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<StructureSection load='2z8q' size='450' side='right' scene='' caption='Ferredoxin with Fe4S4 cluster complex with cobalt hexamine (PDB code [[2z8q]])'>
<StructureSection load='2z8q' size='450' side='right' scene='' caption='Ferredoxin with Fe4S4 cluster complex with cobalt hexamine (PDB code [[2z8q]])'>


==Function==


[[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.
[[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>..   
*'''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>==
==D14C variant of ''Pyrococcus furiosus'' ferredoxin<ref>DOI 10.1007/s00775-011-0778-7</ref>==
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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 ''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.
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.
</StructureSection>


==3D structures of ferredoxin==
==3D structures of ferredoxin==
[[Ferredoxin 3D structures]]


Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
</StructureSection>
{{#tree:id=OrganizedByTopic|openlevels=0|
 
*2Fe-2S containing ferredoxins
 
**[[2kaj]], [[1dox]], [[1doy]] – SyFd +Ga – ''Synechocystis'' – NMR <br />
**[[3hui]], [[4ltu]] – 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 />
**[[1e10]] - Fd – ''Halobacterium halobium''<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]], [[3wcq]] – Fd – ''Cyanidioschyzon merolae''<br />
**[[3b2f]] – mFd – maize<br />
**[[3w5u]], [[3w5v]], [[1gaq]] – mFd + ferredoxin-NADP reductase<br />
**[[3b2g]] – Fd – ''Leptolyngbya boryana''<br />
**[[2mh7]] – Fd – ''Chlamydomonas reinhardtii''<br />
**[[1ewy]] – Fd + ferredoxin-NADP reductase - ''Nostoc''<br />
 
*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 />
**[[1dwl]] – Fd – ''Desulfomicrobium norvegicum''<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
 
**[[2mjd]], [[2mje]] – yADR – yeast<br />
**[[2jqr]] – ADR Fd domain (mutant)+cytochrome c (mutant) – 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 />
**[[4jws]] - PpPUT + cytochrome P450cam<br />
**[[3w9c]], [[4jwu]] - PpPUT (mutant) + cytochrome P450cam<br />
**[[2m56]] - PpPUT (mutant) + cytochrome P450cam - NMR<br />
**[[4jx1]] - PpPUT (mutant) + cytochrome P450cam + camphor + hydroxycamphor<br />
 
*Terpredoxin


**[[1b9r]] – TER – ''Pseudomonas'' - NMR <br />
}}
==References==
==References==
<references/>
<references/>

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Joel L. Sussman, David Canner, Eran Hodis, Jaime Prilusky, Alexander Berchansky, Wayne Decatur
Retrieved from "https://proteopedia.openfox.io/w/Ferredoxin"