Structures, Biosynthesis and Biofunctions of Iron-sulfer proteins
Yiming Chen, Brown University, May 11th, 2011

I. Introduction
Iron-sulfur proteins are the proteins which contain iron-sulfur clusters, like sulfide-linked di-, tri-, and tetrairon centers with various oxidative states 1. An excess of 120 distinct types of enzymes and proteins are known to contain Fe-S clusters2. Iron-sulfur proteins are known for the role of the oxidation-reduction reactions of mitochondrial electron transportation. They are also discovered in a series of metalloproteins procedures, for example, ferredoxins 3, Coenzyme Qcytochrome c reductase 4, succinate-coenzyme Q reductase
5

and nitrogenase 6. The iron-sulfur

proteins have many functions including catalysis, generate radicals, and also can play as sulfur donors in the biosynthesis of lipoic acid and biotin. Additionally some of the Fe-S proteins are able to regulate the gene expression. Furthermore, the discoveries of new iron-sulfur proteins and iron-sulfur clusters has led to lots of interests of their amazing functional and structural diversity, which reflects the versatility of both iron and sulfur in biochemical processes.

Since these iron-sulfur proteins are vey common on the metabolic pathways of most organisms, it leads some scientific interests that iron-sulfur compounds had a significant role in the origin of life in the Iron-sulfur world theory 7. Thus theory claims that the early life on earth probaby formed on the surface of some iron sulfide minerals. It has been well developed by retrodiction from extant biochemistry and some chemical experiments. It has been reported that Fe-S proteins presumably were involved in the first catalysts that nature had to work with8.

1

II. Structures of iron-sulfur clusters
The core of iron/sulfur protein is iron-sulfur cluster9. Iron-sulfur clusters are complexes of iron atoms and sulfide centres, Fe2S2, FeS and Fe4S4 are basic unit of more complicated iron-sulfur clusters, the iron atoms are connected by sulfur bridge bonds, that’s an important structural feature. At the same time, the thiol groups of cysteine residue coordinates with iron atoms as ligands. All the Fe (II) and Fe (III) atoms in clusters are at high-spin states, so such a iron-sulfur clusters are usually mixed valence compounds, ferromagnetic or antiferromagnetic, and shows complicated spin-spin coupling interactions. Due to this complex characteristics of spin coupling interaction and environmental proteins’ regulation, the iron-sulfur clusters show abundant redox properties and catalytic activities. In most of all iron-sulfur clusters, the configurations of iron atoms are tetrahedral. The bridge bonded sulfide groups are either 2- or 3-coordinated.

Iron-sulfur clusters are versatile, ancient co-factors of proteins which are involved in electron transportation, bio-catalysis and gene expression regulation. In 1960s, when people investigated nitrogen-fixing bacteria, they found a highly efficient redox proteins, and proved to be ironsulfur protein. Since then, the studies of iron-sulfur clusters developed rapidly. The in vitro chemistry of Fe-S clusters has been thoroughly documented10, many Fe-S clusters are used as precursors to synthetic analogues of some biological clusters in organometallic chemistry. Holm and co-workers have studied the experimental conditions to synthesize the simpler iron-sulfur clusters, which can be readily synthesized from ferric iron compound, thiols, and sulfide (Fig. 1).

2

FeCl3 5 RS3.5 RS-

2RS Fe RS SR RS S R RS SR R S R S Fe Fe

2SR Fe RS S S R Fe SR R

S

4S 22SR

RS Fe RS

S Fe S

SR SR

MeOH

RS Fe RS S

S S Fe Fe

Fe S

SR

Fig. 1 Reactions which resulting in assembly of [Fe4S4(SR)4]2clusters via the intermediates [Fe(SR)4]2-, [Fe2S2(SR)4]2-, and [Fe4(SR)10]2-.38

1. 2Fe-2S cluster The 2Fe-2S cluster is the simplest iron-sulfur cluster (Fig. 2), which is constituted by two iron ions bridged by two sulfide ions. The iron ions are also coordinated by four ligands: by 4 cysteinyl ligands in ferredoxins, or by two cysteines and two histidines in Rieske proteins. In oxidized proteins, the oxidative states of two iron ions are +3/+3; after reduction, the oxidative states will change to +2/+3. There are a series of proteins contain one or more 2Fe-2S clusters as active sites, for examples, adrenodoxin-type ferredoxins, iron hydrogenases, plant-type ferredoxins, Fe2S2 Rieske proteins.

3

2-/3L Fe L S S Fe L L

Fig. 2 Structure of 2Fe-2S clusters, two iron ions are connected by 2 sulfide bridge bonds.

2. 4Fe-4S cluster The common structural unit of 4Fe-4S cluster is a four iron ions and four sulfide ions placed at the vertices of a cubane-type structure (Fig. 3). And in typical Fe-S proteins which contain a 4Fe-4S cluster, the iron ions are typically connected with thiol ligands.

Due to the increasing number of iron ions, the oxidative states of 4Fe-4S clusters become more complicated. Based on the similarity between reduced high potential iron-sulfur proteins (HiPIP) and oxidized ferredoxin, three oxidative states have been reported independently11. For the cluster (Fe4S4)n+, n=1, 2, 3. Some studies also show other oxidative states12. The proteins which contain one or more 4Fe-4S centers include aldehyde ferredoxin oxidoreductase, bacterial-type ferredoxins, endonuclease III, iron hydrogenases, sirohaem-Fe4S4 enzymes and trimethylamine dehydrogenase.

S S Fe S S S Fe S Fe S Fe S

Fig. 3 Structure of 4Fe-4S clusters, 4 iron ions are placed in a cubane-like framwork.

4

1. 3Fe-4S clusters Proteins are also known to contain the 3Fe-4S clusters, which has one iron less than the 4Fe-4S cores. Three sulfide ions bridge two iron ions each through covalent bond, while the fourth sulfide ione bridges three iron ions in the right center (Fig. 4). Their formal oxidation states of iron ions in 3Fe-4S clusters vary from Fe3S4+ (all iron ions are Fe (III)) to Fe3S42- (all Fe (II) form). Due to the structural similarity with 4Fe-4S clusters, 3Fe-4S could be converted to 4Fe-4S cluster reversibly 13.

L Fe S S Fe L S Fe L S

Fig. 4 Structure of 3Fe-4S clusters, one iron ion less than the 4Fe-4S cluster.

4. Other iron-sulfur clusters Besides the types of iron-sulfur clusters introduced above, some other categories of unusual ironsulfur clusters are also involved in biochemistry processes. For instance, Fe8S7 clusters in Monitrogenase component I (MoFe protein, Fig. 5)14, synthesized 6Fe-6S prismatic cluster (Fig. 6)15, as well as the 7Fe center in nitrogenase16.

5

L

L Fe Fe S S Fe S

S Fe S s Fe Fe L L

L

L
Fig. 5 Structure of 8Fe-7S clusters in Monitrogenase component I.

Fig. 6 Prismatic structure of a synthesized ironsulfur 6Fe-6S cluster.

III. Biosynthesis of iron-sulfur proteins
Biosynthesis of iron-sulfur proteins occurs in two major steps: the first step takes place in the cytoplasm of prokaryotic organisms or in the mitochondria of eukaryotic organisms, in which the iron-sulfur clusters will be assembled; then the clusters will be transfered to the apoproteins17. Lots of in vitro experiments have been done to investigate the mechanism of iron-sulfur protein assembly. It has been reported that inactive apo forms of 2Fe-2S and 4Fe-4S proteins could be activated by adding Fe2+, Fe3+ and S2-2. This result suggests that iron-sulfur clusters can form spontaneously with the existence of iron ions and sulfide, however, the concentration sand toxicity levels are not compatible with biological environment. Another reasonable explanation is specific carriers will bind with iron ions and sulfide, sequester the iron ions and sulfide in nontoxic forms. It is very likely that the sulfur donor is a persulfide located on a cysteine of a cysteine desulfurase system. However, nothing is known regarding the iron donor and thus all in vitro studies use a ferrous salt as the iron source

Nowadays, three special biosynthetic pathways of iron-sulfur proteins have been identified, namely NIF, ISC, and SUF systems. The first discovered biosynthetic system, nitrogen-fixation (NIF) machinery is utilized to assemble the nitrogenase, which is responsible for the conversion

6

of N2 to NH3 in some nitrogen-fixing bacteria 18. Secondly, the ISC(iron sulfur cluster) assembly system is required for production of the majority of cellular iron-sulfur proteins19. Finally, the SUF (sulfur-mobilization) system was investigated that might be used predominantly under ironinsufficient conditions 20.

1. Catalytic formation of a nitrogenase iron-sulfur cluster

Nitrogen fixation in biological organisms is catalyzed by nitrogenase, an enzyme which comprised of two component proteins called the Fe protein and the MoFe protein. Both of these two component proteins contain metalloclusters. Based on the sequence homology with the nif genes that specifically target nitrogenase Fe-S cluster biosynthesis, an isc (iron-sulfur cluster) gene cluster was identified in a wide range of nitrogen-fixing and non-nitrogen-fixing prokaryotes and proposed to be responsible for general Fe-S cluster biosynthesis. Two of the nine isc genes, iscS and iscU, encode homodimeric proteins whose sequences are homologous to NifS and NifU, respectively. Furthermore, in common with NifU and NifS, the gene products IscU and IscS have been shown to produce a heterotetrameric complex.

The Azotobacter vinelundii nifS gene product, which is required for activation of the nitrogenase component proteins, is able to catalyze the desulfurization of L-cysteine to yield sulfur and Lalanin6 through a bounded persulfide intermediate, which has been suggested as a possible Sdonor in biosynthesis of iron-sulfur clusters. It has been reported that apo form of Fe protein without iron-sulfur cluster could be reconstituted with the existence of NifS L-cysteine, ferrous ion, dithiothreitol, and MgATP. However, when an altered NifS protein, NifS-Ala which does not have ability to catalyze desulfurization reaction, is not able to catalyze reconstitution of the apoFe protein.

Another work monitored the synthesis procedures of 4Fe-4S cluster with the IscU product. Results show sequential cluster assembly with the initial IscU product containing one 2Fe-2S2+

7

cluster per dimer turning to a form which containing two 2Fe-2S2+ clusters per dimer. And then, finally to a form that contains one 4Fe-4S2+ cluster per dimer21.

2. ISC related biosynthesis of iron-sulfur cluster This operon which involved in ISC machinery (iscS–iscU–iscA–hscB–hscA–fdx)17 contains a series of genes for the molecular chaperones, and an electron transferring 2Fe-2S ferredoxin19,
21-22.

ISC machinery is essential for general biosynthesis of Fe–S clusters in bacteria19.

Homologues of these proteins involved in biosynthesis have been characterized in eukaryotes suggesting a highly conserved mechanism.

ISC related Iron-sulfur cluster biosynthesis in both prokaryotic and eukaryotic organisms is known to be regulated by two highly conserved proteins: IscS and IscU. Both IscS and IscU exhibit significant similarity with proteins NifS and NifU, which are relate to the nif operon. IscS is closely related to NifS, and both have been shown to be homodimeric, pyridoxyl phosphatedependent L-cysteine desulfurases, catalyzing the reductive conversion of cysteine to alanine and sulfide via an enzyme-bound persulfide intermediate21. When IscS catalyzes desulfurization reaction, Cys-328 of IscS attacks the sulfur atom of L-cysteine, and then then sulfane sulfur derived from L-cysteine connects to the S atom of Cys-328. In the course of the cluster synthesis, IscS and IscU form a covalent complex, and a sulfur atom derived from L-cysteine is transferred from IscS to IscU. The covalent complex is thought to be essential for the cluster biogenesis, but neither the nature of the bond connecting IscS and IscU nor the residues involved in the complex formation have been determined, which have thus far precluded the mechanistic analyses of the cluster assembly23.

And for IscU, which provides a scaffold for IscS-directed assembly of clusters that can be inserted intact into apo forms of Fe-S cluster-containing proteins, possibly via other associated carrier proteins24. Moreover, it is clear that IscS mediated cluster synthesis in IscU proceeds in sequential steps involving well-defined forms of IscU containing one 2Fe-2S2+ cluster per dimer,

8

two 2Fe-2S2+ clusters per dimer, and one 4Fe-4S2+ cluster per dimer. Similar models have been proposed for the SUF system from studies on both SufA and SufE (Fig. 9).

In summary (Fig. 7), the experiment results indicate a general mechanism for Fe-S cluster biosynthesis in which IscU provides a scaffold for IscS-mediated assembly of [Fe2(µ2-S)2] cores. These units constitute the fundamental building blocks of biological Fe2S2, Fe3S4, and Fe4S4 centers24b. These iron-sulfur units are proposed to be transferred intact into apoproteins. However, the details about the transfer step is still unclear. The most likely candidates of the transportation carrier are the IscA protein that contains three conserved cysteine residues and the heat shock proteins HscA and HscB that bear sequence homology to the molecular chaperones. Investigation over how the Fe3+ ion is obtained by IscU and how the Fe2S2 cores assembled in IscU are released and transferred into apoproteins still present fascinating challenges24b.

Fig. 7 Proposed scheme for the formation of the covalent IscS/IscU complex. Details of the processes indicated by dotted arrows are not known. The type of iron-sulfur clusters on IscU serving as iron-sulfur cluster precursor(s) has not been determined23.

9

3. SUF related biosynthesis of iron-sulfur clusters The SUF (sufA–sufB–sufC–sufD–sufS–sufE) machinery works under iron limitation and oxidative stress25. However, still very little is known about the molecular details of the two SufA-dependent reactions: cluster assembly on SufA and cluster transfer. The SUF machinery has the involvement of a cysteine desulfurase (IscS, SufS/E) for the utilization of cysteine as a source of sulfur26. Sulfur from free cysteine is transferred to an essential cysteine of the cysteine desulfurase, generating persulfide/polysulfide intermediate. There are also scaffold proteins (SufA, IscA/U) which provide an effective intermediate assembly site for Fe–S clusters27. From these proteins, the synthesized clusters are transferred to apo recipient proteins. Finally, the SUF and ISC systems contain some helper proteins (like HscA/B, Ferredoxin, SufBCD), which are linked with ATPase or electron transfer activity28.

Two different molecular mechanisms by which Fe and S are assembled into the scaffold protein at the cluster binding site have been postulated29. The first one is named as “Fe first, S second” model (Fig. 8); and the second is ‘‘S first, Fe second’’ model (Fig. 9).

Fig. 8 The ‘‘Fe first, S second’’ model. (R-SH= Cys51 of SufE)29

Fig. 9 The ‘‘S first, Fe second’’ model. (R-SH= Cys51 of SufE)29

10

In first mechanism, two Fe2+ irons are chelated by the cysteine ligands. In second step, a sulfur atom is transferred from the persulfide of SufE to SufA generating a sulfide-bridged diferric species, during a reaction implying a 2-electron reduction of the sulfane sulfur to sulfide by the ferrous ions. A second S atom needs to be provided by SufE but formation of the second sulfide bridge requires two more electrons. They can come from either an exogenous source or a redox active dithiol group, in agreement with the presence of three conserved cysteines per polypeptide29.

In the second mechanism (‘‘S first, Fe second’’) (Fig. 9), the first step consists of a transpersulfuration reaction, during which the nucleophilic cysteines of SufA acquire the S atoms of SufE by the attack of SufE persulfides, generating persulfides on SufA; In a second step, two ferrous ions get chelated by these persulfide moieties. Formation of a 2Fe–2S cluster at the interface then occurs after 2-electron reduction of each of the sulfane S atoms, two electrons provided by the two ferrous iron and two by a redox dithiol for example. Similar models have been proposed for the Isc system from studies on both IscA and IscU data available, the second mechanism is favored17.
30.

From the experiment

About the cluster transportation mechanism, the information available is still very limited. The proposed mechanism can be interpreted as shown in Fig. 10. In this case, SufA is supposed to harbor a 4Fe–4S cluster bridging two subunits. The first step of the reaction of holoSufA with an apoprotein recipient, such as biotin synthase (apoBioB), is the fast formation of a rather tight complex between the two proteins. However, in vitro experiment, no complex could be observed during incubation of holoSufA with holoBioB, apoSufA with apoBioB, apoSufA with holoBioB, showing that the cluster content of the proteins controls the association, in a manner which remains to be understood at the molecular level29. Finally, the drastic stabilization of the complex as the result of mutations of BioB cysteines suggests that the cluster transfer is driven by the direct attack of cysteinates of BioB on the cluster of SufA and thus can be described as a nucleophilic substitution during which the cysteines of SufA are released and replaced by those of BioB.

11

Fig. 10 Proposed mechanism for cluster transfer from a scaffold protein (SufA) to an apo protein target

IV. Biofunctions of Iron-Sulfur Proteins
TABLE 1. Inventory of known Fe–S proteins in (non-photosynthetic) eukaryotes: localization and function. From 31.
Fe-S Protein Mitochondrial Fe–S proteins Aconitase Homoaconotase Dihydroxy-acid dehydratase Lipoate synthase 4Fe-4S 4Fe-4S 4Fe-4S 2Fe-2S, 4Fe-4S Citric acid cycle Biosynthesis of lysine Biosynthesis of branched-chain amino acids Biosynthesis of lipoic acid Cluster Type Function

12

Fe-S Protein Biotin synthase Ferredoxin Cytosolic Fe–S proteins Isopropylmalate isomeras Iron regulatory protein 1 Sulfite reductase Glutamate dehydrogenase ABC protein Rli1 P-loop NTPase Nbp35 Hydrogenase-like Nar1 MOCS1A Dihydro-pyrimidine dehydrogenase CMP-N-acetyl-neuraminic acid hydroxylase Xanthine dehydrogenase Nuclear Fe–S proteins DNA glycosylase

Cluster Type 2Fe-2S, 4Fe-4S 2Fe-2S

Function Biosynthesis of biotin Maturation of Fe–S proteins, biosynthesis of haeme A, steroid biosynthesis in mammals (adrenodoxin)

4Fe-4S 4Fe-4S 4Fe-4S 4Fe-4S ? ? 4Fe-4S 4Fe-4S 4 x 4Fe-4S 2Fe-2S 2 x 2Fe-2S

Biosynthesis of leucine Post-transcriptional control of iron uptake, storage and use in mammals (‘cytosolic aconitase’) Biosynthesis of methionine, contains siroheme Biosynthesis of glutamate Biogenesis of ribosomes, rRNA processing, translation initiation Maturation of cytosolic and nuclear Fe–S proteins Maturation of cytosolic and nuclear Fe–S proteins Biosynthesis of Moco (molybdenum co-factor) Degradation of pyrimidine nucleotides Biosynthesis of N-glycolyl neuraminic acid, Rieskelike protein Degradation of xanthine to urate, contains FAD and molybdopterin

4Fe-4S

DNA repair (endonuclease III-like glycosylase 2)

In TABLE I, a series of iron-sulfur proteins and their biofunctions are listed. Some of the most common iron-sulfur proteins will be selected as example, the biological processes they are involved will be introduced in detail.

13

1. Electron transfer process mediated by ferredoxin Ferredoxins (Fds) are iron-sulfur proteins that mediate electron transfer in a series of metabolic reactions. It is called “capacitors” since ferredoxin proteins are able to accept or discharge electron, thus it can play as electron transfer agent in biological redox reactions. For instance, reduced ferredoxin can be used to reduce thioredoxin with existence of ferredoxin:thioredoxin reductase (FTR).

FTR has a vital position in light-induced enzyme regulation in chloroplasts. The photosynthetic electron transfer chain reduces ferredoxin by photosystem I32. Ferredoxin can then reduce ferredoxin:thioredoxin reductase (FTR), which can reduces the chloroplast thioredoxins m and f. Finally, the thioredoxins are able to activate or deactivate target enzymes, switching the metabolism to anabolic pathways. The whole procedure are shown in Fig. 1133.

Fig. 11 Biochemical pathway of enzyme activation through ferredoxin and ferredoxin:thioredoxin reductase in lightinduced switching of metabolism33.

14

Model of reduction reaction chain of thioredoxin is shown in Fig. 12. FTR is a thin molecule, a concave disk with dimensions 40 Å x 50 Å but 10 Å across the center of the molecule33. The disk-shaped structure of the FTR allows docking of a ferredoxin on one side of the molecule (red), while thioredoxin binds to the other side (yellow). This intermediate can be reduced by a second ferredoxin molecule. The iron-sulfur centers and disulfide bridges are shown in stick- ball model.

Fig. 12 Catalytic33 model of ferredoxin:thioredoxin reductase (FTP). Ferredoxin (red) and thioredoxin (yellow) bind with disk-shape FTR from opposite sides, then electron provided by second ferrdoxin will reduce the thioredoxin33.

In ferredoxin:thiolredoxin reductase (FTR), the irons of the iron-sulfur center are coordinated by cysteines 55, 74, 76, and 85 in a normal cubane-type geometry. The active-site disulfide bridge between residues 57 and 87 is in van der Waals contact with the iron center. The sulfur atom of Cys87 contacts the iron atom bound by Cys55 and the sulfur atom of Cys55, both of which are at 3.1 Å distance. The closest sulfide ion of the cluster is 3.5 Å away from Cys87. Incoming electrons can pass from ferredoxin onto the main chain of Cys74 to the disulfide bridge by way of the iron center33.
15

All other biological disulfide reactions occur by approach of thioldisulfide exchange reactions. The disulfide that is close to one iron atom of the iron-sulfur cluster can pick up an electron from ferredoxin to the iron-sulfur cluster of FTR, but it can also attract one additional electron from the iron-sulfur center to break the disulfide bond. Cys57 becomes then the reactive thiol, while the second cysteine thiol is protected by connecting to the iron-sulfur cluster. Therefore, the oneelectron reduction of FTR by ferredoxin results in an oxidation of the 4Fe-4S2+ cluster to an 4Fe4S3+ cluster34 (Fig. 13).

Fig. 13 The proposed mechanism of action of ferredoxin:thioredoxin reductase35.

The one-electron reduced intermediate with nucleophilic thiol Cys57, will attack the disulfide bridge of thioredoxin to form a hetero-disulfide. The next electron delivered by a new ferredoxin molecule will reduce the iron-sulfur cluster back to its original oxidation state and produce a new nucleophilic sulfide on Cys87, which will attack the disulfide bridge between FTR and thioredoxin and releasing the reduced thioredoxin. Such a mechanism, which requires the
16

simultaneous docking of thioredoxin and ferredoxin, is entirely compatible with the disk-shaped structure of FTR, which allows docking of a second ferredoxin on one side of the molecule as electron-donor, while thioredoxin is bound to the other side by way of the intermolecular disulfide bridge35.

2. Nitrogen-fixation by Fe-Mo cofactor in nitrogenase

Nitrogen is an essential element of biological matter on earth. Despite nitrogen is the major component of atmosphere, we are still short of nitrogen supply, since N2 is exceptionally inert, and only few bacteria in nature have the ability to convert it from N(0) to compound. The triple bond of N2 is one of the strongest covalent bonds while high pressure and high temperature are required to convert N2 into NH3 in the industrial production, on contrary biological nitrogen fixation breaks the N-N triple bond at ambient conditions. For this purpose, the enzyme nitrogenase is employed, one of the most complex bioinorganic catalysts in nature.

Nitrogenase consists of two proteins: (1) the molybdenum-iron protein, which holds the active site; and (2) the iron protein which hydrolyzes MgATP and uses energy to provide the molybdenum-iron protein with electrons as an electron-donors. The structure of active site of FeMo protein is illustrated in Fig. 1436.

Fig. 14 The FeMo cofactor of nitrogenase with its homocitrate ligand and the two residues linking the cofactor to the protein, histidine and cysteine.

17

Johannes Kästner and his co-worker postulated a stepwise molecular mechanism (Fig. 15) for the nitrogen-fixation process, investigated the geometrical and energetic changes during the catalytic reactions37.

Fig. 15 The catalytic cycle of biological nitrogen fixation.Arrows indicate bond rearrangements. The largest barrier in the cycle is, at E≠=66 kJ mol−1, the transition from 3 to 437.

Structure 1 in Fig. 15 represents the cofactor after one reduction and one protonation with respect to the resting state. Only after at least two reductions and two protonations at the sulfur bridges, nitrogen gas molecule binds axially to one of the Fe sites of the cluster (Structure 3). At the same time, to maintain the tetrahedral coordination of the Fe atom, the sulfur bridge between iron ion and sulfide breaks and becomes a non-bridging thiol group and remains isolated throughout the reaction until the very last step, where it plays a crucial role in removing the final reaction product by nucleophilic attack. Then the N2 molecule which coordinate with Fe ion can insert between two Fe sites, by overcoming 66 kJ/mol energetic barrier.

18

After the dinitrogen “bridge” between two iron sites formed, the nitrogen will be protonated as shown in Structure 4-6, Fig. 15. The first and second protons add to different nitrogen atom s which bind with the cofactor in the bridged configuration. The barriers are relative smaller, 4 kJ/ mol and 26 kJ/mol. After protonations, an intramolecular rearrangement occurs: a bond shift rearranges the N2H2 fragment so that it forms π complex (Structure 7) with one Fe site. The N2H2 adduct exposes one pair of lone electrons, which is able to accept the third proton (Structure 8). After third protonation, the bond between Fe and N2H3 transforms into a single bond.

After protonation of the lone pair on nitrogen in Structure 9, the resulting NH3 dissociates with catalytic center and release 204 kJ/mol energy with a small barrier of less than 10 kJ/mol. The breakage of N-N bond requires electron in anti-bond orbital, which can be provided by delocalized electron system of nitrogenase. The nitrogen atom left then will be protonated and disassociates with one Fe site, which will form a new bond with central ligand to maintain the tetrahedron coordination geometry. Once another proton is transferred to nitrogen atom, the sulfide will insert between the two Fe sites, reconstitute the bridge as in original form. As a consequence, the second ammonia molecule is displaced and disassociate from site. A final proton transfer restores the initial configuration (Structure 2) with a protonated SH group that awaits the next nitrogen molecule to begin the next cycle.

V. Summary
In this paper, the structures and biogenesis of a series of iron-sulfur clusters are carefully reviewed. Despite most of the molecular mechanisms involved in biosynthesis of iron-sulfur clusters have been well investigated, however, some crucial steps are still not very clear. For instance, the iron-donor which provides iron ions to scaffold proteins has not been identified yet, since almost all the in vitro experiments use ferrous or ferric salts as iron source. Furthermore, some mechanisms have been proposed for the cluster transportation from scaffold proteins to apo recipient proteins, but some steps still cannot consist with experiment observation, that indicates

19

some other enzymes probably take part in the transportation procedure. In third part, two important biology processes which catalyzed by iron-sulfur clusters are selected, their mechanisms are thoroughly investigated by experiment or theoretical approaches. Iron-sulfur proteins play different roles in a series of redox reactions, the versatility of iron-sulfur proteins in biological processes is exhibited clearly.

20

VI. References
1. Orme-Johnson, W. H.; Hansen, R. E.; Beinert, H.; Tsibris, J. C.; Tsai, R. L.; Bartholomaus, R. C.; Gunsalus, I. C., Metal site of nonheme (iron-sulfur) proteins. Science 1968, 160 (3826), 441-2. 2. Beinert, H.; Holm, R. H.; Munck, E., Iron-Sulfur Clusters: Nature's Modular, Multipurpose Structures. Science 1997, 277 (5326), 653-659. 3. Bruschi, M., Structure, function and evolution of bacterial ferredoxins. FEMS microbiology letters 1988, 54 (2), 155-175. 4. Gao, X.; Wen, X.; Esser, L.; Quinn, B.; Yu, L.; Yu, C.-A.; Xia, D., Structural Basis for the Quinone Reduction in the bc1 Complex: A Comparative Analysis of Crystal Structures of Mitochondrial Cytochrome bc1 with Bound Substrate and Inhibitors at the Qi Site. Biochemistry 2003, 42 (30), 9067-9080. 5. Oyedotun, K. S.; Lemire, B. D., The Quaternary Structure of the Saccharomyces cerevisiae Succinate Dehydrogenase. Journal of Biological Chemistry 2004, 279 (10), 9424-9431. 6. Zheng, L.; Dean, D. R., Catalytic formation of a nitrogenase iron-sulfur cluster. Journal of Biological Chemistry 1994, 269 (29), 18723-18726. 7. Wächtershäuser, G., Evolution of the first metabolic cycles. Proceedings of the National Academy of Sciences 1990, 87 (1), 200-204. 8. Huber, C.; Wächtershäuser, G., Peptides by Activation of Amino Acids with CO on (Ni,Fe)S Surfaces: Implications for the Origin of Life. Science 1998, 281 (5377), 670-672. 9. 10. 11. Lippard, S. J.; Berg, J. M., Principles of Bioinorganic Chemistry. Mill Valley, CA, 1994. Holm, R. H., Adv. Inorg. Chem. 1992, 38. Carter, C. W.; Kraut, J.; Freer, S. T.; Alden, R. A.; Sieker, L. C.; Adman, E.; Jensen, L. H., A Comparison of Fe4S4 Clusters in High-Potential Iron Protein and in Ferredoxin. Proceedings of the National Academy of Sciences 1972, 69 (12), 3526-3529.

21

12.

(a) Averill, B. A.; Herskovitz, T.; Holm, R. H.; Ibers, J. A., Synthetic analogs of the active sites of iron-sulfur proteins. II. Synthesis and structure of the tetra[mercapto-.mu.3sulfido-iron] clusters, [Fe4S4(SR)4]2. Journal of the American Chemical Society 1973, 95 (11), 3523-3534; (b) Frankel, R. B.; Herskovitz, T.; Averill, B. A.; Holm, R. H.; Krusic, P. J.; Phillips, W. D., Synthetic analogs of the active sites of iron-sulfur proteins. VIII. Some electronic properties of [Fe4S4(SR)4]3; analogs of reduced bacterial ferredoxins. Biochemical and Biophysical Research Communications 1974, 58 (4), 974-982.

13.

(a) Rousset, M.; Montet, Y.; Guigliarelli, B.; Forget, N.; Asso, M.; Bertrand, P.; Fontecilla-Camps, J. C.; Hatchikian, E. C., [3Fe-4S] to [4Fe-4S] cluster conversion in Desulfovibrio fructosovorans [NiFe] hydrogenase by site-directed mutagenesis. Proceedings of the National Academy of Sciences 1998, 95 (20), 11625-11630; (b) Bingemann, R.; Klein, A., Conversion of the central [4Fe–4S] cluster into a [3Fe–4S] cluster leads to reduced hydrogen-uptake activity of the F420-reducing hydrogenase of Methanococcus voltae. European Journal of Biochemistry 2000, 267 (22), 6612-6618.

14.

Kim, J.; Woo, D.; Rees, D. C., X-ray crystal structure of the nitrogenase molybdenumiron protein from Clostridium pasteurianum at 3.0 Å resolution. Biochemistry 1993, 32 (28), 7104-7115.

15.

Saak, W.; Henkel, G.; Pohl, S., A New Route to Iron-Sulfur Clusters: Synthesis and Structure of [(C2H5)4N]2Fe6S6I6. Angewandte Chemie International Edition in English 1984, 23 (2), 150-151.

16.

Rees, D. C.; Akif Tezcan, F.; Haynes, C. A.; Walton, M. Y.; Andrade, S.; Einsle, O.; Howard, J. B., Structural basis of biological nitrogen fixation. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 2005, 363 (1829), 971-984.

17.

Sendra, M.; Ollagnier de Choudens, S.; Lascoux, D.; Sanakis, Y.; Fontecave, M., The SUF iron-sulfur cluster biosynthetic machinery: Sulfur transfer from the SUFS-SUFE complex to SUFA. FEBS Letters 2007, 581 (7), 1362-1368.

18.

Rees, D. C.; Howard, J. B., Nitrogenase: standing at the crossroads. Current Opinion in Chemical Biology 2000, 4 (5), 559-566.

22

19.

Zheng, L.; Cash, V. L.; Flint, D. H.; Dean, D. R., Assembly of Iron-Sulfur Clusters. Journal of Biological Chemistry 1998, 273 (21), 13264-13272.

20.

Takahashi, Y.; Tokumoto, U., A Third Bacterial System for the Assembly of Iron-Sulfur Clusters with Homologs in Archaea and Plastids. Journal of Biological Chemistry 2002, 277 (32), 28380-28383.

21.

Agar, J. N.; Krebs, C.; Frazzon, J.; Huynh, B. H.; Dean, D. R.; Johnson, M. K., IscU as a Scaffold for Iron-Sulfur Cluster Biosynthesis: Sequential Assembly of [2Fe-2S] and [4Fe-4S] Clusters in IscU. Biochemistry 2000, 39 (27), 7856-7862.

22.

Hoff, K. G.; Silberg, J. J.; Vickery, L. E., Interaction of the iron–sulfur cluster assembly protein IscU with the Hsc66/Hsc20 molecular chaperone system of Escherichia coli. Proceedings of the National Academy of Sciences 2000, 97 (14), 7790-7795.

23.

Kato, S.-i.; Mihara, H.; Kurihara, T.; Takahashi, Y.; Tokumoto, U.; Yoshimura, T.; Esaki, N., Cys-328 of IscS and Cys-63 of IscU are the sites of disulfide bridge formation in a covalently bound IscS/IscU complex: Implications for the mechanism of iron-sulfur cluster assembly. Proceedings of the National Academy of Sciences 2002, 99 (9), 5948-5952.

24.

(a) Yuvaniyama, P.; Agar, J. N.; Cash, V. L.; Johnson, M. K.; Dean, D. R., NifS-directed assembly of a transient [2Fe-2S] cluster within the NifU protein. Proceedings of the National Academy of Sciences 2000, 97 (2), 599-604; (b) Agar, J. N.; Zheng, L.; Cash, V. L.; Dean, D. R.; Johnson, M. K., Role of the IscU Protein in Iron−Sulfur Cluster Biosynthesis: IscS-mediated Assembly of a [Fe2S2] Cluster in IscU. Journal of the American Chemical Society 2000, 122 (9), 2136-2137.

25.

Outten, F. W.; Djaman, O.; Storz, G., A suf operon requirement for Fe–S cluster assembly during iron starvation in Escherichia coli. Molecular Microbiology 2004, 52 (3), 861-872.

26.

Loiseau, L.; Ollagnier-de-Choudens, S.; Nachin, L.; Fontecave, M.; Barras, F. d. r., Biogenesis of Fe-S Cluster by the Bacterial Suf System. Journal of Biological Chemistry 2003, 278 (40), 38352-38359.

27.

Ollagnier-de-Choudens, S.; Mattioli, T.; Takahashi, Y.; Fontecave, M., Iron-Sulfur Cluster Assembly. Journal of Biological Chemistry 2001, 276 (25), 22604-22607.

23

28.

Outten, F. W.; Wood, M. J.; Muñoz, F. M.; Storz, G., The SufE Protein and the SufBCD Complex Enhance SufS Cysteine Desulfurase Activity as Part of a Sulfur Transfer Pathway for Fe-S Cluster Assembly in Escherichia coli. Journal of Biological Chemistry 2003, 278 (46), 45713-45719.

29.

Fontecave, M.; Choudens, S.; Py, B.; Barras, F., Mechanisms of iron–sulfur cluster assembly: the SUF machinery. Journal of Biological Inorganic Chemistry 2005, 10 (7), 713-721-721.

30.

Krebs, C.; Agar, J. N.; Smith, A. D.; Frazzon, J.; Dean, D. R.; Huynh, B. H.; Johnson, M. K., IscA, an Alternate Scaffold for Fe-S Cluster Biosynthesis. Biochemistry 2001, 40 (46), 14069-14080.

31.

Lill, R.; M¸hlenhoff, U., Iron-sulfur-protein biogenesis in eukaryotes. Trends in Biochemical Sciences 2005, 30 (3), 133-141.

32.

van Thor, J. J.; Geerlings, T. H.; Matthijs, H. C. P.; Hellingwerf, K. J., Kinetic Evidence for the PsaE-Dependent Transient Ternary Complex Photosystem I/Ferredoxin/ Ferredoxin:NADP+ Reductase in a Cyanobacterium. Biochemistry 1999, 38 (39), 12735-12746.

33.

Dai, S.; Schwendtmayer, C.; Schürmann, P.; Ramaswamy, S.; Eklund, H., Redox Signaling in Chloroplasts: Cleavage of Disulfides by an Iron-Sulfur Cluster. Science 2000, 287 (5453), 655-658.

34.

Staples, C. R.; Ameyibor, E.; Fu, W.; Gardet-Salvi, L.; Stritt-Etter, A.-L.; Schürmann, P.; Knaff, D. B.; Johnson, M. K., The Function and Properties of the Iron‚àíSulfur Center in Spinach Ferredoxin:Thioredoxin Reductase: A New Biological Role for Iron‚àíSulfur Clusters. Biochemistry 1996, 35 (35), 11425-11434.

35.

Staples, C. R.; Gaymard, E.; Stritt-Etter, A.-L.; Telser, J.; Hoffman, B. M.; Schürmann, P.; Knaff, D. B.; Johnson, M. K., Role of the [Fe4S4] Cluster in Mediating Disulfide Reduction in Spinach Ferredoxin:Thioredoxin Reductase. Biochemistry 1998, 37 (13), 4612-4620.

24

36.

Einsle, O.; Tezcan, F. A.; Andrade, S. L. A.; Schmid, B.; Yoshida, M.; Howard, J. B.; Rees, D. C., Nitrogenase MoFe-Protein at 1.16 Å Resolution: A Central Ligand in the FeMo-Cofactor. Science 2002, 297 (5587), 1696-1700.

37.

Kästner, J.; Blöchl, P. E., Towards an Understanding of the Workings of Nitrogenase from DFT Calculations. ChemPhysChem 2005, 6 (9), 1724-1726.

38.

Hagen, K. S.; Reynolds, J. G.; Holm, R. H., Definition of reaction sequences resulting in self-assembly of [Fe4S4(SR)4]2- clusters from simple reactants. Journal of the American Chemical Society 1981, 103 (14), 4054-4063.

25