Nomenclature Committee of the International Union of Biochemistry (NC-IUB)

Nomenclature of Iron-Sulfur Proteins

Recommendations, 1978

Recommendations for the nomenclature of iron- sulfur proteins were formulated in 1971 and published in 1973 [l]. Since that time, a number of major contri- butions to the field have reported structure determina- tions by X-ray crystallography, elaboration of a series of model compounds, and the discovery of novel examples of these proteins. On the basis of the new information, it has become desirable to revise the nomenclature of the iron-sulfur proteins and thereby take into accounts the more precise description of known species while retaining flexibility for future discoveries. For this purpose. a group of experts’ was asked to construct proposals for the Nomencla- ture Committee of the International. Union of Bio- chemistry.

Wherever possible, terms that have gained wide acceptance have been retained and particular attention has been given to the development of a useful short- hand notation. However, in order to comply with the established rules for the nomenclature of inorganic compounds [2], it was necessary to make some changes from what is presently used in the biochemical literature’.

1. Proteins containing iron are divided into three groups: hemoproteins, iron-sulfur proteins, and other iron-containing proteins (Scheme 1). The last group includes ferritin, transferrin and the oxygenases. The term ‘iron-sulfur proteins’ refers only to those proteins in which a non-heme iron is ligated with inorganic sulfur or cysteine sulfur.

2. The iron-.&fir proteins (abbreviations: Fe-S proteins) are in two major categories: simple iron- sulfur proteins and complex iron-sulfur proteins. Simple’ need only be used when the difference from complex iron-sulfur proteins is emphasized. Simple iron-sulfur proteins contain only one or more Fe-S clusters2 whereas the complex proteins bear such addi- tional active groups as flavin or heme.

3. Simple iron-su&irproteins fall into three groups: rubredoxins, ferredoxins, and other (simple) iron- sulfur proteins (see Scheme 1).

3.1. Rubredoxins (abbreviation: Rd). This group comprises those iron-sulfur proteins without acid labile sulfur that are characterized by having iron in a typical mercaptide coordination, i.e. an iron center’ surrounded by four cysteine residues or sulfur-contain- ing ligands. More than one iron center of this type may exist in the molecule. Oxidized rubredoxin has a distinctive electron paramagnetic resonance (EPR) spectrum with a line at g = 4.3, whereas the reduced form gives no discernible EPR signal. Only negative redox potentials at pH 7 have been noted for those rubredoxins presently characterized.

The full name should be listed as follows: (source) rubredoxin (function), e.g. Pseudomonas oleovorans rubredoxin, alkane o-hydroxylation.

Document of the Nomenclature CommIttee of the Internattonal Union of Biochemistry. Comments on and suggestions for future revismns may be sent to any member of the committee: P. Karlson (Chairman). H. Bielka. B. L. Horecker, W B. Jakoby, B. Keil. C. LiCbecq (as Chairman of the IUB Committee of Editors of Bio- chemical Journals). B. Lindberg and E. C. Webb, or its secretary: H. B. F. Dixon. University Department of Biochemistry, Tennis Court Road. Cambridge, England, CB2- 1QW.

’ H. Bemert (Convener), R. Cammack. R. H. Helm. L. H. Jen- sen, J. Kraut. W. Lovenberg. W. H. Orme-Johnson. J. C. Rabino- wiu. and E. C. Slater.

’ According to these rules [2]. the Fe& or Fe& unit ofa 2.iron or 4-iron ferredoxm, respectively, is to be considered as the row sulfur cluster, thereby excluding the cystein residues lmked to the won In this sense then. rubredoxin does not contain an iron-sulfur cluster. merely an iron center. When the cluster charge is calculated, the exclusion of the cyst&e ligands makes it necessary to digress from present widespread use in btochemistry in that the charge of a 2-iron ferredoxin. e.g.. spinach ferredoxin, in its normally isolated ondized state is now (+2) Instead of (-2) and that of reduced spmach ferredoxin, (+ I) instead of (- 3). In inorganic nomencla- ture a ‘center’ is understood as a single atom to which ligands are attached, as It exists. for example, m rubredoxin. In the recent bio- chemical hterature. Iron-sulfur clusters of complex iron-sulfur pro- teins have been called ‘iron-sulfur centers’ in the sense of enzymatic or redox ‘active centers’ of these proteins. Although this use deviates from that established ininorganic chemistry, the use of ‘center 1.2. etc.’ of complex proteins in the sence of ‘active center’ as used in enzymology is sufficiently entrenched and reasonable that it may be contmued colloquially. However, the correct nomenclature would be ‘cluster I, 2, etc.

607

Reprinted from Eur. J. Biochem. 93, 427-430 (1979).

608 Nomenclature of Iron-Sulfur Protems

Iron-conlainmg protems

Iron-sulfur protan\ Other ran-contaming proteins

I----- --Lpp- ~/

Simple Iron-sulfur protems Complex iron-wlfur proteins

Rubredoxms FClTlXiOXlllS Other (simple) iron-sulfur proteins

;lm-, I

I-center Rd 2.cenkr Rd

I-- L-. ~~,

2 iron Fd 4 roi,, Fd

I-clustcl- Fd 2.clusw Fd I-clurter Fd 2.clurtel- Fd etc (2Fe;cluster) (2Fc clurter) (4Fe,cluster) (4Fe clwrr)

Iron-a;llfur Ravoproteins

3.2. Ferredosins (abbreviation: Fe). This group comprises those iron-sulfur proteins that contain an equal number of iron and labile-sulfur atoms and that exclusively display electron-carrier activity but not classical enzyme function. Thus, since hydrogenases (iron-sulfur proteins containing one or more Fe-S clusters) are enzymes, they are not classified as ferre- doxins.

The criterion that ferredoxins must have negative oxidation-reduction midpoint potentials at pH 7 has been abandoned; there is no need to distinguish between ferredoxins and the previously designated ‘high-potential iron-sulfur proteins’3 as exemplified

’ The group of ‘h&potential iron-sulfur proteins‘ has been deleted on the following barlr. (a) The three-ditnen~ional structure of the active center of thlr protem ha\ ken found to be e\\entiall) the same as that of ferredoxins 13.4). The magnetic properttes dilkr because the Fe-S clusters may assume three different oxidation levels [3,5]. Thus, an oxidized ferredoxin (diamagnetic) corresponds to the reduced Chromorium tdno.sum high-potential Iron-sulfur pro- tein (diamagnetic): the extreme oxidation levels. 1.e. those of reduced ferredoxin and oxidized C. vinosum high-potential Iron-sulfur pro- tein, have one electron more or one electron less. respectwely. than this oxidation level and are paramagnetlc. (b) After the original study [6] with the Clvomurium high-potential Iron-sulfur protein, It became apparent that other iron-sulfur proteins may have the unusual oxidation level of the Chromarium protein without a high midpoint oxidation-reduction potential (71. Conversely. ferredoxms wth the usual oxidation level and magnettc properties, may have high-mldpoint potent& (Xl. The expression. ‘htgh-potential FeS protem’ (or Hipip) has been used mcreasingly in the literature to indxzate the ablbty to form the higher oxidation level of the Clvvmu- urn protein. This practice is mappropnate since it uses a term applying to a redox potential for the description of a magnets property or an oxidatton level.

--7- --- 1 ~~~ in I--- 1 IrOn-WllLr Iron-sulfur IW-WlfUr OIhk

molybdenum molybdenum hemoflavo- protetns flavoprotelns proteins

by an iron-sulfur protein from C/r,omurium rinosum [6]. Ferredoxins may contain one or more clusters of two or four iron and labile-sulfur atoms.

3.3. All simple iron-sulfur proteins that are neither rubredoxins nor ferredoxins fall into the category of other iron-sulfur proteins.

SPECIFIC RECOMMENDATIONS, ABBREVIATIONS AND SYMBOLS

4. If any iron-sulfur protein has been given another name previously, this should be stated to minimize confusion.

5. The term, ‘high-potential iron-sulfur protein’ (abbreviated Hipip), may continue to be used for the original iron-sulfur protein of photosynthetic bacteria that had been given this name initially. Otherwise, the use of the terms Hipip or ‘high-potential Fe-S protein’ is discouraged ; there are ferredoxins occurring natu- rally at the oxidation level of oxidized and reduced spinach ferredoxin that have oxidation-reduction po- tentials as high as the original Hipip of bacteria.

6. At least once in a report, the source of the protein should precede the term rubredoxin, ferredoxin, or iron-sulfur protein. Similarly, for iron-sulfur clusters, or ‘centers” of complex iron-sulfur proteins, the proper designation of the parent protein or enzyme should be given, preferably along with the source, e.g. beef-heart NADH-dehydrogenase Fe-S cluster 1. Thereafter. the designation, cluster 1, may be used. The proliferation of such other abbreviations as center N-l, S-l. or bc-1 is discouraged. With regard to more

complex systems, including the complex iron-sulfur proteins, it appears to be neither suitable nor desirable to present designations for Fe-S clusters that are in- adequately characterized.

7. Iron-sulfur proteins from the same source that have the same type of Fe-S cluster are numbered sequentially with Roman numerals. A newly isolated iron-sulfur protein that is not fully characterized should be called ‘iron-sulfur protein’ and given the lowest unused numeral. By analogy, the various iron- sulfur clusters, or ‘centers’ of an iron-sulfur protein. should be designated Fe-S center 1 (or Fe-S cluster l), Fe-S center 2 (cluster 2), and so on in the order of discovery. Arabic numerals should be used for the different clusters of the same protein or complex, since iron-sulfur proteins and the complexes of the respira- tory chain are designated by Roman numerals.

8. The designation of a cluster’ in an iron-sulfur protein containing labile-sulfur atoms. should consist of square brackets about the number of iron and labile- sulfur atoms. Thus. [2Fe-2S] represents a two-iron.

two-labile-sulfur cluster and [4Fe-4S]. B four-iron. four-labile-sulfur clusterJ. The protein incorporating such a cluster may be called a ‘two-iron-two-sulfur’ or ‘four-iron-four-sulfur‘ ferredoxin or iron-sulfur protein. For ferredoxins, it is sufficient simply to refer to a ‘two-iron’ or ‘four-iron’ ferredoxin.

C‘omn~cr~/. The use of hyphens and parentheses is firmly codified in the nomenclature of inorganic chem- istry [2]. In order to avoid confusion with established practices in coordination chemistry. a short hyphen is used to write Fe-S and the term is placed between square brackets instead of parentheses.

9. The presence of several clusters. as in clostridial ferredoxin, is indicated as follows: 2[4Fe-4S]. This may be called a two-cluster four-iron four-sulfur ferredoxin or iron-sulfur protein or, simply, a two- cluster-four-iron ferredoxin.

10. When the formal charge of the cluster is calcu- lated, the sulfur atoms of the bound cysteine residues are no/ included in the calculation. contrary to the widespread practice in the current literature. Thus. for the oxidized and reduced forms. respectively. we have :

Spmach ferredoun [Fe-31’ ’ [2Fc-2SJ’ Bm I//!/$ ~wll I,I,‘,u ferredoxm (4Fe-4S]’ ’ [4Fe-4S]’ ’ ~%l\rrldwlt pn,/l~u~klllrrrlr f~rredmwl 2[4Fc-4S]’ ’ ?[4Fe-4SJ’ *

(hmmmt. The charges referred to are those within the entire cluster. This is in contrast with usage in inorganic chemistry where a charge shown in a formula refers to the whole compound [2]. There is also a possi- bility for misunderstanding the codified use of the term, oxidation state. which always characterizes a single atom but never a group of atoms [2]. In order

a In Ilngh\h lhey would he pronounced a\ ‘IV,,>-eke-IW-e,‘ and ‘four-ef-ee-four-e,‘.

to avoid confusion, the term, ‘oxidation level’ is used to refer io the cluster.

1 I. For ferredoxins at the oxidation level typical of C’hromtrtium Hipip, the expression, [4Fe-4S]” +,

will differentiate between what was formerly called Hipip and a ferredoxin.

12. If the oxidation levels in which a ferredoxin can occur are known, this may be indicated as follows for a [4Fe-4S] ferredoxin that is generally obtained on isolation at the (2 +) level: [4Fe-4S]“‘J’~*‘.“‘. This designation implies that the ferredoxin can occur at all three possible oxidation levels. However, these designations should only be used to refer to oxidation levels that can be reached in a biological milieu, i.e.. in the absence of agents denaturing the protein. even though artificial oxidants may be used to attain such oxidation levels. By this designation, the highest oxi- dation levels normally found in Cllromatium Hipip and the protein from Buc,i//u.~po!,,n?~,.\-u. both [4Fe-4S] ferredoxins. may be differentiated:

(‘Ill 1~,>1~,,,!,,?1 I,,,, ~,1,,>, HIpIp ,4ke.4S]’ + C.! + 1 *

Bm 1//11\ /‘1’/‘1~1, \(I fc!rredoiln [jke.jS]’ f 12 + I )

This shorthand denotes that C‘h,-omcr/iu~~~ ferre- doxin occurs in the reduced (3 +) state but also can be

found at the (2+ ) state whereas B. /JCJ/&?I~‘YCI ferre- doxin occurs in the oxidized (2 +) state. has not been found in the (3 +) but can exist in the (1 +) state. The (2+) state is diamagnetic. whereas both the (3+) and (1 +) states are paramagnetic and detectable by EPR measurements. It is recommended that the desig- nation for the oxidation level. whether (3 +). (2 +) or (1 +), when used in a publication, should be that occurring in the experiments described. In spoken language. such terms as reduced, oxidized, and super-

~‘l~~.rrrdrun~ pu~fcwriumm 2[4Fe-4S]‘+ Fd or. I” a \pecxtic ConteY,. 2[4Fe-4S]” ” + ’ t ‘Fd

610 Nomenclature of Iron-Sulfur Protems

reduced may be used during a transition period; the formal charge designations should be used when the new recommendations become familiar.

13. Rubredoxins are treated in an analogous fashion, except that the basic center is designated [Rd] since there is no ambiguity concerning numbers of metal atoms involved. Rubredoxins with multiple clusters are denoted as n[Rd]. The formal charges of rubredoxins are [Rd]‘+ and [Rd]” for the oxidized and reduced forms, respectively.

14. It is useful to present midpoint redox potentials, light-absorption and EPR characteristics, particularly when an iron-sulfur protein is first mentioned in a publication.

15. The examples given in Table 1 illustrate and contrast the new designations with those previously applied.

Iron-sulfur proteins with clusters of different types may be designated in a similar manner. For instance, a protein from Azofobacter vine/andii [7] has two Fe-S clusters which assume the same range of oxidation

levels, although one is found ‘reduced’ and the other ‘oxidized’: [4Fe-4S]” @+.‘+)[4Fe-4S13+ @+.‘+)Fd I.

REFERENCES I. IUPAC-IUB Commission on Blochernial Nomenclature (1973)

Eur. J. Biwhem. 35, I ~ 2, and J. Bd. Chem. 248, 5907 -590X. 2. International Umon of Pure and Applied Chemistry (1970)

Nomenrlarur~ f>f Inor~anrc Chrmrstry. 2nd edn. Butterworths. London.

3. Carter. C. W., Jr, Kraut. J , Freer. S. T, Alden. R A., Slekrr, L. C.. Adman, E. & Jensen, L. H. (1972) Pro<. Nurl Aad. .%I. U S.A. 69. 3526-3529.

4. Carter, C W.. Jr, Kraut. 1.. Freer, S T. & Alden, R. A. (1974) J. Bid Chrm. 249, 6339-6346.

5. Herskowtz. T.. Aver~ll. B.A. Holm. R. H.. Ibers. J. A.. Phll- bps. W. D. & Weiher. J F. (1972) Proc. Nurl Am/ SC; l’S.A.69 2347-2441

6. Bartsch. R. G (1963) tn Bucrrwal Phora~ynrhrw (Gest. H.. San Pletro. A. & Vernon, L. P., eds) p. 315. Antloch Press. Yellow Sprmgs. Ohlo

7 Sweeney, W. V.. Rahinowitz. J. C & Yoch, D C. (1975) J. Bd. chlw7. 250. 7x42 - 7847

X. Laph. J. S., Jr & Frcclnska, M (1975) Bwc~hwn Biophj,.s. Ac,ru. 3X7. 95 106.