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PDBsum entry 2nyb

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
2nyb
Jmol
Contents
Protein chains
192 a.a. *
Ligands
__O ×4
Metals
FE2 ×4
Waters ×1144
* Residue conservation analysis
PDB id:
2nyb
Name: Oxidoreductase
Title: Crystal structure of e.Coli iron superoxide dismutase q69e at 1.1 angstrom resolution
Structure: Superoxide dismutase [fe]. Chain: a, b, c, d. Synonym: iron superoxide dismutase. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: sodb, b1656, jw1648. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
1.10Å     R-factor:   0.160     R-free:   0.174
Authors: J.C.Porta,A.Vahedi-Faridi,G.E.O.Borgstahl
Key ref: E.Yikilmaz et al. (2007). How can a single second sphere amino acid substitution cause reduction midpoint potential changes of hundreds of millivolts? J Am Chem Soc, 129, 9927-9940. PubMed id: 17628062 DOI: 10.1021/ja069224t
Date:
20-Nov-06     Release date:   05-Dec-06    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AGD3  (SODF_ECOLI) -  Superoxide dismutase [Fe]
Seq:
Struc:
193 a.a.
193 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.1.15.1.1  - 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/ja069224t J Am Chem Soc 129:9927-9940 (2007)
PubMed id: 17628062  
 
 
How can a single second sphere amino acid substitution cause reduction midpoint potential changes of hundreds of millivolts?
E.Yikilmaz, J.Porta, L.E.Grove, A.Vahedi-Faridi, Y.Bronshteyn, T.C.Brunold, G.E.Borgstahl, A.F.Miller.
 
  ABSTRACT  
 
The active site metal ion of superoxide dismutase (SOD) is reduced and reoxidized as it disproportionates superoxide to dioxygen and hydrogen peroxide. Thus, the reduction midpoint potential (Em) is a critical determinant of catalytic activity. In E. coli Fe-containing SOD (FeSOD), reduction of Fe3+ is accompanied by protonation of a coordinated OH-, to produce Fe2+ coordinated by H2O. The coordinated solvent's only contact with the protein beyond the active site is a conserved Gln residue. Mutation of this Gln to His or Glu resulted in elevation of the Em by 220 mV and more than 660 mV, respectively [Yikilmaz et al., Biochemistry 2006, 45, 1151-1161], despite the fact that overall protein structure was preserved, His is a chemically conservative replacement for Gln, and neutral Glu is isostructural and isoelectronic with Gln. Therefore, we have investigated several possible bases for the elevated Em's, including altered Fe electronic structure, altered active site electrostatics, altered H-bonding and altered redox-coupled proton transfer. Using EPR, MCD, and NMR spectroscopies, we find that the active site electronic structures of the two mutants resemble that of the WT enzyme, for both oxidation states, and Q69E-FeSOD's apparent deviation from WT-like Fe3+ coordination in the oxidized state can be explained by increased affinity for a small anion. Spontaneous coordination of an exogenous anion can only stabilize oxidized Q69E-Fe3+SOD and, therefore, cannot account for the increased Em of Q69E FeSOD. WT-like anion binding affinities and active site pK's indicate that His69 of Q69H-FeSOD is neutral in both oxidation states, like Gln69 of WT-FeSOD, whereas Glu69 appears to be neutral in the oxidized state but ionized in the reduced state of Q69E-FeSOD. A 1.1 A resolution crystal structure of Q69E-Fe2+SOD indicates that Glu69 accepts a strong H-bond from coordinated solvent in the reduced state, in contrast to the case in WT-FeSOD where Gln69 donates an H-bond. These data and DFT calculations lead to the proposal that the elevated Em of Q69E-FeSOD can be substantially explained by (1) relief from enforced H-bond donation in the reduced state, (2) Glu69's capacity to provide a proton for proton-coupled Fe3+ reduction, and (3) strong hydrogen bond acceptance in the reduced state, which stabilizes coordinated H2O. Our results thus support the hypothesis that the protein matrix can apply significant redox tuning via its influence over redox-coupled proton transfer and the energy associated with it.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21153851 A.J.Fielding, E.G.Kovaleva, E.R.Farquhar, J.D.Lipscomb, and L.Que (2011).
A hyperactive cobalt-substituted extradiol-cleaving catechol dioxygenase.
  J Biol Inorg Chem, 16, 341-355.
PDB codes: 3ojj 3ojk 3ojn 3ojt
19297238 K.L.Stone, and A.S.Borovik (2009).
Lessons from nature: unraveling biological CH bond activation.
  Curr Opin Chem Biol, 13, 114-118.  
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.  
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.