5vq4: Difference between revisions

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<StructureSection load='5vq4' size='340' side='right'caption='[[5vq4]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='5vq4' size='340' side='right'caption='[[5vq4]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5vq4]] 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=5VQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VQ4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5vq4]] 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=5VQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VQ4 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]] 2.3&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5vpw|5vpw]], [[5vq3|5vq3]]</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='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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5vq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vq4 OCA], [https://pdbe.org/5vq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vq4 RCSB], [https://www.ebi.ac.uk/pdbsum/5vq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vq4 ProSAT]</span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5vq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vq4 OCA], [http://pdbe.org/5vq4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vq4 RCSB], [http://www.ebi.ac.uk/pdbsum/5vq4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vq4 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: Morrison CN]]
[[Category: Morrison, C N]]
[[Category: Rees DC]]
[[Category: Rees, D C]]
[[Category: Spatzal T]]
[[Category: Spatzal, T]]
[[Category: Av1]]
[[Category: Mofe protein]]
[[Category: Molybdenum-iron protein]]
[[Category: Oxidoreductase]]

Latest revision as of 16:55, 4 October 2023

Nitrogenase Av1 at pH 5Nitrogenase Av1 at pH 5

Structural highlights

5vq4 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 2.3Å
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

Protonated states of the nitrogenase active site are mechanistically significant since substrate reduction is invariably accompanied by proton uptake. We report the low pH characterization by X-ray crystallography and EPR spectroscopy of the nitrogenase molybdenum iron (MoFe) proteins from two phylogenetically distinct nitrogenases (Azotobacter vinelandii, Av, and Clostridium pasteurianum, Cp) at pHs between 4.5 and 8. X-ray data at pHs of 4.5-6 reveal the repositioning of side chains along one side of the FeMo-cofactor, and the corresponding EPR data shows a new S = 3/2 spin system with spectral features similar to a state previously observed during catalytic turnover. The structural changes suggest that FeMo-cofactor belt sulfurs S3A or S5A are potential protonation sites. Notably, the observed structural and electronic low pH changes are correlated and reversible. The detailed structural rearrangements differ between the two MoFe proteins, which may reflect differences in potential protonation sites at the active site among nitrogenase species. These observations emphasize the benefits of investigating multiple nitrogenase species. Our experimental data suggest that reversible protonation of the resting state is likely occurring, and we term this state "E0H+", following the Lowe-Thorneley naming scheme.

Reversible Protonated Resting State of the Nitrogenase Active Site.,Morrison CN, Spatzal T, Rees DC J Am Chem Soc. 2017 Aug 9;139(31):10856-10862. doi: 10.1021/jacs.7b05695. Epub, 2017 Jul 26. PMID:28692802[1]

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

See Also

References

  1. ↑ Morrison CN, Spatzal T, Rees DC. Reversible Protonated Resting State of the Nitrogenase Active Site. J Am Chem Soc. 2017 Aug 9;139(31):10856-10862. doi: 10.1021/jacs.7b05695. Epub, 2017 Jul 26. PMID:28692802 doi:http://dx.doi.org/10.1021/jacs.7b05695

5vq4, resolution 2.30Å

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