1MNG

STRUCTURE-FUNCTION IN E. COLI IRON SUPEROXIDE DISMUTASE: COMPARISONS WITH THE MANGANESE ENZYME FROM T. THERMOPHILUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure-function in Escherichia coli iron superoxide dismutase: comparisons with the manganese enzyme from Thermus thermophilus.

Lah, M.S.Dixon, M.M.Pattridge, K.A.Stallings, W.C.Fee, J.A.Ludwig, M.L.

(1995) Biochemistry 34: 1646-1660

  • DOI: 10.1021/bi00005a021
  • Primary Citation of Related Structures:  
    1ISB, 1ISA, 1ISC, 1MNG

  • PubMed Abstract: 
  • The crystal structure of dimeric Fe(III) superoxide dismutase (SOD) from Escherichia coli (3006 protein atoms, 2 irons, and 281 solvents) has been refined to an R of 0.184 using all observed data between 40.0 and 1.85 A (34,879 reflections). Features of this structure are compared with the refined structure of MnSOD from Thermus thermophilus ...

    The crystal structure of dimeric Fe(III) superoxide dismutase (SOD) from Escherichia coli (3006 protein atoms, 2 irons, and 281 solvents) has been refined to an R of 0.184 using all observed data between 40.0 and 1.85 A (34,879 reflections). Features of this structure are compared with the refined structure of MnSOD from Thermus thermophilus. The coordination geometry at the Fe site is distorted trigonal bipyramidal, with axial ligands His26 and solvent (proposed to be OH-), and in-plane ligands His73, Asp156, and His160. Reduction of crystals to the Fe(II) state does not result in significant changes in metal-ligand geometry (R = 0.188 for data between 40.0 and 1.80 A). The arrangement of iron ligands in Fe(II) and Fe(III)SOD closely matches the Mn coordination found in MnSOD from T. thermophilus [Ludwig, M.L., Metzger, A.L., Pattridge, K.A., & Stallings, W.C. (1991) J. Mol. Biol. 219, 335-358]. Structures of the Fe(III) azide (40.0-1.8 A, R = 0.186) and Mn(III) azide (20.0-1.8 A, R = 0.179) complexes, reported here, reveal azide bound as a sixth ligand with distorted octahedral geometry at the metal; the in-plane ligand-Fe-ligand and ligand-Mn-ligand angles change by 20-30 degrees to coordinate azide as a sixth ligand. However, the positions of the distal azide nitrogens are different in the FeSOD and MnSOD complexes. The geometries of the Fe(III), Fe(II), and Fe(III)-azide species suggest a reaction mechanism for superoxide dismutation in which the metal alternates between five- and six-coordination. A reaction scheme in which the ligated solvent acts as a proton acceptor in the first half-reaction [formation of Fe(II) and oxygen] is consistent with the pH dependence of the kinetic parameters and spectroscopic properties of Fe superoxide dismutase.


    Related Citations: 
    • Manganese Superoxide Dismutase from Thermus Thermophilus. A Structural Model Refined at 1.8 Angstroms Resolution
      Ludwig, M.L., Metzger, A.L., Pattridge, K.A., Stallings, W.C.
      (1991) J Mol Biol 219: 335
    • Iron and Manganese Superoxide Dismutases: Catalytic Inferences from the Structures
      Stallings, W.C., Bull, C., Fee, J.A., Lah, M.S., Ludwig, M.L.
      (1992) Molecular Biology Of Free Radical Scavenging Systems --: 193
    • Structure-Function Relationships in Fe-and Mn-Superoxide Dismutases
      Stallings, W.C., Metzger, A.L., Pattridge, K.A., Fee, J.A., Ludwig, M.L.
      (1991) Free Radic Res Commun 12: 259
    • The Structure of Manganese Superoxide Dismutase from Thermus Thermophilus at 2.4 Angstroms Resolution
      Stallings, W.C., Pattridge, K.A., Strong, R.K., Ludwig, M.L.
      (1985) J Biol Chem 260: 16424
    • Manganese and Iron Superoxide Dismutases are Structural Homologs
      Stallings, W.C., Pattridge, K.A., Strong, R.K., Ludwig, M.L.
      (1984) J Biol Chem 259: 10695

    Organizational Affiliation

    Biophysics Research Division, University of Michigan, Ann Arbor 48109.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MANGANESE SUPEROXIDE DISMUTASEA, B203Thermus thermophilusMutation(s): 0 
EC: 1.15.1.1
Find proteins for P61503 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P61503 
Go to UniProtKB:  P61503
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
AZI
Query on AZI

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.8α = 90
b = 146.8β = 90
c = 55.6γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other