1BZO

THREE-DIMENSIONAL STRUCTURE OF PROKARYOTIC CU,ZN SUPEROXIDE DISMUTASE FROM P.LEIOGNATHI, SOLVED BY X-RAY CRYSTALLOGRAPHY.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Evolutionary constraints for dimer formation in prokaryotic Cu,Zn superoxide dismutase.

Bordo, D.Matak, D.Djinovic-Carugo, K.Rosano, C.Pesce, A.Bolognesi, M.Stroppolo, M.E.Falconi, M.Battistoni, A.Desideri, A.

(1999) J.Mol.Biol. 285: 283-296

  • DOI: 10.1006/jmbi.1998.2267

  • PubMed Abstract: 
  • Prokaryotic Cu,Zn superoxide dismutases are characterized by a distinct quaternary structure, as compared to that of the homologous eukaryotic enzymes. Here we report a newly determined crystal structure of the dimeric Cu,Zn superoxide dismutase from ...

    Prokaryotic Cu,Zn superoxide dismutases are characterized by a distinct quaternary structure, as compared to that of the homologous eukaryotic enzymes. Here we report a newly determined crystal structure of the dimeric Cu,Zn superoxide dismutase from Photobacterium leiognathi (crystallized in space group R32, refined at 2.5 A resolution, R-factor 0.19) and analyse it in comparison with that of the monomeric enzyme from Escherichia coli. The dimeric assembly, observed also in a previously studied monoclinic crystal form of P. leiognathi Cu,Zn superoxide dismutase, is based on a ring-shaped subunit contact region, defining a solvated interface cavity. Three clusters of neighbouring residues play a direct role in the stabilization of the quaternary assembly. The present analysis, extended to the amino acid sequences of the other 11 known prokaryotic Cu,Zn superoxide dismutases, shows that at least in five other prokaryotic enzymes the interface residue clusters are under strong evolutionary constraint, suggesting the attainment of a quaternary structure coincident with that of P. leiognathi Cu,Zn superoxide dismutase. Calculation of electrostatic fields for both the enzymes from E. coli and P. leiognathi shows that the monomeric/dimeric association behaviour displayed by prokaryotic Cu, Zn superoxide dismutases is related to the distribution of surface charged residues. Moreover, Brownian dynamics simulations reproduce closely the observed enzyme:substrate association rates, highlighting the role of the active site neighbouring residues in determining the dismutase catalytic properties.


    Related Citations: 
    • Novel Dimeric Interface and Electrostatic Recognition in Bacterial Cu,Zn Superoxide Dismutase
      Bourne, Y.,Redford, S.M.,Steinman, H.M.,Lepock, J.R.,Tainer, J.A.,Getzoff, E.D.
      (1996) Proc.Natl.Acad.Sci.USA 93: 12774


    Organizational Affiliation

    Department of Physics - INFM and Advanced Biotechnology Center - IST, University of Genova, Largo R. Benzi, 10, Genova, I-16132, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (SUPEROXIDE DISMUTASE)
A
151Photobacterium leiognathiGene Names: sodC
EC: 1.15.1.1
Find proteins for P00446 (Photobacterium leiognathi)
Go to UniProtKB:  P00446
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A
URANYL (VI) ION
O2 U
IZLHQJIUOZHTLW-UHFFFAOYSA-N
 Ligand Interaction
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: 2.1 Å
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 86.890α = 90.00
b = 86.890β = 90.00
c = 99.010γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-04-09
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance