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| | <StructureSection load='6bbl' size='340' side='right'caption='[[6bbl]], [[Resolution|resolution]] 1.68Å' scene=''> | | <StructureSection load='6bbl' size='340' side='right'caption='[[6bbl]], [[Resolution|resolution]] 1.68Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6bbl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BBL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6bbl]] 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=6BBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BBL 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=C2H:acetylene'>C2H</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>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.68Å</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=1CL:FE(8)-S(7)+CLUSTER,+OXIDIZED'>1CL</scene>, <scene name='pdbligand=C2H:acetylene'>C2H</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>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6bbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bbl OCA], [http://pdbe.org/6bbl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bbl RCSB], [http://www.ebi.ac.uk/pdbsum/6bbl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bbl 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=6bbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bbl OCA], [https://pdbe.org/6bbl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bbl RCSB], [https://www.ebi.ac.uk/pdbsum/6bbl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bbl 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: De Gioia L]] |
| - | [[Category: Eilers, B J]] | + | [[Category: Eilers BJ]] |
| - | [[Category: Gioia, L De]]
| + | [[Category: Karamatullah D]] |
| - | [[Category: Karamatullah, D]] | + | [[Category: Keable SM]] |
| - | [[Category: Keable, S M]] | + | [[Category: Peters JW]] |
| - | [[Category: Peters, J W]] | + | [[Category: Rasmussen AJ]] |
| - | [[Category: Rasmussen, A J]] | + | [[Category: Seefeldt LC]] |
| - | [[Category: Seefeldt, L C]] | + | [[Category: Vertemara J]] |
| - | [[Category: Vertemara, J]] | + | [[Category: Zadvornyy OA]] |
| - | [[Category: Zadvornyy, O A]] | + | [[Category: Zampella G]] |
| - | [[Category: Zampella, G]] | + | |
| - | [[Category: Acetylene]]
| + | |
| - | [[Category: Electron transport]]
| + | |
| - | [[Category: Femo-cofactor]]
| + | |
| - | [[Category: N2 reduction]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Substrate binding]]
| + | |
| Structural highlights
6bbl 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 1.68Å |
| 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 biological reduction of dinitrogen (N2) to ammonia is catalyzed by the complex metalloenzyme nitrogenase. Structures of the nitrogenase component proteins, Iron (Fe) protein and Molybdenumiron (MoFe) protein, and the stabilized complexes these component proteins, have been determined, providing a foundation for a number of fundamental aspects of the complicated catalytic mechanism. The reduction of dinitrogen to ammonia is a complex process that involves the binding of N2 followed by reduction with multiple electrons and protons. Electron transfer into nitrogenase is typically constrained to the unique electron donor, the Fe protein. These constraints have prevented structural characterization of the active site with bound substrate. Recently it has been realized that selected amino acid substitutions in the environment of the active site metal cluster (Ironmolybdenum cofactor, FeMo-co) allow substrates to persist even in the resting state. Reported here is a 1.70A crystal structure of a nitrogenase MoFe protein alpha-96(ArgGln) variant with the alternative substrate acetylene trapped in a channel in close proximity to FeMo-co. Complementary theoretical calculations support the validity of the acetylene interaction at this site and is also consistent with more favorable interactions in the variant MoFe protein compared to the native MoFe protein. This work represents the first structural evidence of a substrate trapped in the nitrogenase MoFe protein and is consistent with earlier assignments of proposed substrate pathways and substrate binding sites deduced from biochemical, spectroscopic, and theoretical studies.
Structural characterization of the nitrogenase molybdenum-iron protein with the substrate acetylene trapped near the active site.,Keable SM, Vertemara J, Zadvornyy OA, Eilers BJ, Danyal K, Rasmussen AJ, De Gioia L, Zampella G, Seefeldt LC, Peters JW J Inorg Biochem. 2017 Dec 13;180:129-134. doi: 10.1016/j.jinorgbio.2017.12.008. PMID:29275221[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Keable SM, Vertemara J, Zadvornyy OA, Eilers BJ, Danyal K, Rasmussen AJ, De Gioia L, Zampella G, Seefeldt LC, Peters JW. Structural characterization of the nitrogenase molybdenum-iron protein with the substrate acetylene trapped near the active site. J Inorg Biochem. 2017 Dec 13;180:129-134. doi: 10.1016/j.jinorgbio.2017.12.008. PMID:29275221 doi:http://dx.doi.org/10.1016/j.jinorgbio.2017.12.008
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