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	PROSITE documentation PDOC00175 [for PROSITE entry PS51085]

2Fe-2S ferredoxin-type iron-sulfur binding domain signature and profile

Ferredoxins are small, acidic, electron transfer proteins that are ubiquitous in biological redox systems. They have either 4Fe-4S, 3Fe-4S, or 2Fe-2S cluster. Among them, ferredoxin with one 2Fe-2S cluster per molecule are present in plants, animals, and bacteria, and form a distinct 2Fe-Ferredoxin family [1,2]. They are proteins of around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This conserved region is also found as a domain in various metabolic enzymes.

Several structures of the 2Fe-2S ferredoxin domain have been determined (see for example <PDB:4FXC>) [3]. The domain is classified as a β-grasp which is characterized as having a β-sheet comprised of four β-strands and one α-helix flanking the sheet [4]. The two Fe atoms are coordinated tetrahedrally by the two inorganic S atoms and four cysteinyl S atoms.

Some proteins that contains a 2Fe-2S ferredoxin-type domain are listed below:

• Ferredoxin from photosynthetic organisms; namely plants and algae where it is located in the chloroplast or cyanelle; and cyanobacteria.
• Ferredoxin from archaebacteria of the Halobacterium genus.
• Ferredoxin IV (gene pftA) and V (gene fdxD) from Rhodobacter capsulatus.
• Ferredoxin in the toluene degradation operon (gene xylT) and naphthalene degradation operon (gene nahT) of Pseudomonas putida.
• Hypothetical Escherichia coli protein yfaE.
• The N-terminal domain of the bifunctional ferredoxin/ferredoxin reductase electron transfer component of the benzoate 1,2-dioxygenase complex (gene benC) from Acinetobacter calcoaceticus, the toluene 4-monooxygenase complex (gene tmoF), the toluate 1,2-dioxygenase system (gene xylZ), and the xylene monooxygenase system (gene xylA) from Pseudomonas.
• The N-terminal domain of phenol hydroxylase protein p5 (gene dmpP) from Pseudomonas Putida.
• The N-terminal domain of methane monooxygenase component C (gene mmoC) from Methylococcus capsulatus .
• The C-terminal domain of the vanillate degradation pathway protein vanB in a Pseudomonas species.
• The N-terminal domain of bacterial fumarate reductase iron-sulfur protein (gene frdB).
• The N-terminal domain of CDP-6-deoxy-3,4-glucoseen reductase (gene ascD) from Yersinia pseudotuberculosis.
• The central domain of eukaryotic succinate dehydrogenase (ubiquinone) iron- sulfur protein.
• The N-terminal domain of eukaryotic xanthine dehydrogenase.
• The N-terminal domain of eukaryotic aldehyde oxidase.

Three of the four conserved cysteines are clustered together in the same region of the protein. Our signature pattern spans that iron-sulfur binding region. We also developed a profile that covers the whole domain.

Note:

Ferredoxins from the adrenodoxin subfamily are slightly divergent and are not picked up by our pattern (but they are recognized by the profile). We have thus developed a second pattern specific for this subfamily (see <PDOC00642>).

Last update:

March 2005 / Text revised; profile added.

PROSITE methods (with tools and information) covered by this documentation:

2FE2S_FER_2, PS51085; 2Fe-2S ferredoxin-type iron-sulfur binding domain profile  (MATRIX)

• Sequences in UniProtKB/Swiss-Prot known to belong to this class: 459
  • detected by PS51085: 435 (true positives)
  • undetected by PS51085: 24 (14 false negatives and 10 'partials')
• Other sequence(s) in UniProtKB/Swiss-Prot detected by PS51085:
  NONE.
• Domain architecture view of Swiss-Prot proteins matching PS51085
  
• Retrieve an alignment of UniProtKB/Swiss-Prot true positive hits:
  Clustal format, color, condensed view  /  Clustal format, color  /  Clustal format, plain text  /  Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic distribution of all UniProtKB (Swiss-Prot + TrEMBL) entries matching PS51085
• Retrieve a list of all UniProtKB (Swiss-Prot + TrEMBL) entries matching PS51085
• Scan UniProtKB (Swiss-Prot and/or TrEMBL) entries against PS51085
• View ligand binding statistics of PS51085
• Matching PDB structures: 1A70 1AWD 1AYF 1B9R ... [ALL]

2FE2S_FER_1, PS00197; 2Fe-2S ferredoxin-type iron-sulfur binding region signature  (PATTERN)

• Consensus pattern:
  C-{C}-{C}-[GA]-{C}-C-[GAST]-{CPDEKRHFYW}-C
  The 3 C's are 2Fe-2S ligands
• Sequences in UniProtKB/Swiss-Prot known to belong to this class: 419
  • detected by PS00197: 286 (true positives)
  • undetected by PS00197: 133 (121 false negatives and 12 'partials')
• Other sequence(s) in UniProtKB/Swiss-Prot detected by PS00197:
  56 false positives and 1 unknown.
• Retrieve an alignment of UniProtKB/Swiss-Prot true positive hits:
  Clustal format, color, condensed view  /  Clustal format, color  /  Clustal format, plain text  /  Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic distribution of all UniProtKB (Swiss-Prot + TrEMBL) entries matching PS00197
• Retrieve a list of all UniProtKB (Swiss-Prot + TrEMBL) entries matching PS00197
• Scan UniProtKB (Swiss-Prot and/or TrEMBL) entries against PS00197
• View ligand binding statistics of PS00197
• Matching PDB structures: 1A70 1AWD 1CZP 1DOI ... [ALL]

1	Authors	Meyer J.
	Source	Trends Ecol. Evol. 3:222-226(1988).

2	Authors	Harayama S., Polissi A., Rekik M.
	Title	Divergent evolution of chloroplast-type ferredoxins.
	Source	FEBS Lett. 285:85-88(1991).
	PubMed ID	2065785

3	Authors	Fukuyama K., Ueki N., Nakamura H., Tsukihara T., Matsubara H.
	Title	Tertiary structure of [2Fe-2S] ferredoxin from Spirulina platensis refined at 2.5 A resolution: structural comparisons of plant-type ferredoxins and an electrostatic potential analysis.
	Source	J. Biochem. 117:1017-1023(1995).
	PubMed ID	8586613

4	Authors	Overington J.P.
	Source	Curr. Opin. Struct. Biol. 2:394-401(1992).

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