEROXIDE DISMUTASE FROM ACTINOBACILLUS PLEUROPNEUMONIAE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cu,Zn superoxide dismutase structure from a microbial pathogen establishes a class with a conserved dimer interface.

Forest, K.T.Langford, P.R.Kroll, J.S.Getzoff, E.D.

(2000) J.Mol.Biol. 296: 145-153

  • DOI: 10.1006/jmbi.1999.3448

  • PubMed Abstract: 
  • Macrophages and neutrophils protect animals from microbial infection in part by issuing a burst of toxic superoxide radicals when challenged. To counteract this onslaught, many Gram-negative bacterial pathogens possess periplasmic Cu,Zn superoxide di ...

    Macrophages and neutrophils protect animals from microbial infection in part by issuing a burst of toxic superoxide radicals when challenged. To counteract this onslaught, many Gram-negative bacterial pathogens possess periplasmic Cu,Zn superoxide dismutases (SODs), which act on superoxide to yield molecular oxygen and hydrogen peroxide. We have solved the X-ray crystal structure of the Cu,Zn SOD from Actinobacillus pleuropneumoniae, a major porcine pathogen, by molecular replacement at 1.9 A resolution. The structure reveals that the dimeric bacterial enzymes form a structurally homologous class defined by a water-mediated dimer interface, and share with all Cu,Zn SODs the Greek-key beta-barrel subunit fold with copper and zinc ions located at the base of a deep loop-enclosed active-site channel. Our structure-based sequence alignment of the bacterial enzymes explains the monomeric nature of at least two of these, and suggests that there may be at least one additional structural class for the bacterial SODs. Two metal-mediated crystal contacts yielded our C222(1) crystals, and the geometry of these sites could be engineered into proteins recalcitrant to crystallization in their native form. This work highlights structural differences between eukaryotic and prokaryotic Cu,Zn SODs, as well as similarities and differences among prokaryotic SODs, and lays the groundwork for development of antimicrobial drugs that specifically target periplasmic Cu,Zn SODs of bacterial pathogens.


    Organizational Affiliation

    Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, Mail Drop MB-4, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. forest@bact.wisc.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (CU,ZN SUPEROXIDE DISMUTASE)
A, B
162Actinobacillus pleuropneumoniaeMutation(s): 0 
Gene Names: sodC
EC: 1.15.1.1
Find proteins for P24702 (Actinobacillus pleuropneumoniae)
Go to UniProtKB:  P24702
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.221 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 58.050α = 90.00
b = 123.880β = 90.00
c = 107.250γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-25
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance