PDBsum entry 2bkb

Oxidoreductase

PDB id: 2bkb

Contents

Protein chains

192 a.a. *

Metals

FE2 ×4

Waters ×629

* Residue conservation analysis

PDB id:

2bkb

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

Resolution:

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

Date:

14-Feb-05 Release date: 03-Jan-07

Protein chains

P0AGD3  (SODF_ECOLI) -  Superoxide dismutase [Fe] from Escherichia coli (strain K12)

Seq: 193 a.a.

Struc: 192 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.15.1.1 - superoxide dismutase.
• Reaction: 2 superoxide + 2 H⁺ = H2O2 + O2
• Cofactor: Fe cation or Mn(2+) or (Zn(2+) and Cu cation)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

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.

ABSTRACT

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.