1frf: Difference between revisions

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~~[[Image:1frf.gif|left|200px]]<br /><applet load="1frf" size="450" color="white" frame="true" align="right" spinBox="true"~~

~~caption="1frf, resolution 2.70Å" />~~

~~'''CRYSTAL STRUCTURE OF THE NI-FE HYDROGENASE FROM DESULFOVIBRIO FRUCTOSOVORANS'''<br />~~

==~~Overview~~==

==CRYSTAL STRUCTURE OF THE NI-FE HYDROGENASE FROM DESULFOVIBRIO FRUCTOSOVORANS==

The role of the high potential [3Fe-4S]1+,0 cluster of [NiFe] hydrogenase, from Desulfovibrio species located halfway between the proximal and distal, low potential [4Fe-4S]2+,1+ clusters has been investigated by using, site-directed mutagenesis. Proline 238 of Desulfovibrio fructosovorans, [NiFe] hydrogenase, which occupies the position of a potential ligand of, the lacking fourth Fe-site of the [3Fe-4S] cluster, was replaced by a, cysteine residue. The properties of the mutant enzyme were investigated in, terms of enzymatic activity, EPR, and redox properties of the iron-sulfur, centers and crystallographic structure. We have shown on the basis of both, spectroscopic and x-ray crystallographic studies that the [3Fe-4S] cluster, of D. fructosovorans hydrogenase was converted into a [4Fe-4S] center in, the P238 mutant. The [3Fe-4S] to [4Fe-4S] cluster conversion resulted in a, lowering of approximately 300 mV of the midpoint potential of the modified, cluster, whereas no significant alteration of the spectroscopic and redox, properties of the two native [4Fe-4S] clusters and the NiFe center, occurred. The significant decrease of the midpoint potential of the, intermediate Fe-S cluster had only a slight effect on the catalytic, activity of the P238C mutant as compared with the wild-type enzyme. The, implications of the results for the role of the high-potential [3Fe-4S], cluster in the intramolecular electron transfer pathway are discussed.

== Structural highlights ==

<table><tr><td colspan='2'>[[1frf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Solidesulfovibrio_fructosivorans Solidesulfovibrio fructosivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FRF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FRF FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1frf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1frf OCA], [https://pdbe.org/1frf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1frf RCSB], [https://www.ebi.ac.uk/pdbsum/1frf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1frf ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/PHNS_SOLFR PHNS_SOLFR] Involved in hydrogen uptake for the anaerobic reduction of sulfate to hydrogen sulfide in an electron transport chain. Cytochrome c3 is the physiological electron acceptor.

== Evolutionary Conservation ==

[[Image:Consurf_key_small.gif|200px|right]]

Check<jmol>

<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fr/1frf_consurf.spt"</scriptWhenChecked>

<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>

<text>to colour the structure by Evolutionary Conservation</text>

</jmolCheckbox>

</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1frf ConSurf].

== Publication Abstract from PubMed ==

The role of the high potential [3Fe-4S]1+,0 cluster of [NiFe] hydrogenase from Desulfovibrio species located halfway between the proximal and distal low potential [4Fe-4S]2+,1+ clusters has been investigated by using site-directed mutagenesis. Proline 238 of Desulfovibrio fructosovorans [NiFe] hydrogenase, which occupies the position of a potential ligand of the lacking fourth Fe-site of the [3Fe-4S] cluster, was replaced by a cysteine residue. The properties of the mutant enzyme were investigated in terms of enzymatic activity, EPR, and redox properties of the iron-sulfur centers and crystallographic structure. We have shown on the basis of both spectroscopic and x-ray crystallographic studies that the [3Fe-4S] cluster of D. fructosovorans hydrogenase was converted into a [4Fe-4S] center in the P238 mutant. The [3Fe-4S] to [4Fe-4S] cluster conversion resulted in a lowering of approximately 300 mV of the midpoint potential of the modified cluster, whereas no significant alteration of the spectroscopic and redox properties of the two native [4Fe-4S] clusters and the NiFe center occurred. The significant decrease of the midpoint potential of the intermediate Fe-S cluster had only a slight effect on the catalytic activity of the P238C mutant as compared with the wild-type enzyme. The implications of the results for the role of the high-potential [3Fe-4S] cluster in the intramolecular electron transfer pathway are discussed.

~~==About this Structure==~~

[3Fe-4S] to [4Fe-4S] cluster conversion in Desulfovibrio fructosovorans [NiFe] hydrogenase by site-directed mutagenesis.,Rousset M, Montet Y, Guigliarelli B, Forget N, Asso M, Bertrand P, Fontecilla-Camps JC, Hatchikian EC Proc Natl Acad Sci U S A. 1998 Sep 29;95(20):11625-30. PMID:9751716<ref>PMID:9751716</ref>

~~1FRF is a~~ [~~http://en.wikipedia.org/wiki/Protein_complex Protein complex~~] ~~structure of sequences from~~ [~~http://en.wikipedia.org/wiki/Desulfovibrio_fructosovorans~~ Desulfovibrio fructosovorans] ~~with FE~~, NI, MG, ~~SF4 and F3S as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase]~~, ~~with~~ EC ~~number [http~~:~~//www.brenda~~-~~enzymes~~.~~info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2] Full crystallographic information is available from [http~~:/~~/ispc.weizmann.ac.il/oca-bin/ocashort?id=1FRF OCA].~~

~~==Reference==~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

~~[3Fe-4S] to [4Fe-4S] cluster conversion in Desulfovibrio fructosovorans [NiFe] hydrogenase by site-directed mutagenesis.~~, ~~Rousset M, Montet Y, Guigliarelli B, Forget N, Asso M, Bertrand P, Fontecilla-Camps JC, Hatchikian EC, Proc Natl Acad Sci~~ U S A. ~~1998 Sep 29;95(20):11625~~-~~30. PMID:[http~~://~~ispc.weizmann.ac.il//pmbin~~/~~getpm?pmid=9751716 9751716]~~

</div>

[[Category: ~~Desulfovibrio fructosovorans~~]]

[[Category: ~~Ferredoxin hydrogenase]]~~

== References ==

~~[[Category: Protein complex~~]]

[[Category: Fontecilla~~, J.C.~~]]

__TOC__

[[Category: Frey, M.]]

</StructureSection>

[[Category: Hatchikian~~, E.C.~~]]

[[Category: Large Structures]]

[[Category: Montet, Y.]]

[[Category: Solidesulfovibrio fructosivorans]]

[[Category: Piras, C.]]

[[Category: Fontecilla JC]]

[[Category: Volbeda, A.]]

[[Category: Frey M]]

~~[[Category: F3S]]~~

[[Category: Hatchikian EC]]

~~[[Category: FE]]~~

[[Category: Montet Y]]

~~[[Category: MG]]~~

[[Category: Piras C]]

~~[[Category: NI]]~~

[[Category: Volbeda A]]

~~[[Category: SF4]]~~

~~[[Category: ni-fe hydrogenase]]~~

~~''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:11:26 2007''~~

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@@ Line 1: / Line 1: @@
-[[Image:1frf.gif|left|200px]]<br /><applet load="1frf" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1frf, resolution 2.70&Aring;" />
-'''CRYSTAL STRUCTURE OF THE NI-FE HYDROGENASE FROM DESULFOVIBRIO FRUCTOSOVORANS'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF THE NI-FE HYDROGENASE FROM DESULFOVIBRIO FRUCTOSOVORANS==
-The role of the high potential [3Fe-4S]1+,0 cluster of [NiFe] hydrogenase, from Desulfovibrio species located halfway between the proximal and distal, low potential [4Fe-4S]2+,1+ clusters has been investigated by using, site-directed mutagenesis. Proline 238 of Desulfovibrio fructosovorans, [NiFe] hydrogenase, which occupies the position of a potential ligand of, the lacking fourth Fe-site of the [3Fe-4S] cluster, was replaced by a, cysteine residue. The properties of the mutant enzyme were investigated in, terms of enzymatic activity, EPR, and redox properties of the iron-sulfur, centers and crystallographic structure. We have shown on the basis of both, spectroscopic and x-ray crystallographic studies that the [3Fe-4S] cluster, of D. fructosovorans hydrogenase was converted into a [4Fe-4S] center in, the P238 mutant. The [3Fe-4S] to [4Fe-4S] cluster conversion resulted in a, lowering of approximately 300 mV of the midpoint potential of the modified, cluster, whereas no significant alteration of the spectroscopic and redox, properties of the two native [4Fe-4S] clusters and the NiFe center, occurred. The significant decrease of the midpoint potential of the, intermediate Fe-S cluster had only a slight effect on the catalytic, activity of the P238C mutant as compared with the wild-type enzyme. The, implications of the results for the role of the high-potential [3Fe-4S], cluster in the intramolecular electron transfer pathway are discussed.
+<StructureSection load='1frf' size='340' side='right'caption='[[1frf]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1frf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Solidesulfovibrio_fructosivorans Solidesulfovibrio fructosivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FRF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FRF FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1frf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1frf OCA], [https://pdbe.org/1frf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1frf RCSB], [https://www.ebi.ac.uk/pdbsum/1frf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1frf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PHNS_SOLFR PHNS_SOLFR] Involved in hydrogen uptake for the anaerobic reduction of sulfate to hydrogen sulfide in an electron transport chain. Cytochrome c3 is the physiological electron acceptor.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fr/1frf_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1frf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The role of the high potential [3Fe-4S]1+,0 cluster of [NiFe] hydrogenase from Desulfovibrio species located halfway between the proximal and distal low potential [4Fe-4S]2+,1+ clusters has been investigated by using site-directed mutagenesis. Proline 238 of Desulfovibrio fructosovorans [NiFe] hydrogenase, which occupies the position of a potential ligand of the lacking fourth Fe-site of the [3Fe-4S] cluster, was replaced by a cysteine residue. The properties of the mutant enzyme were investigated in terms of enzymatic activity, EPR, and redox properties of the iron-sulfur centers and crystallographic structure. We have shown on the basis of both spectroscopic and x-ray crystallographic studies that the [3Fe-4S] cluster of D. fructosovorans hydrogenase was converted into a [4Fe-4S] center in the P238 mutant. The [3Fe-4S] to [4Fe-4S] cluster conversion resulted in a lowering of approximately 300 mV of the midpoint potential of the modified cluster, whereas no significant alteration of the spectroscopic and redox properties of the two native [4Fe-4S] clusters and the NiFe center occurred. The significant decrease of the midpoint potential of the intermediate Fe-S cluster had only a slight effect on the catalytic activity of the P238C mutant as compared with the wild-type enzyme. The implications of the results for the role of the high-potential [3Fe-4S] cluster in the intramolecular electron transfer pathway are discussed.
-==About this Structure==
+[3Fe-4S] to [4Fe-4S] cluster conversion in Desulfovibrio fructosovorans [NiFe] hydrogenase by site-directed mutagenesis.,Rousset M, Montet Y, Guigliarelli B, Forget N, Asso M, Bertrand P, Fontecilla-Camps JC, Hatchikian EC Proc Natl Acad Sci U S A. 1998 Sep 29;95(20):11625-30. PMID:9751716<ref>PMID:9751716</ref>
-FRF is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Desulfovibrio_fructosovorans Desulfovibrio fructosovorans] with FE, NI, MG, SF4 and F3S as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1FRF OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[3Fe-4S] to [4Fe-4S] cluster conversion in Desulfovibrio fructosovorans [NiFe] hydrogenase by site-directed mutagenesis., Rousset M, Montet Y, Guigliarelli B, Forget N, Asso M, Bertrand P, Fontecilla-Camps JC, Hatchikian EC, Proc Natl Acad Sci U S A. 1998 Sep 29;95(20):11625-30. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9751716 9751716]
+</div>
-[[Category: Desulfovibrio fructosovorans]]
+<div class="pdbe-citations 1frf" style="background-color:#fffaf0;"></div>
-[[Category: Ferredoxin hydrogenase]]
+== References ==
-[[Category: Protein complex]]
+<references/>
-[[Category: Fontecilla, J.C.]]
+__TOC__
-[[Category: Frey, M.]]
+</StructureSection>
-[[Category: Hatchikian, E.C.]]
+[[Category: Large Structures]]
-[[Category: Montet, Y.]]
+[[Category: Solidesulfovibrio fructosivorans]]
-[[Category: Piras, C.]]
+[[Category: Fontecilla JC]]
-[[Category: Volbeda, A.]]
+[[Category: Frey M]]
-[[Category: F3S]]
+[[Category: Hatchikian EC]]
-[[Category: FE]]
+[[Category: Montet Y]]
-[[Category: MG]]
+[[Category: Piras C]]
-[[Category: NI]]
+[[Category: Volbeda A]]
-[[Category: SF4]]
-[[Category: ni-fe hydrogenase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:11:26 2007''