1pc5: Difference between revisions

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 ==Crystal Structure of the P50G Mutant of Ferredoxin I at 1.8 A Resolution==
-<StructureSection load='1pc5' size='340' side='right' caption='[[1pc5]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='1pc5' size='340' side='right'caption='[[1pc5]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1pc5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_478 Atcc 478]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PC5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PC5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1pc5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PC5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PC5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1pc4|1pc4]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pc5 OCA], [http://pdbe.org/1pc5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pc5 RCSB], [http://www.ebi.ac.uk/pdbsum/1pc5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pc5 ProSAT]</span></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=1pc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pc5 OCA], [https://pdbe.org/1pc5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pc5 RCSB], [https://www.ebi.ac.uk/pdbsum/1pc5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pc5 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/FER1_AZOVI FER1_AZOVI]] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions. This ferredoxin could play a role in regulating gene expression by interacting directly with DNA.
+[https://www.uniprot.org/uniprot/FER1_AZOVI FER1_AZOVI] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions. This ferredoxin could play a role in regulating gene expression by interacting directly with DNA.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 20: / Line 20: @@
 </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=1pc5 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The 7Fe ferredoxin from Azotobacter vinelandii (AvFdI) contains a [3Fe-4S](+/0) cluster that binds a single proton in its reduced level. Although the cluster is buried, and therefore inaccessible to solvent, proton transfer from solvent to the cluster is fast. The kinetics and energetics of the coupled electron-proton transfer reaction at the cluster have been analyzed in detail by protein-film voltammetry, to reveal that proton transfer is mediated by the mobile carboxylate of an adjacent surface residue, aspartate-15, the pK of which is sensitive to the charge on the cluster. This paper examines the role of a nearby proline residue, proline-50, in proton transfer and its coupling to electron transfer. In the P50A and P50G mutants, a water molecule has entered the cluster binding region; it is hydrogen bonded to the backbone amide of residue-50 and to the Asp-15 carboxylate, and it is approximately 4 A from the closest sulfur atom of the cluster. Despite the water molecule linking the cluster more directly to the solvent, proton transfer is not accelerated. A detailed analysis reveals that Asp-15 remains a central part of the mechanism. However, the electrostatic coupling between cluster and carboxylate is almost completely quenched, so that cluster reduction no longer induces such a favorable shift in the carboxylate pK, and protonation of the base no longer induces a significant shift in the pK of the cluster. The electrostatic coupling is crucial for maintaining the efficiency of proton transfer both to and from the cluster, over a range of pH values.
-Mechanisms of redox-coupled proton transfer in proteins: role of the proximal proline in reactions of the [3Fe-4S] cluster in Azotobacter vinelandii ferredoxin I.,Camba R, Jung YS, Hunsicker-Wang LM, Burgess BK, Stout CD, Hirst J, Armstrong FA Biochemistry. 2003 Sep 16;42(36):10589-99. PMID:12962482<ref>PMID:12962482</ref>
+==See Also==
+*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1pc5" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 478]]
+[[Category: Azotobacter vinelandii]]
-[[Category: Armstrong, F A]]
+[[Category: Large Structures]]
-[[Category: Burgess, B K]]
+[[Category: Armstrong FA]]
-[[Category: Camba, R]]
+[[Category: Burgess BK]]
-[[Category: Chen, K]]
+[[Category: Camba R]]
-[[Category: Hirst, J]]
+[[Category: Chen K]]
-[[Category: Hunsicker-Wang, L M]]
+[[Category: Hirst J]]
-[[Category: Jung, Y S]]
+[[Category: Hunsicker-Wang LM]]
-[[Category: Stout, C D]]
+[[Category: Jung YS]]
-[[Category: Electron transport]]
+[[Category: Stout CD]]
-[[Category: Ferredoxin]]
-[[Category: Iron-sulfur protein]]
-[[Category: Mutant]]