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| <StructureSection load='6cdk' size='340' side='right'caption='[[6cdk]], [[Resolution|resolution]] 2.10Å' scene=''> | | <StructureSection load='6cdk' size='340' side='right'caption='[[6cdk]], [[Resolution|resolution]] 2.10Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
- | <table><tr><td colspan='2'>[[6cdk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5ijy 5ijy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CDK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6cdk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5ijy 5ijy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CDK FirstGlance]. <br> |
- | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> |
- | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </span></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='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=6cdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cdk OCA], [http://pdbe.org/6cdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cdk RCSB], [http://www.ebi.ac.uk/pdbsum/6cdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cdk 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=6cdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cdk OCA], [https://pdbe.org/6cdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cdk RCSB], [https://www.ebi.ac.uk/pdbsum/6cdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cdk ProSAT]</span></td></tr> |
| </table> | | </table> |
| == Function == | | == Function == |
- | [[http://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. [[http://www.uniprot.org/uniprot/NIFK_AZOVI NIFK_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;"> | | <div style="background-color:#fffaf0;"> |
| == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| [[Category: Azotobacter vinelandii]] | | [[Category: Azotobacter vinelandii]] |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
- | [[Category: Nitrogenase]]
| + | [[Category: Danyal K]] |
- | [[Category: Danyal, K]] | + | [[Category: Eilers BJ]] |
- | [[Category: Eilers, B J]] | + | [[Category: Keable SM]] |
- | [[Category: Keable, S M]] | + | [[Category: LeVan AX]] |
- | [[Category: LeVan, A X]] | + | [[Category: Peters JW]] |
- | [[Category: Peters, J W]] | + | [[Category: Prussia GA]] |
- | [[Category: Prussia, G A]] | + | [[Category: Rasmussen AJ]] |
- | [[Category: Rasmussen, A J]] | + | [[Category: Seefeldt LC]] |
- | [[Category: Seefeldt, L C]] | + | [[Category: Zadvornyy OA]] |
- | [[Category: Zadvornyy, O A]] | + | |
- | [[Category: Electron transport]]
| + | |
- | [[Category: Metalloprotein]]
| + | |
- | [[Category: Nitrogen fixation]]
| + | |
- | [[Category: Oxidoreductase]]
| + | |
- | [[Category: P-cluster of mofe protein]]
| + | |
- | [[Category: Poised state]]
| + | |
- | [[Category: Redox mediator]]
| + | |
| Structural highlights
Function
NIFD_AZOVI This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.
Publication Abstract from PubMed
Nitrogenase is the enzyme that reduces atmospheric dinitrogen (N2) to ammonia (NH3) in biological systems. It catalyzes a series of single-electron transfers from the donor iron protein (Fe protein) to the molybdenum-iron protein (MoFe protein) that contains the iron-molybdenum cofactor (FeMo-co) sites where N2 is reduced to NH3 The [8Fe-7S] P-cluster in the MoFe protein functions in nitrogenase catalysis as an intermediate electron carrier between the external electron donor, the Fe protein, and the FeMo-co sites of the MoFe protein. Previous work has revealed that the P-cluster undergoes redox dependent structural changes and that the transition from the all-ferrous resting (P(N)) state to the two electron oxidized P(2+) state is accompanied by protein serince hydroxyl and backbone amide ligation to Fe. In this work, the MoFe protein was poised at defined potentials with redox mediators in an electrochemical cell, and the three distinct structural states of the P-cluster (P(2+), P(1+), and P(N)) were characterized by X-ray crystallography and confirmed by computational analysis. These analyses revealed that the three oxidation states differ in coordination implicating that the P(1+) state retains the serine hydroxyl coordination but lacks the backbone amide coordination observed in the P(2+) states. These results provide a complete picture of the redox-dependent ligand rearrangements of the three P-cluster redox states.
Structural characterization of the P(1+) intermediate state of the P-cluster of nitrogenase.,Keable SM, Zadvornyy OA, Johnson LE, Ginovska B, Rasmussen AJ, Danyal K, Eilers BJ, Prussia GA, LeVan AX, Raugei S, Seefeldt LC, Peters JW J Biol Chem. 2018 May 2. pii: RA118.002435. doi: 10.1074/jbc.RA118.002435. PMID:29720402[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Keable SM, Zadvornyy OA, Johnson LE, Ginovska B, Rasmussen AJ, Danyal K, Eilers BJ, Prussia GA, LeVan AX, Raugei S, Seefeldt LC, Peters JW. Structural characterization of the P(1+) intermediate state of the P-cluster of nitrogenase. J Biol Chem. 2018 May 2. pii: RA118.002435. doi: 10.1074/jbc.RA118.002435. PMID:29720402 doi:http://dx.doi.org/10.1074/jbc.RA118.002435
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