8e3t: Difference between revisions

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<table><tr><td colspan='2'>[[8e3t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Azotobacter_vinelandii_DJ Azotobacter vinelandii DJ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8E3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8E3T FirstGlance]. <br>
<table><tr><td colspan='2'>[[8e3t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Azotobacter_vinelandii_DJ Azotobacter vinelandii DJ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8E3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8E3T 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]] 2.2&#8491;</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]] 2.2&#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=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=ICS:IRON-SULFUR-MOLYBDENUM+CLUSTER+WITH+INTERSTITIAL+CARBON'>ICS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=UFF:FE(7)-S(7)+CLUSTER'>UFF</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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=8e3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8e3t OCA], [https://pdbe.org/8e3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8e3t RCSB], [https://www.ebi.ac.uk/pdbsum/8e3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8e3t 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=8e3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8e3t OCA], [https://pdbe.org/8e3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8e3t RCSB], [https://www.ebi.ac.uk/pdbsum/8e3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8e3t ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[https://www.uniprot.org/uniprot/NIFD_AZOVI NIFD_AZOVI] This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.
[https://www.uniprot.org/uniprot/NIFD_AZOVI NIFD_AZOVI] This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Nitrogenase catalyzes the multielectron reduction of dinitrogen to ammonia. Electron transfer in the catalytic protein (MoFeP) proceeds through a unique [8Fe-7S] cluster (P-cluster) to the active site (FeMoco). In the reduced, all-ferrous (P(N)) state, the P-cluster is coordinated by six cysteine residues. Upon two-electron oxidation to the P(2+) state, the P-cluster undergoes conformational changes in which a highly conserved oxygen-based residue (a Ser or a Tyr) and a backbone amide additionally ligate the cluster. Previous studies of Azotobacter vinelandii (Av) MoFeP revealed that when the oxygen-based residue, betaSer188, was mutated to a noncoordinating residue, Ala, the P-cluster became redox-labile and reversibly lost two of its eight Fe centers. Surprisingly, the Av strain with a MoFeP variant that lacked the serine ligand (Av betaSer188Ala MoFeP) displayed the same diazotrophic growth and in vitro enzyme turnover rates as wild-type Av MoFeP, calling into question the necessity of this conserved ligand for nitrogenase function. Based on these observations, we hypothesized that betaSer188 plays a role in protecting the P-cluster under nonideal conditions. Here, we investigated the protective role of betaSer188 both in vivo and in vitro by characterizing the ability of Av betaSer188Ala cells to grow under suboptimal conditions (high oxidative stress or Fe limitation) and by determining the tendency of betaSer188Ala MoFeP to be mismetallated in vitro. Our results demonstrate that betaSer188 (1) increases Av cell survival upon exposure to oxidative stress in the form of hydrogen peroxide, (2) is necessary for efficient Av diazotrophic growth under Fe-limiting conditions, and (3) may protect the P-cluster from metal exchange in vitro. Taken together, our findings suggest a structural adaptation of nitrogenase to protect the P-cluster via Ser ligation, which is a previously unidentified functional role of the Ser residue in redox proteins and adds to the expanding functional roles of non-Cys ligands to FeS clusters.
Role of Serine Coordination in the Structural and Functional Protection of the Nitrogenase P-Cluster.,Rutledge HL, Field MJ, Rittle J, Green MT, Tezcan FA J Am Chem Soc. 2022 Dec 7;144(48):22101-22112. doi: 10.1021/jacs.2c09480. Epub , 2022 Nov 29. PMID:36445204<ref>PMID:36445204</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8e3t" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Nitrogenase 3D structures|Nitrogenase 3D structures]]
*[[Nitrogenase 3D structures|Nitrogenase 3D structures]]
== References ==
<references/>
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</StructureSection>
</StructureSection>

Latest revision as of 15:05, 13 August 2026

Gallium-reconstituted nitrogenase MoFeP mutant S188A from Azotobacter vinelandii after IDS oxidation

8e3t, resolution 2.20Å

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