Nomenclature of iron-sulfur proteins Recommendations, 1978

101

Biochimica et Biophysica Acta, 549 (1979) 101-105 Elsevier/North-Holland Biomedical Press

NOMENCLATURE OF IRON-SULFUR PROTEINS

RECOMMENDATIONS, 1978

NOMENCLATURE COMMITTEE OF THE INTERNATIONAL UNION OF BIOCHEMISTRY (NC-IUB)

R e c o m m e n d a t i o n s for the n o m e n c l a t u r e o f iron-sulfur proteins were f o r m u l a t e d in 1971 and published in 1973 [1]. Since that time, a n u m b e r o f major c o n t r i b u t i o n s to the field have reported structure d e t e r m i n a t i o n s by X-ray crystallography, elaboration o f a series o f m o d e l c o m p o u n d s , and the discovery o f novel examples o f these proteins. On the basis o f the new i n f o r m a t i o n , it has b e c o m e desirable to revise the n o m e n c l a t u r e o f the iron-sulfur proteins and thereby take into account the m o r e precise description o f k n o w n species while retaining flexibility for future discoveries. For this purpose, a group o f experts * was asked to c o n s t r u c t proposals for the N o m e n c l a t u r e C o m m i t t e e o f the International U n i o n o f Biochemistry. Wherever possible, terms that have gained wide acceptance have been retained and particular a t t e n t i o n has been given to the d e v e l o p m e n t o f a useful shorthand n o t a t i o n . However, in order to c o m p l y w i t h the established rules for the n o m e n c l a t u r e o f inorganic c o m p o u n d s [2], it was necessary to make some changes from w h a t is presently used in the biochemical literature ** Document of the Nomenclature Committee of the International Union of Biochemistry. Comments on and suggestions for future revisions may be sent to any member of the committee: P. Karlson (Chairman), H. Bielka, B.L. Horecker, W.B. Jakoby, B. Keil, C. Li~becq (as Chairman of the IUB Committee of Editors of Biochemical 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. Beinert (Convener) R. Cammack, R.H. Holm, L.H. Jensen, J. Kraut, W. Lovenberg, W.H. OrmeJohnson, J.C. Rabinowitz, and E.C. Slater. ** According to these rules [2], the Fe2S 2 or Fe4S4 unit of a 2-iron or 4-iron ferredoxin, respectively, is to be considered as the iron-sulfur cluster, thereby excluding the cysteine residueslinked to the iron. 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 cysteine ligands makes it necessary to digress from present widespread use in biochemistry in that the charge of a 2-iron ferredoxin, e.g., spinach ferredoxin, in its normally isolated oxidized state is now (+2) instead of ( - 2 ) and that of reduced spinach ferredoxin, (+1) instead of (-3). In inorganic nomenclature a 'center' is understood as a single atom to which ligands are attached, as it exists, for example, in rubredoxin. In the recent biochemical literature, iron-sulfur clusters of complex iron-sulfur proteins 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 in inorganic chemistry, the use of 'center 1, 2, etc.' of complex proteins in the sense of 'active center' as used in enzymology is sufficiently entrenched and reasonable that it may be continued colloquially. However, the correct nomenclature would be 'cluster 1, 2, etc.'

102 Iron-containing proteins

[ Hemoproteins

Iron-sulfur proteins l. . . . . . . . . .

r

Simple iron-sulfur proteins

7---'

.....

Rubredoxins

1........

~

Ferredoxins

Other (simple) kon-sulfur proteins

] 2-center Rd F 2 iron Fd

7-

I

i

Complex iron-sulfur proteins

/

I 1-center Rd

Other iron-containing proteins

1 4 iron Fd

F

F

I

I

1-cluster Fd 2-cluster Fd 1-cluster Fd 2-cluster Ed etc. (2Fe/cluster) (2Fe/cluster) (4Fe/cluster)(4Fe/cluster) Iron-sulfur flavoproteins

Iron-sulfur molybdenum pro teins

Iron-sulfur molybdenum flavoproteins

1

Iron-sulfur hemoflavoproteins

1

Others

SCHEME I. Iron-containing proteins

1. Proteins containing iron are divided into three groups: hemoproteins, iron-sulfur proteins, and other iron-containing proteins (Scheme I). 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-sulfur 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 clusters (see footnote ** on p. 1) whereas the complex proteins bear such additional active groups as flavin or heme. 3. Simple iron-sulfur proteins fall into three groups: rubredoxins, ferredoxins, and other (simple) iron-sulfur proteins (see Scheme I). 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 (see footnote ** on p. 1) surrounded by four cysteine residues or sulfur-containing 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. Pseudornonas oleovorans rubredoxin, alkane a>hydroxylation. 3.2. Ferredoxins (abbreviation: Fd). 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

103 (iron-sulfur proteins containing one or more Fe-S clusters) are enzymes, they are not classified as ferredoxins. 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' * as exemplified by an ironsulfur protein from Chromatium vinosum [6]. Ferredoxins may contain one or more clusters o f 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 o f 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 o f photosynthetic bacteria that had been given this name initially. Otherwise, the use o f the terms Hipip or 'high-potential Fe-S protein' is discouraged; there are ferredoxins occurring naturally at the oxidation level o f oxidized and reduced spinach ferredoxin that have oxidation-reduction potentials as high as the original Hipip o f bacteria. 6. At least once in a report, the source o f the protein should precede the term rubredoxin, ferredoxin, or iron-sulfur protein. Similarly, for iron-sulfur clusters, or 'centers' (see footnote ** on p. 1) o f complex iron-sulfur proteins, the proper designation o f the parent protein or enzyme should be given, preferably along with the source, e.g. beefheart NADH-dehydrogenase Fe-S cluster 1. Thereafter, the designation, cluster 1, may be used. The proliferation o f 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 inadequately characterized. 7. Iron-sulfur proteins from the same source that have the same type o f 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' o f an iron-sulfur protein, should be designated Fe-S center 1 (or Fe-S cluster 1), Fe-S center 2 (cluster 2), * The group of 'high-potential iron-sulfur proteins' has been deleted on the following basis: (a) The three-dimensional structure of the active center of these proteins has been found to be essentially the same as that of ferredoxins [3,4]. The magnetic properties differ because the Fe-S clusters may assume three different oxidation levels [3,5]. Thus, an oxidized ferredoxin (diamagnetic) corresponds to the reduced Chromatium vinosum high-potential iron-sulfur protein (diamagnetic): the extreme oxidation levels, i.e. those of reduced ferredoxin and oxidized C. vinosum high-potential iron-sulfur protein, have one electron more or one electron less, respectively, than this oxidation level and are paramagnetic. (b) After the original study [6] with the Chrornatium high-potential iron-sulfur protein, it became apparent that other iron-sulfur proteins may have the unusual oxidation level of the Chromatium protein without a high midpoint oxidation-reduction potential [7]. Conversely, ferredoxins with the usual oxidation level and magnetic properties may have highmidpoint potentials [8]. The expression, 'high-potential Fe-S protein' (or Hipip) has been used increasingly in the literature to indicate the ability to form the higher oxidation level of the Chromatium protein. This practice is inappropriate since it uses a term applying to a redox potential for the description of a magnetic property or an oxidation level.

104, 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 respiratory chain are designated by Roman numerals. 8. The designation of a cluster (see footnote ** on p. 1) in an iron-sulfur protein containing labile-sulfur atoms should consist of square brackets about the number o f iron and labile-sulfur atoms. Thus, [2Fe-2S] represents a two-iron, two-labile-sulfur cluster and [4Fe-4S], a four-iron, four-labile-sulfur cluster *. The protein incorporating such a cluster may be called a 'two-iron-two-sulfur' or 'four-iron-four-sulfur' ferredoxin or ironsulfur protein. For ferredoxins, it is sufficient simply to refer to a 'two-iron' or 'four-iron' ferredoxin. Comment. The use of hyphens and "parentheses is firmly codified in the nomenclature of inorganic chemistry [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: 214Fe-4S]. This may be called a two-cluster four-iron four-sulfur ferredoxin or ironsulfur protein or, simply, a two-cluster-four-iron ferredoxin. 10. When the formal charge of the cluster is calculated, the sulfur atoms of the bound cysteine residues are not included in the calculation, contrary to the widespread practice in the current literature. Thus, for the oxidized and reduced forms, respectively, we have: Spinach ferredoxin: Bacilluspolymyxa ferredoxin: Clostridium pasteurianurn ferredoxin:

[2Fe-2S] 2+. [4Fe-4S]2+'; 214Fe-4S]2+;

[2Fe-2S] 1+ [4Fe-4S] 1+ 214Fe-4S] 1+

Comment. 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 possibility 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 to avoid confusion, the term, 'oxidation level' is used to refer to the cluster. 11. For ferredoxins at the oxidation level typical of Chromatium Hipip, the expression, [4Fe-4S] 3+, 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] 2÷(3+,2+,1+). 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 oxidation levels normally found in Chromatium Hipip and the protein from Bacillus polymyxa, both [4Fe-4S] ferredoxins, may be differentiated: Chromatium vinosum Hipip: [4Fe.4S]2+ (3+, 2+) Bacillus polymyxa ferredoxin: [4Fe.4S]2+ (2+, 1+) This shorthand denotes that Chromatium ferredoxin occurs in the reduced (2+)state but also can be found at the (3+) state, whereas B. polymyxa ferredoxin occurs m the * In English they would be pronounced as 'two-ef-ee-two-es' and 'four-ef-ee-four-es'.

105 TABLE I DESIGNATION OF IRON-SULFUR PROTEINS AS GENERALLY OBTAINED ON ISOLATION Previous designation

Recommended designation

Spinach chloroplast ferredoxin

Spinach chloroplast [2Fe-2S]2÷Fd or, in a specific context, [2Fe-2S]2+(2+,I+)Fd

Azotobacter vinelandii

Azotobacter vinelandii

iron-sulfur protein I

[2Fe-2S]2÷Fe-S protein I

Chromatium vinosum

Chromatium vinosum [4Fe-4S] 2*Fd

high-potential iron-sulfur protein

or, in a specific context, [4Fe-4S] 2+(3+,2+)Fd

Clostridium pasteurianum

Clostridium pasteurianum

ferredoxin

2[4Fe-4S]2+Fd or, in a specific context, 214Fe-4S]2+(2+,I+)Fd

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 designation 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 superreduced 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 o f rubredoxins are [Rd] 3+ and [Rd] 2. 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 I illustrate and contrast the new designations with those previously applied. Iron-sulfur proteins with clusters o f different types may be designated in a similar manner. F o r instance, a protein from Azotobacter vinelandii [7] has two Fe-S clusters which assume the same range o f oxidation levels, although one is found 'reduced' and the other 'oxidized': [4Fe-4S]2+(a*'2+) [4Fe-4S]a+(a+'2+)FdI.

References 1 IUPAC-IUB Commission on Biochemical Nomenclature (1973) Eur. J. Biochem. 35, 1-2, and J. Biol. Chem. 248, 5907-5908 2 International Union of Pure and Applied Chemistry (1970) Nomenclature of Inorganic Chemistry, 2nd edn., Butterworths, London 3 Carter, C.W., Jr., Kraut, J., Freer, S.T., Alden, R.A., Sieker, L.C., Adman, E. and Jensen, L.H. (1972) Proc. Natl. Acad. Sci. U.S. 69, 3526-3529 4 Carter, C.W., Jr., Kraut, J., Freer, S.T. and Alden, R.A. (1974) J. Biol. Chem. 249, 6339-6346 5 Herskovitz, T., Averill, B.A., Holm, R.H., lbers, J.A., Phillips, W.D. and Weiher, J.F. (1972) Proc. Natl. Acad. Sci. U.S. 69, 2347-2441 6 Bartsch, R.G. (1963) in Bacterial Photosynthesis (Gest, H., San Pietro, A. and Vernon, L.P., eds.), p. 315, Antioch Press, Yellow Springs, Ohio 7 Sweeney, W.V., Rabinowitz, J.C. and Yoch, D.C. (1975) J. Biol. Chem. 250, 7842-7847 8 Leigh, J.S., Jr. and Erecinska, M. (1975) Biochim. Biophys. Acta 387, 95-106