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Last modified: 11 February 1999

Bacterial­type mono­, di­ and polycluster ferredoxins
Iron-sulphur cluster Formal oxidation states
Fe4S4 image
[Fe4S4](SgammaCys)4
[Fe4S4]+; [Fe4S4]2+
[Fe4S4]Cys3COOH image
[Fe4S4](SgammaCys)3OdeltaAsp
[Fe4S4]+; [Fe4S4]2+
Fe3S4 image
[Fe3S4](SgammaCys)3
[Fe3S4]2-; [Fe3S4]0; [Fe3S4]+

Ferredoxins [1, 2] are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s). One group, originally found in bacteria, has been termed `bacterial­type', in which the active centre is a [Fe4S4] cluster. Bacterial­type ferredoxins may in turn be subdivided into further groups, based on their sequence properties [2]. Most contain at least one conserved domain, including four cysteine residues that bind to a [Fe4S4] centre. In Pyrococcus furiosus [Fe4S4] ferredoxin, one of conserved Cys residues is substituted with aspartic acid [3].

During the evolution of bacterial­type ferredoxins, intrasequence gene duplication, transposition and fusion events occurred [2], resulting in the appearance of proteins with multiple iron-sulphur centres, e.g., dicluster­type (2×[Fe4S4]) polyferredoxins; iron-sulphur subunits of bacterial succinate dehydrogenase / fumarate reductase; formate hydrogenlyase and formate dehydrogenase complexes; pyruvate­flavodoxin oxidoreductase; NADH:ubiquinone reductase and others. In some bacterial ferredoxins, one of the duplicated domains has lost one or more of the four conserved Cys residues. These domains have either lost their iron-sulphur binding property, or bind to a [Fe3S4] centre instead of a [Fe4S4] centre.
. . .
. . .
fusion
fusion
|
|
[Fe4S4]
duplication
2×[Fe4S4]
duplication
n×(2×[Fe4S4])
|
|
Cys loss
Cys loss
[Fe3S4]
[Fe3S4]+[Fe4S4]

3­D structures are now known both for a number of monocluster­type [4] and dicluster­type [5] Fe4S4 ferredoxins. The fold belongs to the alpha+ß class, with 2-7 alpha­helices and four ß­strands forming a barrel­like structure, and an extruded loop containing three "proximal" cysteinyl residues of the iron-sulphur cluster: 

                             I II III
                      +H3N---C--C--C.
                              \ | /  |
                              [FeS]  |
                                  \  |        
                      ¯OOC---------C'
                                   IV
In dicluster ferredoxins, which have arisen via duplication of ancestral bacterial­type ferredoxin, the iron-sulphur clusters are related according to the following scheme: 
                          I II III  IV 
                  +H3N----C--C--C---C----.
                           \ | /   /      |
                           [FeS] [FeS]    |
                             /   / | \    |        
                  ¯OOC------C---C--C--C--'
                           IV' III'II'I'
i.e. "distal" cysteines binding the iron-sulphur clusters are "swapped".

A number of oxidoreductases contain redox domains similar to bacterial­type ferredoxins, including the iron-sulphur proteins of the succinate dehydrogenase and the fumarate reductase complexes, enzymes of the dimethylsulphoxide reductase family and Fe hydrogenases.

Bacterial­type ferredoxins in motif databases

PRINTS ID PRINTS AC PROSITE/BLOCKS ID PROSITE AC BLOCKS AC
3FE4SFRDOXIN PR00352
-
-
-
4FE4SFRDOXIN PR00353 4FE4S_FERREDOXIN PS00198 BL00198
7FE8SFRDOXIN PR00354

Bacterial­type ferredoxins in alignment databases

Protein Superfamily Protein Homology Domain Pfam LPFC 3­D
alignment
00030; ferredoxin 2[4Fe-4S]
00031; polyferredoxin 6×2[4Fe-4S]
00101; fumarate reductase Fe-S protein 		00121; ferredoxin 2[4Fe-4S]
PF00037; fer4
fer4

Bacterial­type ferredoxins in 3­D databases

All bacterial­type (Fe4S4 / Fe3S4) ferredoxins contain one or several cubane­like iron-sulphur prosthetic groups:

PDB scop BSM RELI
Base		 Header MMS Abstract ¹
1a6l#
-
 1a6l# 1a6l# Ferredoxin (FdI) (T14C mutant); Azotobacter vinelandii, strain JG100
-
1axq#
-
 1axq# 1axq# Ferredoxin (FdI) (partially oxidised); Azotobacter vinelandii, strain JG100
-
1b0t#
-
 1b0t#
-
#		 Ferredoxin (FdI) (D15K, K84D mutant); Azotobacter vinelandii, strain DJ138/PBS3A1
-
1bc6#
-
 1bc6#
-
 Ferredoxin (oxidised); Bacillus schlegelii, strain ATCC 43741 (recombinant form expressed in Escherichia coli)
-
1bd6#
-
 1bd6#
-
 Ferredoxin (oxidised); Bacillus schlegelii, strain ATCC 43741 (recombinant form expressed in Escherichia coli)
-
1blu 1blu 1blu 1blu Ferredoxin; Chromatium vinosum
-
1bqx
-
 1bqx
-
 Ferredoxin (D13C mutant, artificial [Fe8S8] ferredoxin); Bacillus schlegelii, strain ATCC 43741 (recombinant form expressed in Escherichia coli)
-
1bwe
-
 1bwe
-
 Ferredoxin (D13C mutant, artificial [Fe8S8] ferredoxin); Bacillus schlegelii, strain ATCC 43741 (recombinant form expressed in Escherichia coli)
-
1clf 1clf 1clf 1clf Ferredoxin; Closridium pasteurianum MS6HK14
1dax×
-
 1dax×
-
 Ferredoxin I (oxidised); Desulfovibrio africanus, strain Benghazi
-
1dfd×
-
 1dfd×
-
 Ferredoxin I (oxidised); Desulfovibrio africanus, strain Benghazi
-
1fca 1fca 1fca 1fca Ferredoxin; Closridium acidiurici MS6LBC23
1fd2# 1fd2# 1fd2# 1fd2# Ferredoxin (C20A mutant); Azotobacter vinelandii
-
1fda# 1fda# 1fda# 1fda# Ferredoxin (oxidised) (pH 6); Azotobacter vinelandii
-
1fdb# 1fdb# 1fdb# 1fdb# Ferredoxin (reduced) (pH 6); Azotobacter vinelandii
-
1fdc# 1fdc# 1fdc# 1fdc# Ferredoxin (reduced) (pH 8); Azotobacter vinelandii
-
1fdd# 1fdd# 1fdd# 1fdd# Ferredoxin (D15N mutant); Azotobacter vinelandii
-
1fdn 1fdn 1fdn 1fdn Ferredoxin; Clostridium acidurici MS5PD7
1fdx 1fdx 1fdx 1fdx Ferredoxin; Peptococcus aerogenes
-
1fer# 1fer# 1fer# 1fer# Ferredoxin I (pH 6.5); Azotobacter vinelandii
-
1frh# 1frh# 1frh# 1frh# Ferredoxin (FdI) (F2Y mutant); Azotobacter vinelandii, strain JG100
-
1fri# 1fri# 1fri# 1fri# Ferredoxin (FdI) (D23N mutant); Azotobacter vinelandii, strain JG100
-
1frj# 1frj# 1frj# 1frj# Ferredoxin (FdI) (F25I mutant); Azotobacter vinelandii, strain JG100
-
1frk# 1frk# 1frk# 1frk# Ferredoxin (FdI) (H35D mutant); Azotobacter vinelandii, strain JG100
-
1frl# 1frl# 1frl# 1frl# Ferredoxin (FdI) (E38S mutant); Azotobacter vinelandii, strain JG100
-
1frm# 1frm# 1frm# 1frm# Ferredoxin (FdI) (E46A mutant); Azotobacter vinelandii, strain JG100
-
1frx# 1frx# 1frx# 1frx# Ferredoxin (FdI) (C20S mutant); Azotobacter vinelandii, strain JG100
-
1ftc# 1ftc# 1ftc# 1ftc# Ferredoxin (FdI) (Y13C [cysteine persulphide] mutant); Azotobacter vinelandii, strain JG100
-
1fxd* 1fxd* 1fxd* 1fxd* Ferredoxin II (modified Cys­11); Desulfovibrio gigas
-
1fxr× 1fxr× 1fxr× 1fxr× Ferredoxin I (complex with sulphate); Desulfovibrio africanus, strain Benghazi MS5MM13×
1rof× 1rof× 1rof× 1rof× Ferredoxin; Thermatoga maritima MS7KSC19×
1vjw× 1vjw× 1vjw× 1vjw× Ferredoxin; Thermatoga maritima MS7MMC14×
1xer* 1xer* 1xer*
-
 Ferredoxin (contains N­methyl­Lys­29) (complex with Zn2+); Sulfolobus acidocaldarius MS7MB5*
2fd2# 2fd2# 2fd2# 2fd2# Ferredoxin (C24A mutant); Azotobacter vinelandii
-
2fxb× 2fxb× 2fxb× 2fxb× Ferredoxin; Bacillus thermoproteolyticus
-
5fd1# 5fd1# 5fd1# 5fd1# Ferredoxin (oxidised) (pH 8); Azotobacter vinelandii
-
6fd1#
-
 6fd1#
-
 Ferredoxin (100 K, pH 8); Azotobacter vinelandii
-
6fdr#
-
 6fdr#
-
 Ferredoxin (sodium dithionite reduced) (100 K, pH 8.5); Azotobacter vinelandii
-
7fd1#
-
 7fd1#
-
 Ferredoxin (100 K, pH 8.5); Azotobacter vinelandii
-
7fdr#
-
 7fdr#
-
 Ferredoxin (sodium dithionite reduced) (100 K, pH 8.5); Azotobacter vinelandii
-
-
-
-
-
 Ferredoxin [Fe4S4]; Thermococcus litoralis MS7KSC23×

¹ Macromolecular Structures abstract. Full text is available to BioMedNet Members

References

  1. Otaka, E. and Ooi, T. (1989) Examination of protein sequence homologies: V. New perspectives on evolution between bacterial and chloroplast­type ferredoxins inferred from sequence evidence. J. Mol. Evol. 29, 246-254.
  2. George, D.G., Hunt, L.T., Yeh, L.S. and Barker, W.C. (1985) New perspectives on bacterial ferredoxin evolution. J. Mol. Evol. 22, 20-31.
  3. Zhou, Z.­H. and Adams, M.W.W. (1997) Site­directed mutations of the 4Fe­ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus: Role of the cluster­coordinating aspartate in physiological electron transfer reactions. Biochemistry 36, 10892-10900.
  4. Fukuyama, K., Matsubara, H., Tsukihara, T. and Katsube, Y. (1989) Structure of [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus refined at 2.3 Å resolution. Structural comparisons of bacterial ferredoxins. J. Mol. Biol. 210, 383-398.
  5. Duée, E.D., Fanchon, E., Vicat, J., Sieker, L.C., Meyer, J. and Moulis, J.­M. (1994) Refined crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici at 1.84 Å resolution. J. Mol. Biol. 243, 683-695.
Bibliography on structural studies of bacterial­type ferredoxins
Reviews on bacterial­type ferredoxins