Ferredoxin - Revision history

Michal Harel at 05:50, 23 June 2024

2024-06-23T05:50:36Z

← Older revision		Revision as of 05:50, 23 June 2024
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	[[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.		[[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>..		*'''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.		*'''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>==

Michal Harel at 05:49, 23 June 2024

2024-06-23T05:49:35Z

← Older revision		Revision as of 05:49, 23 June 2024
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	[[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.		[[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.		*'''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.

	==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>==

Michal Harel at 05:39, 23 June 2024

2024-06-23T05:39:14Z

← Older revision		Revision as of 05:39, 23 June 2024
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	==Function==		==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.

	==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>==

Michal Harel at 08:28, 27 June 2019

2019-06-27T08:28:32Z

@@ Line 32: / Line 32: @@
 </StructureSection>
 ==References==
 <references/>

Michal Harel at 08:27, 27 June 2019

2019-06-27T08:27:09Z

← Older revision		Revision as of 08:27, 27 June 2019
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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. '''Putidaredoxin''' (PUT) and '''terpredoxin''' (TER) are involved in the same reaction in bacteria and contain a 2Fe-2S group.
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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.

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

	</StructureSection>		</StructureSection>

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	**[[5bok]] - Fd – ''Diaphorobacter''<br />		**[[5bok]] - Fd – ''Diaphorobacter''<br />
	**[[4zhp]] - Fd – potato<br />		**[[4zhp]] - Fd – potato<br />
	**[[4zho]] – Fd-2 – ''Arabidopsis thaliana''<br />		**[[4zho]] – AtFd-2 – ''Arabidopsis thaliana''<br />
			**[[6b03]], [[6b05]], [[6brs]] – AtFd-2 + zinc protease<br />
			**[[6e6s]], [[6e6r]], [[6e6q]] – PaFd (mutant)_- ''Pseudomonas aeruginosa''<br />

	*4Fe-4S containing ferredoxins		*4Fe-4S containing ferredoxins
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	**[[1siz]] - PfFd<br >		**[[1siz]] - PfFd<br >
	**[[3pni]] - PfFd (mutant)<br />		**[[3pni]] - PfFd (mutant)<br />
	**[[2fgo]] - ~~Fd– ''Pseudomonas aeruginosa''~~ <br />		**[[2fgo]] - PaFd <br />
	**[[1iqz]], [[1ir0]] - BtFd – ''Bacillus thermoproteolyticus'' <br />		**[[1iqz]], [[1ir0]] - BtFd – ''Bacillus thermoproteolyticus'' <br />
	**[[1rgv]] - Fd – ''Thauera aromatica'' <br />		**[[1rgv]] - Fd – ''Thauera aromatica'' <br />

Michal Harel at 09:50, 14 May 2017

2017-05-14T09:50:13Z

← Older revision		Revision as of 09:50, 14 May 2017
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	**[[1awd]] - Fd – ''Chlorella fusca'' <br />		**[[1awd]] - Fd – ''Chlorella fusca'' <br />
	**[[2cjn]], [[2cjo]], [[1roe]] – SyFd – NMR <br />		**[[2cjn]], [[2cjo]], [[1roe]] – SyFd – NMR <br />
	**[[1rof]] – SyFd – ''Synechococcus elongates'' <br />		**[[1rof]], [[5aui]], [[5auk]] – SyFd – ''Synechococcus elongates'' <br />
	**[[1doi]] - Fd – ''Haloarcula marismortui'' <br />		**[[1doi]] - Fd – ''Haloarcula marismortui'' <br />
	**[[4fxc]] – Fd – ''Spirulina platensi''s <br />		**[[4fxc]] – Fd – ''Spirulina platensi''s <br />
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	**[[3dqy]], [[2qpz]], [[3ah7]] - Fd – ''Pseudomonas putida'' <br />		**[[3dqy]], [[2qpz]], [[3ah7]] - Fd – ''Pseudomonas putida'' <br />
	**[[3ab5]], [[3wcq]] – Fd – ''Cyanidioschyzon merolae''<br />		**[[3ab5]], [[3wcq]] – Fd – ''Cyanidioschyzon merolae''<br />
	**[[3b2f]] – mFd – maize<br />		**[[3b2f]], [[5h57]] – mFd – maize<br />
	**[[3w5u]], [[3w5v]], [[1gaq]] – mFd + ferredoxin-NADP reductase<br />		**[[3w5u]], [[3w5v]], [[1gaq]], [[5h5j]] – mFd + ferredoxin-NADP reductase<br />
			**[[5h92]], [[5h8y]] – mFd + sulfite reductase<br />
	**[[3b2g]] – Fd – ''Leptolyngbya boryana''<br />		**[[3b2g]] – Fd – ''Leptolyngbya boryana''<br />
	**[[2mh7]] – Fd – ''Chlamydomonas reinhardtii''<br />		**[[2mh7]] – Fd – ''Chlamydomonas reinhardtii''<br />
	**[[1ewy]] – Fd + ferredoxin-NADP reductase - ''Nostoc''<br />		**[[1ewy]] – Fd + ferredoxin-NADP reductase - ''Nostoc''<br />
			**[[5ffi]], [[5abr]] - AvFd – ''Azotobacter vinelandii''<br />
			**[[5bok]] - Fd – ''Diaphorobacter''<br />
			**[[4zhp]] - Fd – potato<br />
			**[[4zho]] – Fd-2 – ''Arabidopsis thaliana''<br />


	*4Fe-4S containing ferredoxins		*4Fe-4S containing ferredoxins
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	**[[1cje]], [[1ayf]] - cADR <br />		**[[1cje]], [[1ayf]] - cADR <br />
	**[[3na0]], [[3n9y]], [[3n9z]], [[3na1]] - hADR +cholesterol side-chain cleavage enzyme – human<br />		**[[3na0]], [[3n9y]], [[3n9z]], [[3na1]] - hADR +cholesterol side-chain cleavage enzyme – human<br />
	**[[3p1m]] - hADR		**[[3p1m]] - hADR<br />
			**[[5uj5]] – ADR – ''Encephalitozoon cuniculi''<br />

	*Putidaredoxin		*Putidaredoxin

Michal Harel at 09:03, 2 April 2015

2015-04-02T09:03:47Z

← Older revision		Revision as of 09:03, 2 April 2015
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	**[[2mjd]], [[2mje]] – yADR – yeast<br />		**[[2mjd]], [[2mje]] – yADR – yeast<br />
	**[[2jqr]] – ~~ADR~~ Fd domain (mutant)+cytochrome c (mutant) – NMR <br />		**[[2jqr]] – yADR Fd domain (mutant)+cytochrome c (mutant) – NMR <br />
	**[[2bt6]] – cADR1 modified – cow <br />		**[[2bt6]] – cADR1 modified – cow <br />
	**[[1l6u]], [[1l6v]] – cADR1 – NMR <br />		**[[1l6u]], [[1l6v]] – cADR1 – NMR <br />

Michal Harel at 09:00, 2 April 2015

2015-04-02T09:00:08Z

← Older revision		Revision as of 09:00, 2 April 2015
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	**[[2kaj]], [[1dox]], [[1doy]] – SyFd +Ga – ''Synechocystis'' – NMR <br />		**[[2kaj]], [[1dox]], [[1doy]] – SyFd +Ga – ''Synechocystis'' – NMR <br />
	**[[3hui]] – Fd – ''Rhodopseudomonas palustris'' <br />		**[[3hui]], [[4ltu]] – Fd – ''Rhodopseudomonas palustris'' <br />
	**[[1off]] – SyFd <br />		**[[1off]] – SyFd <br />
	**[[3gce]] – Fd – ''Nocardioides aromaticivorans'' <br />		**[[3gce]] – Fd – ''Nocardioides aromaticivorans'' <br />
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	**[[3ab5]], [[3wcq]] – Fd – ''Cyanidioschyzon merolae''<br />		**[[3ab5]], [[3wcq]] – Fd – ''Cyanidioschyzon merolae''<br />
	**[[3b2f]] – mFd – maize<br />		**[[3b2f]] – mFd – maize<br />
	**[[3w5u]], [[3w5v]] – mFd + ferredoxin-NADP reductase<br />		**[[3w5u]], [[3w5v]], [[1gaq]] – mFd + ferredoxin-NADP reductase<br />
	**[[3b2g]] – Fd – ''Leptolyngbya boryana''		**[[3b2g]] – Fd – ''Leptolyngbya boryana''<br />
			**[[2mh7]] – Fd – ''Chlamydomonas reinhardtii''<br />
			**[[1ewy]] – Fd + ferredoxin-NADP reductase - ''Nostoc''<br />

	*4Fe-4S containing ferredoxins		*4Fe-4S containing ferredoxins
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	*Adrenoredoxin		*Adrenoredoxin

	**[[2jqr]] – ADR Fd domain (mutant)+cytochrome c (mutant) ~~– yeast~~ – NMR <br />		**[[2mjd]], [[2mje]] – yADR – yeast<br />
			**[[2jqr]] – ADR Fd domain (mutant)+cytochrome c (mutant) – NMR <br />
	**[[2bt6]] – cADR1 modified – cow <br />		**[[2bt6]] – cADR1 modified – cow <br />
	**[[1l6u]], [[1l6v]] – cADR1 – NMR <br />		**[[1l6u]], [[1l6v]] – cADR1 – NMR <br />

Michal Harel at 07:09, 25 November 2014

2014-11-25T07:09:01Z

Show changes

Michal Harel at 08:09, 27 August 2014

2014-08-27T08:09:30Z

← Older revision		Revision as of 08:09, 27 August 2014
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	</StructureSection>		</StructureSection>

	===3D structures of ferredoxin===		==3D structures of ferredoxin==

	Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}		Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}