Ferredoxin: Difference between revisions

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Michal Harel, Joel L. Sussman, David Canner, Eran Hodis, Jaime Prilusky, Alexander Berchansky, Wayne Decatur

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-[[Image:1vjw.png|left|150px]]<br />
+<StructureSection load='2z8q' size='450' side='right' scene='' caption='Ferredoxin with Fe4S4 cluster complex with cobalt hexamine (PDB code [[2z8q]])'>
-{{STRUCTURE_1vjw|  PDB=1vjw  | SIZE=400|  SCENE=Ferredoxin/Cv/1|right|CAPTION=Fe4S4 ferredoxin, [[1vjw]] }}
-[[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 (''e.g.'' 4Fe-4S ''Thermotoga maritima'' [[1vjw]] to the right).  '''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.
+==Function==
-{{TOC limit|limit=2}}
+[[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<ref>PMID:22556163</ref>..
-<StructureSection load='2Z8Qa.pdb' size='500' side='right' scene='Journal:JBIC:10/Cv1/2' caption='4Fe-4S ferredoxin complex with Co (III) hexamine [[2z8q]]'>
+*'''Putidaredoxin''' (PUT) and '''terpredoxin''' (TER) are involved in the same reaction in bacteria and contain a 2Fe-2S group<ref>PMID:10220356</ref>.
 ==D14C variant of ''Pyrococcus furiosus'' ferredoxin<ref>DOI 10.1007/s00775-011-0778-7</ref>==
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 [[Image:Schem1.png|left|300px|thumb|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.]]
+{{Clear}}
-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 at the left). 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 <scene name='Journal:JBIC:10/Cv1/13'>monomeric form, which resembles molecule A of D14C [4Fe-4S] Pyrococcus furiosus ferredoxin</scene>. Crystal packing in <scene name='Journal:JBIC:10/Cv2/7'>D14C [3Fe-4S] ferredoxin is as extended beta-sheet dimers of adjacent molecules</scene> (shown in <font color='red'><b>red</b></font> and <font color='orange'><b>orange</b></font>), which is the same as <scene name='Journal:JBIC:10/Cv2/9'>WT [3Fe-4S] P. furiosus ferredoxin</scene> ([[1sj1]], shown in <font color='blue'><b>blue</b></font> and <font color='cyan'><b>cyan</b></font>) even though the space groups are different (see also corresponding side views for <scene name='Journal:JBIC:10/Cv2/8'>D14C [3Fe-4S]</scene>) and <scene name='Journal:JBIC:10/Cv2/10'>WT [3Fe-4S]</scene>).
+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 <scene name='Journal:JBIC:10/Cv1/13'>monomeric form, which resembles molecule A of D14C [4Fe-4S] Pyrococcus furiosus ferredoxin</scene>. Crystal packing in <scene name='Journal:JBIC:10/Cv2/7'>D14C [3Fe-4S] ferredoxin is as extended beta-sheet dimers of adjacent molecules</scene> (shown in <font color='red'><b>red</b></font> and <font color='orange'><b>orange</b></font>), which is the same as <scene name='Journal:JBIC:10/Cv2/9'>WT [3Fe-4S] P. furiosus ferredoxin</scene> ([[1sj1]], shown in <font color='blue'><b>blue</b></font> and <font color='cyan'><b>cyan</b></font>) even though the space groups are different (see also corresponding side views for <scene name='Journal:JBIC:10/Cv2/8'>D14C [3Fe-4S]</scene>) and <scene name='Journal:JBIC:10/Cv2/10'>WT [3Fe-4S]</scene>).
-</StructureSection>
-<StructureSection load='1stp' size='500' side='right' scene='Journal:JBIC:12/Cv/2' caption='[2fe-S2] ferredoxin complex with Cl- (green) and Na+ (purple) ions, [[3ah7]]'>
 ==ISC-like [2Fe-2S] ferredoxin (FdxB) dimer from ''Pseudomonas putida'' JCM 20004<ref>DOI:10.1007/s00775-011-0793-8</ref>==
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 [[Image:FdxBFig8.jpg|left|400px|thumb|Skewed orientations of the g<sub>max</sub> component (red) with respect to
 the molecular frame of the [2Fe–2S] cluster of FdxB.]]
+{{Clear}}
 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 <scene name='Journal:JBIC:12/Cv1/15'>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</scene>. 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.
-</StructureSection>
+== Heterometallic [AgFe<sub>3</sub>S<sub>4</sub>] ferredoxin variants – synthesis, characterization and the first crystal structure of an engineered heterometallic iron-sulfur protein <ref >pmid 23296387 </ref>==
+The crystal structure of the ''Pyrococcus furiosus'' (Pf) ferredoxin (Fd) D14C variant with the novel [AgFe<sub>3</sub>S<sub>4</sub>] 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 <scene name='Journal:JBIC:19/Cv/4'>monomeric form</scene> shows that the <scene name='Journal:JBIC:19/Cv/6'>silver (I) ion is part of the cluster</scene> (clearly seen on the electron density map), as predicted from previous spectroscopic and electrochemical studies. The heterometal is coordinated to the <scene name='Journal:JBIC:19/Cv/5'>three inorganic sulfides of the cluster</scene> and to the <scene name='Journal:JBIC:19/Cv/7'>thiolate group of residue 14</scene> (residues <scene name='Journal:JBIC:19/Cv/8'>Cys11, Cys17 and Cys56</scene> are coordinated with Fe ions of heterometal), <scene name='Journal:JBIC:19/Cv/9'>replacing the aboriginal Fe ion in the all-iron coordinated</scene> [Fe<sub>4</sub>S<sub>4</sub>] D14C variant ([[2z8q]], <span style="color:cyan;background-color:black;font-weight:bold;">heterometallic [AgFe<sub>3</sub>S<sub>4</sub>] protein is in cyan</span> and <span style="color:lime;background-color:black;font-weight:bold;">homometallic [Fe<sub>4</sub>S<sub>4</sub>] is in green</span>) and  completing the incomplete cuboidal cluster present in the [Fe<sub>3</sub>S<sub>4</sub>] WT Pf Fd (PDB: [[1sj1]]) and its D14C (PDB: [[3pni]]) variant (for more details see also [http://proteopedia.org/w/Journal:JBIC:10 "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 [AgFe<sub>3</sub>S<sub>4</sub>] protein and the homometallic [Fe<sub>4</sub>S<sub>4</sub>] D14C variant ([[2z8q]]) shows <scene name='Journal:JBIC:19/Cv/10'>very minor differences</scene>, 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 (<span style="color:cyan;background-color:black;font-weight:bold;">heterometallic [AgFe<sub>3</sub>S<sub>4</sub>] protein is in cyan</span> and <span style="color:lime;background-color:black;font-weight:bold;">homometallic [Fe<sub>4</sub>S<sub>4</sub>] is in green</span>). <scene name='Journal:JBIC:19/Cv/14'>More significant difference</scene> can be seen in the superimposed Fe–S clusters (atom colors corresponding to <span style="color:yellow;background-color:black;font-weight:bold;">yellow: S</span>, <span style="color:orange;background-color:black;font-weight:bold;">orange: Fe</span>, <span style="color:gray;background-color:black;font-weight:bold;">gray: Ag</span>) 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, <scene name='Journal:JBIC:19/Cv/12'>because to the longer</scene> Ag – S bond lengths compared to Fe – S bonds. However, the S – Ag – S <scene name='Journal:JBIC:19/Cv/13'>bond angles</scene> are still close to the expected 90° for a primitive cubic system.
-===3D structures of ferredoxin===
+==3D structures of ferredoxin==
+[[Ferredoxin 3D structures]]
-''Update June 2012''
+</StructureSection>
-===2Fe-2S containing ferredoxins===
-[[2kaj]], [[1dox]], [[1doy]] – SyFd +Ga – ''Synechocystis'' – NMR <br />
-[[3hui]] – Fd – ''Rhodopseudomonas palustris'' <br />
-[[1off]] – SyFd  <br />
-[[3gce]] – Fd – ''Nocardioides aromaticivorans'' <br />
-[[3lxf]] – Fd – ''Novosphingobium aromaticivorans''<br />
-[[2e4p]], [[2e4q]] - Fd – ''Pseudomonas sp.'' <br />
-[[2q3w]], [[1vm9]] - PmFd (mutant) – ''Pseudomonas mendocina'' <br />
-[[2i7f]], [[1uwm]] - RcFd  – ''Rhodobacter capsulatus'' <br />
-[[1e9m]] – RcFd - NMR<br />
-[[1rfk]], [[3p63]] - Fd – ''Cyanobacterium'' ''masticogladus laminosus'' <br />
-[[1vck]] - Fd – ''Pseudomonas resinovorans'' <br />
-[[1wri]], [[1frr]] - Fd – E''quisetum arvense'' <br />
-[[1sjg]] - PmFd– NMR <br />
-[[1iue]] - Fd– ''Plasmodium falciparum'' <br />
-[[1m2a]] – AeFd – ''Aquifex aeolicu''s <br />
-[[1m2b]], [[1m2d]], [[1f37]], [[1f5b]], [[1f5c]] – AeFd (mutant) <br />
-[[1l5p]] – Fd –  ''Trichomonas vaginali''s <br />
-[[1i7h]] - Fd  – ''Escherichia coli'' <br />
-[[1czp]], [[1qt9]], [[1frd]], [[1fxa]] - aFd– ''anabaena'' <br />
-[[1j7a]], [[1j7b]], [[1j7c]] , [[1qoa]], [[1qob]], [[1qof]], [[1qog]]- aFd  (mutant)  <br />
-[[1e0z]] – Fd – ''Halobacterium salinarium'' <br />
-[[1pfd]] – Fd – ''Petroselinum crispum'' – NMR <br />
-[[1a70]] - Fd  (mutant) – ''Spinacia oleracea'' <br />
-[[1awd]] - Fd  – ''Chlorella fusca'' <br />
-[[2cjn]], [[2cjo]], [[1roe]] – SyFd – NMR <br />
-[[1rof]] – SyFd – ''Synechococcus elongates'' <br />
-[[1doi]] - Fd  – ''Haloarcula marismortui'' <br />
-[[4fxc]] – Fd – ''Spirulina platensi''s <br />
-[[1fxi]], [[3av8]] – Fd – ''Aphanothece sacrum'' <br />
-[[3dqy]], [[2qpz]], [[3ah7]] - Fd  – ''Pseudomonas putida'' <br />
-[[3ab5]] – Fd – ''Cyanidioschyzon merolae''
-===4Fe-4S containing ferredoxins ===
-[[3eun]] – AvFd  – ''Allochromatium vinosum'' <br />
-[[3exy]] - AvFd (mutant) <br />
-[[2vkr]] - Fd+Zn – ''Acidianus ambivalens'' <br />
-[[2z8q]] - PfFd (mutant) – ''Pyrococcus furiosus'' <br />
-[[1siz]] - PfFd<br >
-[[3pni]] - PfFd (mutant)<br />
-[[2fgo]] - Fd– ''Pseudomonas aeruginosa'' <br />
-[[1iqz]], [[1ir0]] - BtFd   – ''Bacillus thermoproteolyticus'' <br />
-[[1rgv]] - Fd  – ''Thauera aromatica'' <br />
-[[1dax]], [[1dfd]] – DaFd – ''Desulfovibrio africanus'' – NMR <br />
-[[1fxr]] - DaFd  <br />
-[[1vjw]] – Fd – ''Thermotoga maritima'' <br />
-===3Fe-4S containing ferredoxins===
-[[2v2k]] – Fd – ''Mycobacterium smegmatis'' <br />
-[[1wtf]] - BtFd (mutant)  <br />
-[[1sj1]] - PfFd  <br />
-[[1fxd]] - DgFd  – ''Desulfovibrio gigas'' <br />
-[[1f2g]] – DgFd – NMR <br />
-[[1xer]] - Fd  – ''Sulfolobus tokodaii'' <br />
-===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'' <br />
-[[1pc4]], [[1pc5]], [[1g6b]], [[1g3o]], [[1ff2]], [[1b0v]], [[1d3w]], [[1b0t]], [[1a6l]], [[1ftc]], [[1frx]], [[2fd2]], [[1fd2]] - AvFd  (mutant)  <br />
-[[1h98]] – Fd – ''Thermus thermophilus'' <br />
-[[1a8p]], [[1bd6]], [[1bc6]] - BsFd  – ''Bacillus schlegelii'' – NMR <br />
-===4Fe-4S+4Fe-4S containing ferredoxins===
-[[1dur]] – Fd – ''Peptoniphilus asaccarolyticus'' <br />
-[[1bwe]], [[1bqx]] - BsFd  (mutant) – NMR <br />
-[[2fdn]], [[1fca]] , [[1fdn]]- Fd – ''Clostridium acidi-urici'' <br />
-[[1blu]] - Fd – ''Chromatium vinosum'' <br />
-[[1clf ]]– Fd – ''Clostridium pasteurianum'' – NMR <br />
-===Adrenoredoxin===
-[[2jqr]] – ADR Fd domain (mutant)+cytochrome c (mutant) – yeast – NMR <br />
-[[2bt6]] – cADR1 modified – cow <br />
-[[1l6u]], [[1l6v]] – cADR1 – NMR <br />
-[[1e6e]] – cADR (mutant)+ADR reductase <br />
-[[1cje]], [[1ayf]] - cADR <br />
-[[3na0]], [[3n9y]], [[3n9z]], [[3na1]] - hADR +cholesterol side-chain cleavage enzyme – human<br />
-[[3p1m]] - hADR
-===Putidaredoxin===
-[[1yji]], [[1yjj]], [[1pdx]] – PpPUT – NMR <br />
-[[3lb8]] – PpPUT (mutant)+PUT reductase <br />
-[[1xln]], [[1xlo]], [[1xlp]], [[1xlq]], [[1r7s]], [[1oqq]], [[1oqr]] - PpPUT (mutant) <br />
-[[1gpx]], [[1put]]- PpPUT (mutant) - NMR <br />
-===Terpredoxin===
-[[1b9r]] – TER – ''Pseudomonas'' - NMR <br />
 ==References==