# Rubredoxin
**Rubredoxin** (abbreviation: Rd) is a small iron-sulfur protein, typically 45 to 55 amino acids long, in which a single iron ion is tetrahedrally coordinated by the sulfur atoms of four cysteine residues; it contains no acid-labile (inorganic) sulfur and functions as an electron carrier.[1](https://onlinelibrary.wiley.com/doi/10.1002/9781119951438.eibc0562) • [2](https://goldbook.iupac.org/terms/view/RT06793) The name derives from the red color of the protein, which was discovered in 1965.[3](https://edepot.wur.nl/201180)
| Key fact | Detail |
|---|---|
| Active site | One iron atom bonded to four cysteine sulfhydryl groups, the simplest of the iron-sulfur active centers[4](https://www.sciencedirect.com/science/chapter/edited-volume/abs/pii/B9780125152501500138) |
| Size | 45–55 amino acids; molar mass about 6000 Da[1](https://onlinelibrary.wiley.com/doi/10.1002/9781119951438.eibc0562) • [5](https://www.sciencedirect.com/science/article/abs/pii/S0010854513000313) |
| Ligand pattern | Two Cys-x-x-Cys-Gly loops; in sequence terms, two –C–x2–C– motifs separated by 20–30 residues[1](https://onlinelibrary.wiley.com/doi/10.1002/9781119951438.eibc0562) • [6](https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/rubredoxin) |
| Redox chemistry | High-spin Fe(III)/Fe(II) couple; potential typically about −0.06 V vs SCE, substantially higher than ferredoxins[7](https://web.stanford.edu/group/solomon/Publications_files/cr9500390.pdf) • [4](https://www.sciencedirect.com/science/chapter/edited-volume/abs/pii/B9780125152501500138) |
| EPR signature | Oxidized form shows the high-spin Fe(III) rhombic signal at g = 4.3; the reduced form gives no discernible EPR signal[8](https://iubmb.qmul.ac.uk/etp/etp5.html) |
| Distribution | Wide range of Archaea and Bacteria, only exceptionally in Eukarya[1](https://onlinelibrary.wiley.com/doi/10.1002/9781119951438.eibc0562) |
| Function | Electron transfer agent, notably in bacterial alkane hydroxylase systems[1](https://onlinelibrary.wiley.com/doi/10.1002/9781119951438.eibc0562) • [9](https://pmc.ncbi.nlm.nih.gov/articles/PMC134906/) |
## Structure
The polypeptide chain wraps around a single iron atom held by four cysteine thiolate ligands arranged in a distorted tetrahedron. The cysteines occur in two symmetry-related Cys-x-x-Cys-Gly loops, where x stands for residues other than cysteine.[1](https://onlinelibrary.wiley.com/doi/10.1002/9781119951438.eibc0562) The structure of rubredoxin from *Clostridium pasteurianum* has been determined at atomic resolution by [X-ray crystallography](https://www.edgepedia.org/x-ray-crystallography) (PDB code 1IRO), and rubredoxins have also been studied by neutron crystallography, optical spectroscopies, NMR, and other magnetic spectroscopies.[1](https://onlinelibrary.wiley.com/doi/10.1002/9781119951438.eibc0562)
Unlike ferredoxins, rubredoxins contain no inorganic sulfide; the iron is bound only by the protein's cysteine sulfur atoms. This absence of acid-labile sulfur (inorganic sulfide released by acid treatment) is part of the formal definition of the class.[2](https://goldbook.iupac.org/terms/view/RT06793) • [4](https://www.sciencedirect.com/science/chapter/edited-volume/abs/pii/B9780125152501500138) Variations of the canonical structure include lengthening one ligand loop to Cys-x-x-x-x-Cys, shortening it to Cys–Cys, and embedding the rubredoxin-type site in larger proteins containing more than one metal site.[1](https://onlinelibrary.wiley.com/doi/10.1002/9781119951438.eibc0562)
## Redox properties
The iron cycles between the +2 and +3 valence states, both high spin.[10](https://www.sciencedirect.com/topics/chemistry/iron-sulfur-protein) • [11](https://epgp.inflibnet.ac.in/epgpdata/uploads/epgp_content/S000005CH/P000670/M014821/ET/1515747056CHE_P15_M27_e-Text.pdf) The rubredoxin couple [Fe(S·Cys)4]1−/2− has a potential typically about −0.06 V vs SCE, far above the roughly −1.08 V (vs SCE, in acetonitrile) of the synthetic model complex [Fe(SEt)4]2−/2−, illustrating how strongly the protein environment tunes the potential of the same tetrahedral thiolate iron site.[7](https://web.stanford.edu/group/solomon/Publications_files/cr9500390.pdf) Reduction potentials at pH 7 that have been noted for the rubredoxins characterized to date are not exclusively negative; for example, [Clostridium](https://www.edgepedia.org/clostridium) pasteurianum rubredoxin has been reported at +31 mV versus the standard hydrogen electrode.[8](https://iubmb.qmul.ac.uk/etp/etp5.html) • [14](https://pmc.ncbi.nlm.nih.gov/articles/PMC1303563/) Compared with ferredoxins, which carry two or more iron atoms with labile sulfide and generally have low reduction potentials, rubredoxins have a substantially higher redox potential.[4](https://www.sciencedirect.com/science/chapter/edited-volume/abs/pii/B9780125152501500138)
## Function and occurrence
Rubredoxins act as electron transfer agents in a variety of redox processes, many of which remain to be fully characterized.[1](https://onlinelibrary.wiley.com/doi/10.1002/9781119951438.eibc0562) They are found across a wide range of Archaea and Bacteria but only exceptionally in Eukarya.[1](https://onlinelibrary.wiley.com/doi/10.1002/9781119951438.eibc0562)
**Alkane oxidation.** The best-defined role is in bacterial membrane-bound alkane hydroxylase systems, where rubredoxins are essential electron transfer components shuttling electrons from a flavoprotein reductase to the hydroxylase.[9](https://pmc.ncbi.nlm.nih.gov/articles/PMC134906/) In the alkane hydroxylase system of *Pseudomonas putida* GPo1, the ratio of the three components was found to be approximately 1:0.2:0.1 for alkane hydroxylase : Rd 2 (AlkG) : Rd reductase, and all alkane-degrading strains examined contain AlkG2-type rubredoxins able to replace the GPo1 Rd 2 in n-octane hydroxylation.[9](https://pmc.ncbi.nlm.nih.gov/articles/PMC134906/) A rubredoxin with two rubredoxin domains serves as an intermediate electron carrier in ω-hydroxylation of fatty acids.[12](https://www.sciencedirect.com/science/article/pii/S0010854599001575) Rubredoxin has also been reported as an electron acceptor of carbon monoxide dehydrogenase and pyruvate ferredoxin oxidoreductase in *Chlorobium tepidum*.[13](https://pmc.ncbi.nlm.nih.gov/articles/PMC4002152/)
## Related proteins and nomenclature
Simple iron-sulfur proteins fall into three groups: rubredoxins, ferredoxins, and other simple iron-sulfur proteins.[8](https://iubmb.qmul.ac.uk/etp/etp5.html) The {Fe(SγCys)4} core also occurs in larger proteins, and a family of related proteins includes flavorubredoxins, rubrerythrins, nigerythrins, desulfoferrodoxins, and desulforedoxins, the last a variant rubredoxin with somewhat higher symmetry and a distinctive EPR spectrum with g-values of 7.7, 4.1, and 1.8.[5](https://www.sciencedirect.com/science/article/abs/pii/S0010854513000313) • [8](https://iubmb.qmul.ac.uk/etp/etp5.html) In the IUBMB nomenclature, the rubredoxin center is designated [Rd], with formal charges [Rd]3+ and [Rd]2+ for the oxidized and reduced forms, and multiple centers written as n[Rd].[8](https://iubmb.qmul.ac.uk/etp/etp5.html)
## References
1. [Jacques Meyer and Jean-Marc Moulis (2011). Rubredoxin. Encyclopedia of Inorganic and Bioinorganic Chemistry, Wiley.](https://onlinelibrary.wiley.com/doi/10.1002/9781119951438.eibc0562)
2. [Rubredoxin, IUPAC Compendium of Chemical Terminology (Gold Book), RT06793.](https://goldbook.iupac.org/terms/view/RT06793)
3. [Studies on the Iron-Sulfur clusters, Wageningen University thesis (discovery of rubredoxin, 1965).](https://edepot.wur.nl/201180)
4. [Ferredoxin and Rubredoxin, Chapter 8, Microbial Iron Metabolism (1974), Elsevier.](https://www.sciencedirect.com/science/chapter/edited-volume/abs/pii/B9780125152501500138)
5. [Piero Zanello (2013). The competition between chemistry and biology in assembling iron-sulfur derivatives. Part I. {Fe(SγCys)4} proteins. Coordination Chemistry Reviews 257, 1777–1805.](https://www.sciencedirect.com/science/article/abs/pii/S0010854513000313)
6. [Iron-Sulfur Proteins, ScienceDirect Topics overview (primary structure patterns).](https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/rubredoxin)
7. [Solomon et al. (1996). Aspects of Metal Sites in Biology. Chemical Reviews 96, 2259.](https://web.stanford.edu/group/solomon/Publications_files/cr9500390.pdf)
8. [Nomenclature Committee of IUB, Nomenclature of Electron-Transfer Proteins, Section 5: Non-Heme Iron Proteins.](https://iubmb.qmul.ac.uk/etp/etp5.html)
9. [Rubredoxins Involved in Alkane Oxidation, PMC134906.](https://pmc.ncbi.nlm.nih.gov/articles/PMC134906/)
10. [Iron-Sulfur Protein, ScienceDirect Topics overview (chemistry).](https://www.sciencedirect.com/topics/chemistry/iron-sulfur-protein)
11. [Chemistry e-text: Classification of Iron-Sulfur Proteins, INFLIBNET e-PG Pathshala.](https://epgp.inflibnet.ac.in/epgpdata/uploads/epgp_content/S000005CH/P000670/M014821/ET/1515747056CHE_P15_M27_e-Text.pdf)
12. [Protein-bound iron-sulfur centers. Form, function, and assembly, Inorganic Chemistry (1999).](https://www.sciencedirect.com/science/article/pii/S0010854599001575)
13. [Metalloproteins Containing Cytochrome, Iron-Sulfur, or Copper Redox Centers, PMC4002152.](https://pmc.ncbi.nlm.nih.gov/articles/PMC4002152/)
14. [pmc.ncbi.nlm.nih.gov](https://pmc.ncbi.nlm.nih.gov/articles/PMC1303563/)
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*Topic: Encyclopedia › Life and health › Biological foundations › Biochemistry and metabolism › Enzyme classes and activities › Oxidoreductases, dehydrogenases, and cytochrome P450 › Electron-transfer partner proteins of oxidoreductases*
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