Rubredoxin

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 [1Fe-0S] or 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.{{cite journal | vauthors = Calderon RH, García-Cerdán JG, Malnoë A, Cook R, Russell JJ, Gaw C, Dent RM, de Vitry C, Niyogi KK | display-authors = 6 | title = A conserved rubredoxin is necessary for photosystem II accumulation in diverse oxygenic photoautotrophs | journal = The Journal of Biological Chemistry | volume = 288 | issue = 37 | pages = 26688–26696 | date = September 2013 | pmid = 23900844 | pmc = 3772215 | doi = 10.1074/jbc.M113.487629 | doi-access = free }}

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).

:Image:Rubredoxin.svg{{clear-left}}

• {{EC number|1.14.15.2}} 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
• {{EC number|1.14.15.3}} alkane 1-monooxygenase (alkane, reduced-rubredoxin:oxygen 1-oxidoreductase)
• octane + reduced rubredoxin + O₂ = 1-octanol + oxidized rubredoxin + H₂O
• {{EC number|1.15.1.2}} superoxide reductase (rubredoxin:superoxide oxidoreductase)
• reduced rubredoxin + superoxide + 2 H⁺ = rubredoxin + H₂O₂
• {{EC number|1.18.1.1}} rubredoxin—NAD⁺ reductase (rubredoxin:NAD⁺ oxidoreductase)
• reduced rubredoxin + NAD⁺ = oxidized rubredoxin + NADH + H⁺
• {{EC number|1.18.1.4}} rubredoxin—NAD(P)⁺ reductase (rubredoxin:NAD(P)⁺ oxidoreductase)
• reduced rubredoxin + NAD(P)⁺ = oxidized rubredoxin + NAD(P)H + H⁺

The electron exchange rate is accurately determined by standard kinetics measurements of visible absorption (490 nm) spectra.{{cite journal | vauthors = Jacks CA, Bennett LE, Raymond WN, Lovenberg W | title = Electron transport to clostridial rubredoxin: kinetics of the reduction by hexaammineruthenium(II), vanadous and chromous ions | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 71 | issue = 4 | pages = 1118–1122 | date = April 1974 | pmid = 4524621 | pmc = 388174 | doi = 10.1073/pnas.71.4.1118 | doi-access = free | bibcode = 1974PNAS...71.1118J }} The electron transfer rate has three parameters: electronic coupling, reorganization energy and free energy of reaction (ΔG°).

File:Iron_Site_of_Clostridium_pasteurianum.png

File:Leu41_Reduced_Conformation.png

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.{{cite journal | vauthors = Min T, Ergenekan CE, Eidsness MK, Ichiye T, Kang C | title = Leucine 41 is a gate for water entry in the reduction of Clostridium pasteurianum rubredoxin | journal = Protein Science | volume = 10 | issue = 3 | pages = 613–621 | date = March 2001 | pmid = 11344329 | pmc = 2374124 | doi = 10.1110/gad.34501 }}

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.{{cite journal | vauthors = Park IY, Youn B, Harley JL, Eidsness MK, Smith E, Ichiye T, Kang C | title = The unique hydrogen bonded water in the reduced form of Clostridium pasteurianum rubredoxin and its possible role in electron transfer | journal = Journal of Biological Inorganic Chemistry | volume = 9 | issue = 4 | pages = 423–428 | date = June 2004 | pmid = 15067525 | doi = 10.1007/s00775-004-0542-3 }} The substitution of the smaller CH₃ shows that the Leu41 side chain stabilizes the Fe²⁺ oxidation state more than 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. ^[1] 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 [Fe(S-Cys)₄] ^2- 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.

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

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• {{cite book | first1 = Stephen J. | last1 = Lippard | first2 = Jeremy M. | last2 = Berg | name-list-style = vanc | title = Principles of Bioinorganic Chemistry | publisher = University Science Books | year = 1994 | isbn = 978-0-935702-72-9 }}
• {{cite book | first1 = J.J.R. | last1 = Fraústo da Silva | first2 = R.J.P. | last2 = Williams | name-list-style = vanc | title = The biological chemistry of the elements: The inorganic chemistry of life | edition = 2nd | publisher = Oxford University Press | year = 2001 | isbn = 978-0-19-850848-9 }}

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• {{PDB|1IRO}} – X-ray structure of rubredoxin from Clostridium pasteurianum
• {{PDB|1VCX}} – Neutron diffraction structure of rubredoxin from Pyrococcus furiosus
• {{InterPro|IPR001052}} – InterPro entry for rubredoxin
• [http://faculty.washington.edu/stenkamp/rubre.html A little iron-sulfur protein]

Category:Iron–sulfur proteins

Category:Metalloproteins

Category:Cofactors