Rubredoxin

Rubredoxins are a class of low-molecular-weight iron-containing proteins found in sulfur-metabolizing bacteria and archaea. Sometimes rubredoxins are classified as iron-sulfur proteins; however, in contrast to iron-sulfur proteins, rubredoxins do not contain inorganic sulfide. Like cytochromes, ferredoxins and Rieske proteins, rubredoxins participate in electron transfer in biological systems.

Structure

The 3-D structures of a number of rubredoxins have been solved. The fold belongs to the α+β class, with 2 α-helices and 2-3 β-strands. Rubredoxin active site contains an iron ion which is coordinated by the sulfurs of four conserved cysteine residues forming an almost regular tetrahedron. This is sometimes denoted as a Fe-0Sor an Fe₁S₀ system, in analogy to the nomenclature for iron-sulfur proteins. While the vast majority of rubredoxins are soluble, there exists a membrane-bound rubredoxin, referred to as rubredoxin A, in oxygenic photoautotrophs.

Rubredoxins perform one-electron transfer processes. The central iron atom changes between the +2 and +3 oxidation states. In both oxidation states, the metal remains high spin, which helps to minimize structural changes. The reduction potential of a rubredoxin is typically in the range +50 mV to -50 mV.

This iron-sulphur protein is an electron carrier, and it is easy to distinguish its metallic centre changes: the oxidized state is reddish (due to a ligand metal charge transfer), while the reduced state is colourless (because the electron transition has an energy of the infrared level, which is imperceptible to the human eye).

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Rubredoxin in some biochemical reactions

* camphor 1,2-monooxygenase +)-camphor, reduced-rubredoxin:oxygen oxidoreductase (1,2-lactonizing)**(+)-bornane-2,5-dione + reduced rubredoxin + O₂ = 5-oxo-1,2-campholide + oxidized rubredoxin + H₂O
* alkane 1-monooxygenase (alkane, reduced-rubredoxin:oxygen 1-oxidoreductase)
**octane + reduced rubredoxin + O₂ = 1-octanol + oxidized rubredoxin + H₂O
* superoxide reductase (rubredoxin:superoxide oxidoreductase)
**reduced rubredoxin + superoxide + 2 H⁺ = rubredoxin + H₂O₂
* rubredoxin—NAD⁺ reductase (rubredoxin:NAD⁺ oxidoreductase)
**reduced rubredoxin + NAD⁺ = oxidized rubredoxin + NADH + H⁺
* rubredoxin—NAD(P)⁺ reductase (rubredoxin:NAD(P)⁺ oxidoreductase)
**reduced rubredoxin + NAD(P)⁺ = oxidized rubredoxin + NAD(P)H + H⁺

Electron transfer rate

The electron exchange rate is accurately determined by standard kinetics measurements of visible absorption (490 nm) spectra. The electron transfer rate has three parameters: electronic coupling, reorganization energy and free energy of reaction (Δ''G''°).

Protein mechanism and effects

The electron transfer reaction of rubredoxin is carried out by a reversible Fe³⁺/Fe²⁺ redox coupling by the reduction of Fe³⁺ to Fe²⁺ and a gating mechanism caused by the conformational changes of Leu41.

Upon the reduction of Fe³⁺ to Fe²⁺, the four Fe-S bond lengths increase and the amide-NH H-bonding to the S(Cys) become shortened. The reduced Fe²⁺ structure of rubredoxin results in a small increase in electrostatic stabilization of the amide-NH H-bonding to the S-Cys, leading to a lower reorganizational energy that allows faster electron transfer.

A gating mechanism involving the conformational change of the Leu41’s non-polar sidechain further stabilizes the Fe²⁺ oxidation state. A site-directed mutagenesis of Leu41 to Alanine shows a 50mV shift of the Fe^3+/2+redox potential. The substitution of the smaller CH₃ shows that the Leu41 side chain stabilizes the Fe²⁺ oxidation state more then the Fe³⁺ oxidation state. The X-ray structure in the reduced Fe²⁺ state shows the Leu41 side chain adopting two different conformations with 40% in a "open conformation" and 60% in a "closed conformation". The Leu41’s non-polar side chain controls access to the redox site by adopting either an open or closed conformation. In the reduced Fe²⁺ state, the Leu41 side-chain faces away from Cys 9 Sγ, exposing the Cys 9 Sγ and increasing the polarity of the Fe³⁺ /Fe²⁺ center. ^{/sup> The lower Fe2+ cation change of the reduced state leaves a higher negative charge on the Cys 9 Sγ-donor which attracts water strongly. As a result, water is able to penetrate and form H-bonds with the Cys 9 Sγ thiolate that blocks the gate from closing, resulting in an open conformation. In contrast, the oxidized Fe3+ state produces a less negatively charged Cys 9 Sγ-donor that does not attract the water strongly. Without H-bonding of the water to the Cys 9 Sγ, the gate remains closed. Thus, the conformation of Leu41 is determined by the presence of water and the oxidation state of rubredoxin. The proximity of water to the e(S-Cys)₄2- active site stabilizes the higher net negative charge of the Fe2+ oxidation state. The stabilization of the Fe2+ oxidation state shifts the reduction potential to a more positive E0 value.}

See also

* Bioinorganic chemistry
* Iron-sulfur protein
* Ferredoxin
* Cytochrome
* Rieske protein

References

Further reading

*
*

External links

* - X-ray structure of rubredoxin from ''Clostridium pasteurianum''
* - neutron diffraction structure of rubredoxin from ''Pyrococcus furiosus''
* {{InterPro, IPR001052 - InterPro entry for rubredoxin

A Little Iron-Sulfur Protein

Iron–sulfur proteins
Metalloproteins
Cofactors