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| | <StructureSection load='4xpi' size='340' side='right'caption='[[4xpi]], [[Resolution|resolution]] 1.97Å' scene=''> | | <StructureSection load='4xpi' size='340' side='right'caption='[[4xpi]], [[Resolution|resolution]] 1.97Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4xpi]] is a 4 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=4XPI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XPI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4xpi]] is a 4 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=4XPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XPI FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1CL:FE(8)-S(7)+CLUSTER,+OXIDIZED'>1CL</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.97Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nifD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=354 ATCC 478]), nifK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=354 ATCC 478])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1CL:FE(8)-S(7)+CLUSTER,+OXIDIZED'>1CL</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4xpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xpi OCA], [https://pdbe.org/4xpi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xpi RCSB], [https://www.ebi.ac.uk/pdbsum/4xpi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xpi ProSAT]</span></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=4xpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xpi OCA], [http://pdbe.org/4xpi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xpi RCSB], [http://www.ebi.ac.uk/pdbsum/4xpi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xpi 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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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 478]] | + | [[Category: Azotobacter vinelandii]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Nitrogenase]]
| + | [[Category: Danyal K]] |
| - | [[Category: Danyal, K]] | + | [[Category: Dean DR]] |
| - | [[Category: Dean, D R]] | + | [[Category: Duval S]] |
| - | [[Category: Duval, S]] | + | [[Category: Keable SM]] |
| - | [[Category: Keable, S M]] | + | [[Category: Peters JW]] |
| - | [[Category: Peters, J W]] | + | [[Category: Rasmusen AJ]] |
| - | [[Category: Rasmusen, A J]] | + | [[Category: Raugei S]] |
| - | [[Category: Raugei, S]] | + | [[Category: Seefeldt LC]] |
| - | [[Category: Seefeldt, L C]] | + | [[Category: Shaw S]] |
| - | [[Category: Shaw, S]] | + | [[Category: Zadvornyy O]] |
| - | [[Category: Zadvornyy, O]] | + | |
| - | [[Category: Acetylene]]
| + | |
| - | [[Category: Atp-binding]]
| + | |
| - | [[Category: Hydride reduction]]
| + | |
| - | [[Category: Iron]]
| + | |
| - | [[Category: Iron-sulfur]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Mofe protein]]
| + | |
| - | [[Category: Molybdenum]]
| + | |
| - | [[Category: Nitrogen]]
| + | |
| - | [[Category: Nitrogen fixation]]
| + | |
| - | [[Category: Nucleotide-binding]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Proton reduction]]
| + | |
| Structural highlights
4xpi is a 4 chain structure with sequence from Azotobacter vinelandii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.97Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
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
The reduction of substrates catalyzed by nitrogenase normally requires nucleotide-dependent Fe protein delivery of electrons to the MoFe protein, which contains the active site FeMo cofactor. Here, it is reported that independent substitution of three amino acids (beta-98(Tyr-->His), alpha-64(Tyr-->His), and beta-99(Phe-->His)) located between the P cluster and FeMo cofactor within the MoFe protein endows it with the ability to reduce protons to H2, azide to ammonia, and hydrazine to ammonia without the need for Fe protein or ATP. Instead, electrons can be provided by the low-potential reductant polyaminocarboxylate-ligated Eu(II) (Em values of -1.1 to -0.84 V vs the normal hydrogen electrode). The crystal structure of the beta-98(Tyr-->His) variant MoFe protein was determined, revealing only small changes near the amino acid substitution that affect the solvent structure and the immediate vicinity between the P cluster and the FeMo cofactor, with no global conformational changes observed. Computational normal-mode analysis of the nitrogenase complex reveals coupling in the motions of the Fe protein and the region of the MoFe protein with these three amino acids, which suggests a possible mechanism for how Fe protein might communicate subtle changes deep within the MoFe protein that profoundly affect intramolecular electron transfer and substrate reduction.
Fe protein-independent substrate reduction by nitrogenase MoFe protein variants.,Danyal K, Rasmussen AJ, Keable SM, Inglet BS, Shaw S, Zadvornyy OA, Duval S, Dean DR, Raugei S, Peters JW, Seefeldt LC Biochemistry. 2015 Apr 21;54(15):2456-62. doi: 10.1021/acs.biochem.5b00140. Epub , 2015 Apr 7. PMID:25831270[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Danyal K, Rasmussen AJ, Keable SM, Inglet BS, Shaw S, Zadvornyy OA, Duval S, Dean DR, Raugei S, Peters JW, Seefeldt LC. Fe protein-independent substrate reduction by nitrogenase MoFe protein variants. Biochemistry. 2015 Apr 21;54(15):2456-62. doi: 10.1021/acs.biochem.5b00140. Epub , 2015 Apr 7. PMID:25831270 doi:http://dx.doi.org/10.1021/acs.biochem.5b00140
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