1EN4

CRYSTAL STRUCTURE ANALYSIS OF THE E. COLI MANGANESE SUPEROXIDE DISMUTASE Q146H MUTANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Outer sphere mutations perturb metal reactivity in manganese superoxide dismutase.

Edwards, R.A.Whittaker, M.M.Whittaker, J.W.Baker, E.N.Jameson, G.B.

(2001) Biochemistry 40: 15-27

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tyrosine 34 and glutamine 146 are highly conserved outer sphere residues in the mononuclear manganese active site of Escherichia coli manganese superoxide dismutase. Biochemical and spectroscopic characterization of site-directed mutants has allowed ...

    Tyrosine 34 and glutamine 146 are highly conserved outer sphere residues in the mononuclear manganese active site of Escherichia coli manganese superoxide dismutase. Biochemical and spectroscopic characterization of site-directed mutants has allowed functional characterization of these residues in the wild-type (wt) enzyme. X-ray crystallographic analysis of three mutants (Y34F, Q146L, and Q146H) reveal subtle changes in the protein structures. The Y34A mutant, as well as the previously reported Y34F mutant, retained essentially the full superoxide dismutase activity of the wild-type enzyme, and the X-ray crystal structure of Y34F manganese superoxide dismutase shows that mutation of this strictly conserved residue has only minor effects on the positions of active site residues and the organized water in the substrate access funnel. Mutation of the outer sphere solvent pocket residue Q146 has more dramatic effects. The Q146E mutant is isolated as an apoprotein lacking dismutase activity. Q146L and Q146H mutants retain only 5-10% of the dismutase activity of the wild-type enzyme. The absorption and circular dichroism spectra of the Q146H mutant resemble corresponding data for the superoxide dismutase from a hyperthermophilic archaeon, Pyrobaculum aerophilum, which is active in both Mn and Fe forms. Interestingly, the iron-substituted Q146H protein also exhibits low dismutase activity, which increases at lower pH. Mutation of glutamine 146 disrupts the hydrogen-bonding network in the active site and has a greater effect on protein structure than does the Y34F mutant, with rearrangement of the tyrosine 34 and tryptophan 128 side chains.


    Related Citations: 
    • Crystal Structure of Escherichia coli Manganese Superoxide Dismutase at 2.1 A Resolution
      Edwards, R.A.,Baker, H.M.,Whittaker, M.M.,Whittaker, J.W.,Jameson, G.B.,Baker, E.N.
      (1998) J.BIOL.INORG.CHEM. 3: 161
    • Removing a hydrogen bond in the dimer interface of Escherichia coli manganese superoxide dismutase alters structure and reactivity.
      Edwards, R.A.,Whittaker, M.M.,Whittaker, J.W.,Baker, E.N.,Jameson, G.B.
      (2001) Biochemistry 40: 4622


    Organizational Affiliation

    Centre for Structural Biology, Institutes of Fundamental Sciences and Molecular BioSciences, Massey University, Palmerston North, New Zealand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MANGANESE SUPEROXIDE DISMUTASE
A, B, C, D
205Escherichia coli (strain K12)Mutations: Q146H
Gene Names: sodA
EC: 1.15.1.1
Find proteins for P00448 (Escherichia coli (strain K12))
Go to UniProtKB:  P00448
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.169 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 101.766α = 90.00
b = 109.239β = 90.00
c = 180.889γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-06-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-04
    Type: Data collection