5koj: Difference between revisions

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<table><tr><td colspan='2'>[[5koj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Gluconacetobacter_diazotrophicus_PA1_5 Gluconacetobacter diazotrophicus PA1 5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KOJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KOJ 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]] 2.592Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat">~~<scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>,~~ <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA~~</scene>, <scene name='pdbligand=ICS:IRON-SULFUR-MOLYBDENUM+CLUSTER+WITH+INTERSTITIAL+CARBON'>ICS~~</scene></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=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</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=5koj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5koj OCA], [https://pdbe.org/5koj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5koj RCSB], [https://www.ebi.ac.uk/pdbsum/5koj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5koj ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/A9H5W5_GLUDA A9H5W5_GLUDA]

== Publication Abstract from PubMed ==

The P-cluster is a unique iron-sulfur center that likely functions as a dynamic electron (e(-)) relay site between the Fe-protein and the catalytic FeMo-cofactor in nitrogenase. The P-cluster has been shown to undergo large conformational changes upon 2-e(-) oxidation which entail the coordination of two of the Fe centers to a Ser side chain and a backbone amide N, respectively. Yet, how and if this 2-e(-) oxidized state (P(OX)) is involved in catalysis by nitrogenase is not well established. Here, we present the crystal structures of reduced and oxidized MoFe-protein (MoFeP) from Gluconacetobacter diazotrophicus (Gd), which natively possesses an Ala residue in the position of the Ser ligand to the P-cluster. While reduced Gd-MoFeP is structurally identical to previously characterized counterparts around the FeMo-cofactor, oxidized Gd-MoFeP features an unusual Tyr coordination to its P-cluster along with ligation by a backbone amide nitrogen. EPR analysis of the oxidized Gd-MoFeP P-cluster confirmed that it is a 2-e(-) oxidized, integer-spin species. Importantly, we have found that the sequence positions corresponding to the Ser and Tyr ligands are almost completely covariant among Group I nitrogenases. These findings strongly support the possibility that the P(OX) state is functionally relevant in nitrogenase catalysis and that a hard, O-based anionic ligand serves to stabilize this state in a switchable fashion.

Tyrosine-Coordinated P-Cluster in G. diazotrophicus Nitrogenase: Evidence for the Importance of O-Based Ligands in Conformationally Gated Electron Transfer.,Owens CP, Katz FE, Carter CH, Oswald VF, Tezcan FA J Am Chem Soc. 2016 Aug 17;138(32):10124-7. doi: 10.1021/jacs.6b06783. Epub 2016 , Aug 8. PMID:27487256<ref>PMID:27487256</ref>

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

</div>

==See Also==

*[[Nitrogenase 3D structures|Nitrogenase 3D structures]]

== References ==

__TOC__

</StructureSection>

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@@ Line 5: / Line 5: @@
 <table><tr><td colspan='2'>[[5koj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Gluconacetobacter_diazotrophicus_PA1_5 Gluconacetobacter diazotrophicus PA1 5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KOJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KOJ 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]] 2.592&#8491;</td></tr>
-<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=ICS:IRON-SULFUR-MOLYBDENUM+CLUSTER+WITH+INTERSTITIAL+CARBON'>ICS</scene></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=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</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=5koj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5koj OCA], [https://pdbe.org/5koj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5koj RCSB], [https://www.ebi.ac.uk/pdbsum/5koj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5koj ProSAT]</span></td></tr>
 </table>
 == Function ==
 [https://www.uniprot.org/uniprot/A9H5W5_GLUDA A9H5W5_GLUDA]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The P-cluster is a unique iron-sulfur center that likely functions as a dynamic electron (e(-)) relay site between the Fe-protein and the catalytic FeMo-cofactor in nitrogenase. The P-cluster has been shown to undergo large conformational changes upon 2-e(-) oxidation which entail the coordination of two of the Fe centers to a Ser side chain and a backbone amide N, respectively. Yet, how and if this 2-e(-) oxidized state (P(OX)) is involved in catalysis by nitrogenase is not well established. Here, we present the crystal structures of reduced and oxidized MoFe-protein (MoFeP) from Gluconacetobacter diazotrophicus (Gd), which natively possesses an Ala residue in the position of the Ser ligand to the P-cluster. While reduced Gd-MoFeP is structurally identical to previously characterized counterparts around the FeMo-cofactor, oxidized Gd-MoFeP features an unusual Tyr coordination to its P-cluster along with ligation by a backbone amide nitrogen. EPR analysis of the oxidized Gd-MoFeP P-cluster confirmed that it is a 2-e(-) oxidized, integer-spin species. Importantly, we have found that the sequence positions corresponding to the Ser and Tyr ligands are almost completely covariant among Group I nitrogenases. These findings strongly support the possibility that the P(OX) state is functionally relevant in nitrogenase catalysis and that a hard, O-based anionic ligand serves to stabilize this state in a switchable fashion.
+Tyrosine-Coordinated P-Cluster in G. diazotrophicus Nitrogenase: Evidence for the Importance of O-Based Ligands in Conformationally Gated Electron Transfer.,Owens CP, Katz FE, Carter CH, Oswald VF, Tezcan FA J Am Chem Soc. 2016 Aug 17;138(32):10124-7. doi: 10.1021/jacs.6b06783. Epub 2016 , Aug 8. PMID:27487256<ref>PMID:27487256</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 5koj" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Nitrogenase 3D structures|Nitrogenase 3D structures]]
+== References ==
+<references/>
 __TOC__
 </StructureSection>