PDBsum entry 2bkb

Go to PDB code: 
protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
Protein chains
192 a.a. *
FE2 ×4
Waters ×629
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Q69e-fesod
Structure: Superoxide dismutase [fe]. Chain: a, b, c, d. Engineered: yes. Mutation: yes. Other_details: reduced state
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
1.70Å     R-factor:   0.207     R-free:   0.231
Authors: E.Yikilmaz,D.W.Rodgers,A.-F.Miller
Key ref:
E.Yikilmaz et al. (2006). The crucial importance of chemistry in the structure-function link: manipulating hydrogen bonding in iron-containing superoxide dismutase. Biochemistry, 45, 1151-1161. PubMed id: 16430211 DOI: 10.1021/bi051495d
14-Feb-05     Release date:   03-Jan-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0AGD3  (SODF_ECOLI) -  Superoxide dismutase [Fe]
193 a.a.
192 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Superoxide dismutase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 superoxide + 2 H+ = O2 + H2O2
2 × superoxide
+ 2 × H(+)
= O(2)
+ H(2)O(2)
      Cofactor: Fe cation or Mn(2+) or (Zn(2+) and Cu cation)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     oxidoreductase activity     4 terms  


    Added reference    
DOI no: 10.1021/bi051495d Biochemistry 45:1151-1161 (2006)
PubMed id: 16430211  
The crucial importance of chemistry in the structure-function link: manipulating hydrogen bonding in iron-containing superoxide dismutase.
E.Yikilmaz, D.W.Rodgers, A.F.Miller.
Fe-containing superoxide dismutase's active site Fe is coordinated by a solvent molecule, whose protonation state is coupled to the Fe oxidation state. Thus, we have proposed that H-bonding between glutamine 69 and this solvent molecule can strongly influence the redox activity of the Fe in superoxide dismutase (SOD). We show here that mutation of this Gln to His subtly alters the active site structure but preserves 30% activity. In contrast, mutation to Glu otherwise preserves the active site structure but inactivates the enzyme. Thus, enzyme function correlates not with atom positions but with residue identity (chemistry), in this case. We observe strong destabilization of the Q69E-FeSOD oxidized state relative to the reduced state and intermediate destabilization of oxidized Q69H-FeSOD. Indeed, redox titrations indicate that mutation of Gln69 to His increases the reduction potential by 240 mV, whereas mutation to Glu appears to increase it by more than 660 mV. We find that this suffices to explain the mutants' loss of activity, although additional factors may also contribute. The strongly elevated reduction potential of Q69E-FeSOD may reflect reorganization of the active site H-bonding network, including possible reversal of the polarity of the key H-bond between residue 69 and coordinated solvent.

Literature references that cite this PDB file's key reference

  PubMed id Reference
18685763 L.Cuesta, E.Tomat, V.M.Lynch, and J.L.Sessler (2008).
Binuclear organometallic ruthenium complexes of a Schiff base expanded porphyrin.
  Chem Commun (Camb), (), 3744-3746.  
17912757 R.Wintjens, D.Gilis, and M.Rooman (2008).
Mn/Fe superoxide dismutase interaction fingerprints and prediction of oligomerization and metal cofactor from sequence.
  Proteins, 70, 1564-1577.  
17647091 G.Renger (2007).
Oxidative photosynthetic water splitting: energetics, kinetics and mechanism.
  Photosynth Res, 92, 407-425.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.