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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-<StructureSection load='1vjw' size='450' side='right' scene='Journal:JBIC:10/Cv1/2' caption='Ferredoxin with Fe4S4 cluster (PDB code [[1vjw]])'>
+<StructureSection load='2z8q' size='450' side='right' scene='' caption='Ferredoxin with Fe4S4 cluster complex with cobalt hexamine (PDB code [[2z8q]])'>
-[[Image:2z8q.png|left|150px]]<br />
-[[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.
+==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>..
+*'''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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 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.
-</StructureSection>
-__NOTOC__
-===3D structures of ferredoxin===
-Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
+==3D structures of ferredoxin==
+[[Ferredoxin 3D structures]]
-===2Fe-2S containing ferredoxins===
+</StructureSection>
-[[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]], [[3wcq]] – Fd – ''Cyanidioschyzon merolae''<br />
-[[3b2f]] – Fd – maize<br />
-[[3b2g]] – Fd – ''Leptolyngbya boryana''
-===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==