Ferredoxin

spinqualitylabelsall models Ferredoxin with Fe4S4 cluster complex with cobalt hexamine (PDB code 2z8q) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D File:2z8q.png Ferredoxin (Fd) is found in chloroplasts which mediates electron transfer and contains an iron-sulfur cluster. It is involved in the photosynthesis process where its iron atoms accept or discharge electrons when they are being oxidized or reduced. The iron-sulfur cluster can contain 2Fe-2S and is termed plant-like or 3Fe-4S or 4Fe-4S clusters. Adrenodoxin (ADR) is a ferredoxin containing a 2Fe-2S group involved in electron transfer from NADPH+ to a cytochrome P-450 in the adrenal gland. Putidaredoxin (PUT) and terpredoxin (TER) are involved in the same reaction in bacteria and contain a 2Fe-2S group. D14C variant of Pyrococcus furiosus ferredoxin Structures of the all cysteinyl coordinated D14C variant of ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus have been determined for the [4Fe-4S] <-> and [3Fe-4S] forms (click to enlarge). The [4Fe-4S] form diffracted to 1.7 Å and two different types of molecules were found in the crystal (2z8q). They have different crystal packing and intramolecular disulfide bond conformation. The crystal packing reveals a beta-sheet interaction between A molecules (shown in blue and green) in adjacent asymmetric units, while B molecules are packed as monomers in a less rigid position next to the A-A extended beta-sheet dimers (shown in red and yellow). The intramolecular disulfide bond in the A molecules is in a double conformation while the intramolecular disulfide bond in the B molecules is in a single conformation (click to see morph, molecule A is shown in blue and molecule B in green). pH dependent equilibrium of D14C [3Fe-4S] P. furiosus ferredoxin between protonated and deprotonated monomers and formation of a disulfide bonded dimer from deprotonated monomers. Fd is short for ferredoxin. Two forms of D14C [3Fe-4S] Pyrococcus furiosus ferredoxin are obtained when purified at pH 8.0: a monomer and a dimer connected by an intermolecular disulfide bond (see static image above). When purified at pH 5.8, only the monomer is obtained. The [3Fe-4S] form diffracted to 2.8 Å resolution and showed only the monomeric form, which resembles molecule A of D14C [4Fe-4S] Pyrococcus furiosus ferredoxin. Crystal packing in D14C [3Fe-4S] ferredoxin is as extended beta-sheet dimers of adjacent molecules (shown in red and orange), which is the same as WT [3Fe-4S] P. furiosus ferredoxin (1sj1, shown in blue and cyan) even though the space groups are different (see also corresponding side views for D14C [3Fe-4S]) and WT [3Fe-4S]). ISC-like [2Fe-2S] ferredoxin (FdxB) dimer from Pseudomonas putida JCM 20004 Biological iron-sulfur (Fe-S) clusters are functionally versatile, modular prosthetic groups. The electronic structure and the site of iron reduction of these protein-bound cofactors account for the electron transfer function and mechanism. In the present work we have solved the structure of the ISC-like [2Fe-2S] ferredoxin called FdxB from the non-pathogenic gammaproteobacterium Pseudomonas putida JCM 20004 (formerly Pseudomonas ovalis IAM 1002) (3ah7). This FdxB protein contains an adrenodoxin (Adx) like, redox-active [2Fe-2S] cluster, which plays an essential role in the de novo iron-sulfur cluster assembly (ISC) system. It is encoded by the fdxB gene as a constituent of the cognate iscR-iscS1-iscU-iscA-hscB-hscA-fdxB gene cluster for the ISC system (DDBJ-EMBL-GenBank code AB109467). In P. putida the ISC pathway is apparently the sole system for in vivo Fe-S cluster assembly whereas the SUF pathway is missing in the bacterial genome (unlike in Escherichia coli). The FdxB structure has a βαββαβ fold with the β-grasp/ubiquitin-like fold motif as found in regular eukaryal and bacterial [2Fe-2S] ferredoxins (e.g. 1i7h, 1cje, 1e9m). FdxB is folded into an (α+β) core fold domain and an extended C-terminal tail. In the lattice FdxB was found to be homo-dimeric, displaying the isologous association of the extended C-terminal tail from each protomer. Each protomer binds a [2Fe-2S] cluster that is coordinated by four terminal cysteine sulfur atoms, where the outermost iron (Fe1) near the protein surface is coordinated by Cys41S and Cys47S and the innermost iron (Fe2) by Cys50S and Cys86S. In the dimeric structure, two [2Fe-2S] clusters are separated at the closest iron-to-iron (Fe1-Fe1) distance of 25 A, suggesting that a rapid interprotomer electron transfer between them would be unlikely to occur. In the place of the consensus free cysteine usually present near the [2Fe-2S] cluster of ISC-like ferredoxins, FdxB has the Lys45 side chain which forms a salt-bridge interaction with Asp65 Oδ2. Thus, the overall FdxB structural features argue for its primarily electron transfer role in the cognate ISC system, rather than the direct catalytic function. With the molecular structural frame determined from the FdxB structure, our electron-nuclear double resonance (ENDOR) analysis has allowed to determine the average gmax direction of the reduced FdxB, which is skewed, pointing roughly towards Cys50 Cα and forming an angle of about 27.3 (±4) degrees with the normal of the [2Fe-2S] plane, while the gint- and gmin-directions are distributed in a plane tilted toward the cluster plane (see image below). Skewed orientations of the gmax component (red) with respect to the molecular frame of the [2Fe–2S] cluster of FdxB. The site of reduced iron in the reduced FdxB is the outermost Fe1 site with the low negative spin density, while the innermost Fe2 site with the high positive spin population is the non-reducible iron retaining the Fe3+-valence of a reduced cluster. From a structural point of view, the larger number of polarized (or polarizable) bonds (NH, OH) and the extended hydrogen bonding network around Fe1 in FdxB may be the crucial factor favoring the accommodation of the reducing electron at the outermost Fe1 site. These results suggest a significant distortion of the electronic structure of the reduced [2Fe-2S] cluster under the influence of the protein environment around each iron site in general. Heterometallic [AgFe3S4] ferredoxin variants – synthesis, characterization and the first crystal structure of an engineered heterometallic iron-sulfur protein The crystal structure of the Pyrococcus furiosus (Pf) ferredoxin (Fd) D14C variant with the novel [AgFe3S4] heterometallic cluster was determined to 1.95 Å resolution (PBD entry 4dhv), being the first reported structure of an engineered heterometallic iron-sulfur protein. The crystal structure of the monomeric form shows that the silver (I) ion is part of the cluster (clearly seen on the electron density map), as predicted from previous spectroscopic and electrochemical studies. The heterometal is coordinated to the three inorganic sulfides of the cluster and to the thiolate group of residue 14 (residues Cys11, Cys17 and Cys56 are coordinated with Fe ions of heterometal), replacing the aboriginal Fe ion in the all-iron coordinated [Fe4S4] D14C variant (2z8q, heterometallic [AgFe3S4] protein is in cyan and homometallic [Fe4S4] is in green) and completing the incomplete cuboidal cluster present in the [Fe3S4] WT Pf Fd (PDB: 1sj1) and its D14C (PDB: 3pni) variant (for more details see also "Crystal structures of the all cysteinyl coordinated D14C variant of Pyrococcus furiosus ferredoxin: (4Fe-4S) <-> (3Fe-4S) cluster conversion"). Structure alignment of backbone atoms from the heterometallic [AgFe3S4] protein and the homometallic [Fe4S4] D14C variant (2z8q) shows very minor differences, i.e. the root mean square deviation (RMSD) is 0.4 – 0.7 Å, observed due to the alternate conformation of the main chain atoms, flexible loops and small changes at the N- and C-termini (heterometallic [AgFe3S4] protein is in cyan and homometallic [Fe4S4] is in green). More significant difference can be seen in the superimposed Fe–S clusters (atom colors corresponding to yellow: S, orange: Fe, gray: Ag) from these two variants, which is due to the presence of the second row transition metal ion (Ag) coordinated to the four S-ligands, i.e. the presence of Ag results in a distorted geometry of the cluster compared to the all-iron arrangement, because to the longer Ag – S bond lengths compared to Fe – S bonds. However, the S – Ag – S bond angles are still close to the expected 90° for a primitive cubic system.

3D structures of ferredoxin

Updated on 14-August-2014

2Fe-2S containing ferredoxins

2z8q, 1sj1, 3ah7 – SyFd +Ga – Synechocystis – NMR
1i7h – Fd – Rhodopseudomonas palustris
1cje – SyFd
1e9m – Fd – Nocardioides aromaticivorans
4dhv – Fd – Novosphingobium aromaticivorans
2z8q, 1sj1 - Fd – Pseudomonas sp.
3pni, 2z8q - PmFd (mutant) – Pseudomonas mendocina
2i7f, 1uwm - RcFd – Rhodobacter capsulatus
1e9m – RcFd - NMR
1rfk, 3p63 - Fd – Cyanobacterium masticogladus laminosus
1vck - Fd – Pseudomonas resinovorans
1wri, 1frr - Fd – Equisetum arvense
1sjg - PmFd– NMR
1iue - Fd– Plasmodium falciparum
1m2a – AeFd – Aquifex aeolicus
1m2b, 1m2d, 1f37, 1f5b, 1f5c – AeFd (mutant)
1l5p – Fd – Trichomonas vaginalis
1i7h - Fd – Escherichia coli
1czp, 1qt9, 1frd, 1fxa - aFd– anabaena
1j7a, 1j7b, 1j7c , 1qoa, 1qob, 1qof, 1qog- aFd (mutant)
1e0z – Fd – Halobacterium salinarium
1e10 - Fd – Halobacterium halobium
1pfd – Fd – Petroselinum crispum – NMR
1a70 - Fd (mutant) – Spinacia oleracea
1awd - Fd – Chlorella fusca
2cjn, 2cjo, 1roe – SyFd – NMR
1rof – SyFd – Synechococcus elongates
1doi - Fd – Haloarcula marismortui
4fxc – Fd – Spirulina platensis
1fxi, 3av8 – Fd – Aphanothece sacrum
3dqy, 2qpz, 3ah7 - Fd – Pseudomonas putida
3ab5, 3wcq – Fd – Cyanidioschyzon merolae
3b2f – mFd – maize
3w5u, 3w5v – mFd + ferredoxin-NADP reductase
3b2g – Fd – Leptolyngbya boryana

4Fe-4S containing ferredoxins

3eun – AvFd – Allochromatium vinosum
3exy - AvFd (mutant)
2vkr - Fd+Zn – Acidianus ambivalens
2z8q - PfFd (mutant) – Pyrococcus furiosus
1siz - PfFd
3pni - PfFd (mutant)
2fgo - Fd– Pseudomonas aeruginosa
1iqz, 1ir0 - BtFd – Bacillus thermoproteolyticus
1rgv - Fd – Thauera aromatica
1dax, 1dfd – DaFd – Desulfovibrio africanus – NMR
1fxr - DaFd
1vjw – Fd – Thermotoga maritima
1dwl – Fd – Desulfomicrobium norvegicum

3Fe-4S containing ferredoxins

2v2k – Fd – Mycobacterium smegmatis
1wtf - BtFd (mutant)
1sj1 - PfFd
1fxd - DgFd – Desulfovibrio gigas
1f2g – DgFd – NMR
1xer - Fd – Sulfolobus tokodaii

4Fe-4S+3Fe-4S containing ferredoxins

1gao, 6fdr, 7fd1, 7fdr, 1axq, 6fd1, 1frh, 1fri,1frj, 1frk, 1frl, 1frm, 1fda, 1fdb, 1fdd, 5fd1, 1fer – AvFd – Azotobacter vinelandii
1pc4, 1pc5, 1g6b, 1g3o, 1ff2, 1b0v, 1d3w, 1b0t, 1a6l, 1ftc, 1frx, 2fd2, 1fd2 - AvFd (mutant)
1h98 – Fd – Thermus thermophilus
1a8p, 1bd6, 1bc6 - BsFd – Bacillus schlegelii – NMR

4Fe-4S+4Fe-4S containing ferredoxins

1dur – Fd – Peptoniphilus asaccarolyticus
1bwe, 1bqx - BsFd (mutant) – NMR
2fdn, 1fca , 1fdn- Fd – Clostridium acidi-urici
1blu - Fd – Chromatium vinosum
1clf– Fd – Clostridium pasteurianum – NMR

Adrenoredoxin

2jqr – ADR Fd domain (mutant)+cytochrome c (mutant) – yeast – NMR
2bt6 – cADR1 modified – cow
1l6u, 1l6v – cADR1 – NMR
1e6e – cADR (mutant)+ADR reductase
1cje, 1ayf - cADR
3na0, 3n9y, 3n9z, 3na1 - hADR +cholesterol side-chain cleavage enzyme – human
3p1m - hADR

Putidaredoxin

1yji, 1yjj, 1pdx – PpPUT – NMR
3lb8 – PpPUT (mutant)+PUT reductase
1xln, 1xlo, 1xlp, 1xlq, 1r7s, 1oqq, 1oqr - PpPUT (mutant)
1gpx, 1put- PpPUT (mutant) - NMR

Terpredoxin

1b9r – TER – Pseudomonas - NMR

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