PROSITE documentation PDOC00176

4Fe-4S ferredoxin-type iron-sulfur binding domain signature and profile




Description

Ferredoxins [1] are a group of iron-sulfur proteins which mediate electron transfer in a wide variety of metabolic reactions. Ferredoxins can be divided into several subgroups depending upon the physiological nature of the iron-sulfur cluster(s). One of these subgroups are the 4Fe-4S ferredoxins, which are found in bacteria and which are thus often referred as 'bacterial-type' ferredoxins. The structure of these proteins [2] consists of the duplication of a domain of twenty six amino acid residues; each of these domains contains four cysteine residues that bind to a 4Fe-4S center.

Several structures of the 4Fe-4S ferredoxin domain have been determined (see for example <PDB:1FDN>) [3]. The clusters consist of two interleaved 4Fe- and 4S-tetrahedra forming a cubane-like structure, in such a way that the four iron occupy the eight corners of a distorted cube. Each 4Fe-4S is attached to the polypeptide chain by four covalent Fe-S bonds involving cysteine residues.

A number of proteins have been found [4] that include one or more 4Fe-4S binding domains similar to those of bacterial-type ferredoxins. These proteins are listed below:

  • The iron-sulfur proteins of the succinate dehydrogenase and the fumarate reductase complexes (EC 1.3.99.1). These enzyme complexes, which are components of the tricarboxylic acid cycle, each contain three subunits: a flavoprotein, an iron-sulfur protein, and a b-type cytochrome. The iron- sulfur proteins contain three different iron-sulfur centers: a 2Fe-2S, a 3Fe-3S and a 4Fe-4S.
  • Escherichia coli anaerobic glycerol-3-phosphate dehydrogenase (EC 1.1.99.5) This enzyme is composed of three subunits: A, B, and C. The C subunit seems to be an iron-sulfur protein with two ferredoxin-like domains in the N- terminal part of the protein.
  • Escherichia coli anaerobic dimethyl sulfoxide reductase. The B subunit of this enzyme (gene dmsB) is an iron-sulfur protein with four 4Fe-4S ferredoxin-like domains.
  • Escherichia coli formate hydrogenlyase. Two of the subunits of this oligomeric complex (genes hycB and hycF) seem to be iron-sulfur proteins that each contain two 4Fe-4S ferredoxin-like domains.
  • Methanobacterium formicicum formate dehydrogenase (EC 1.2.1.2). This enzyme is used by the archaebacteria to grow on formate. The β chain of this dimeric enzyme probably binds two 4Fe-4S centers.
  • Escherichia coli formate dehydrogenases N and O (EC 1.2.1.2). The β chain of these two enzymes (genes fdnH and fdoH) are iron-sulfur proteins with four 4Fe-4S ferredoxin-like domains.
  • Desulfovibrio periplasmic [Fe] hydrogenase (EC 1.18.99.1). The large chain of this dimeric enzyme binds three 4Fe-4S centers, two of which are located in the ferredoxin-like N-terminal region of the protein.
  • Methanobacterium thermoautrophicum methyl viologen-reducing hydrogenase subunit mvhB, which contains six tandemly repeated ferredoxin-like domains and which probably binds twelve 4Fe-4S centers.
  • Salmonella typhimurium anaerobic sulfite reductase (EC 1.8.1.-) [5]. Two of the subunits of this enzyme (genes asrA and asrC) seem to both bind two 4Fe-4S centers.
  • A Ferredoxin-like protein (gene fixX) from the nitrogen-fixation genes locus of various Rhizobium species, and one from the Nif-region of Azotobacter species.
  • The 9 Kd polypeptide of chloroplast photosystem I [6] (gene psaC). This protein contains two low potential 4Fe-4S centers, referred as the A and B centers.
  • The chloroplast frxB protein which is predicted to carry two 4Fe-4S centers.
  • An ferredoxin from a primitive eukaryote, the enteric amoeba Entamobea histolytica.
  • Escherichia coli hypothetical protein yjjW, a protein with a N-terminal region belonging to the radical activating enzymes family (see <PDOC00834>) and two potential 4Fe-4S centers.

The pattern of cysteine residues in the iron-sulfur region is sufficient to detect this class of 4Fe-4S binding proteins. The profile we developed covers the whole domain.

Note:

In some bacterial ferredoxins, one of the two duplicated domains has lost one or more of the four conserved cysteines. The consequence of such variations is that these domains have either lost their iron-sulfur binding property or bind to a 3Fe-3S center instead of a 4Fe-4S center.

Note:

The last residue of this pattern in most proteins belonging to this group, is a Pro; the only exceptions are the Rhizobium ferredoxin-like proteins which have Gly, and two Desulfovibrio ferredoxins which have Glu. It must also be noted that the three non 4Fe-4S-binding proteins which are picked-up by the pattern have Gly in this position of the pattern.

Last update:

April 2008 / Text revised; profile added.

Technical section

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

4FE4S_FER_2, PS51379; 4Fe-4S ferredoxin-type iron-sulfur binding domain profile  (MATRIX)

4FE4S_FER_1, PS00198; 4Fe-4S ferredoxin-type iron-sulfur binding region signature  (PATTERN)


References

1AuthorsMeyer J.
TitleThe evolution of ferredoxins.
SourceTrends Ecol. Evol. 3:222-226(1988).

2AuthorsOtaka E., Ooi T.
TitleExamination of protein sequence homologies: IV. Twenty-seven bacterial ferredoxins.
SourceJ. Mol. Evol. 26:257-267(1987).
PubMed ID3129571

3AuthorsDuee E.D., Fanchon E., Vicat J., Sieker L.C., Meyer J., Moulis J.M.
TitleRefined crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici at 1.84 A resolution.
SourceJ. Mol. Biol. 243:683-695(1994).
PubMed ID7966291

4AuthorsBeinert H.
TitleRecent developments in the field of iron-sulfur proteins.
SourceFASEB J. 4:2483-2491(1990).
PubMed ID2185975

5AuthorsHuang C.J., Barrett E.L.
TitleSequence analysis and expression of the Salmonella typhimurium asr operon encoding production of hydrogen sulfide from sulfite.
SourceJ. Bacteriol. 173:1544-1553(1991).
PubMed ID1704886

6AuthorsKnaff D.B.
TitleThe photosystem I reaction centre.
SourceTrends Biochem. Sci. 13:460-461(1988).



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