6op3: Difference between revisions
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<StructureSection load='6op3' size='340' side='right'caption='[[6op3]], [[Resolution|resolution]] 1.60Å' scene=''> | <StructureSection load='6op3' size='340' side='right'caption='[[6op3]], [[Resolution|resolution]] 1.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6op3]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[6op3]] 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=6OP3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OP3 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</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>, <scene name='pdbligand=SE:SELENIUM+ATOM'>SE</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</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>, <scene name='pdbligand=SE:SELENIUM+ATOM'>SE</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6op3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6op3 OCA], [https://pdbe.org/6op3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6op3 RCSB], [https://www.ebi.ac.uk/pdbsum/6op3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6op3 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. | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</div> | </div> | ||
<div class="pdbe-citations 6op3" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 6op3" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Nitrogenase 3D structures|Nitrogenase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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[[Category: Azotobacter vinelandii]] | [[Category: Azotobacter vinelandii]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Arias RJ]] | |||
[[Category: Arias | [[Category: Rees DC]] | ||
[[Category: Rees | |||
Latest revision as of 10:14, 11 October 2023
Selenium incorporated FeMo-cofactor of nitrogenase from Azotobacter vinelandii with low concentration of seleniumSelenium incorporated FeMo-cofactor of nitrogenase from Azotobacter vinelandii with low concentration of selenium
Structural highlights
FunctionNIFD_AZOVI This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation. Publication Abstract from PubMedThe size and complexity of Mo-dependent nitrogenase, a multicomponent enzyme capable of reducing dinitrogen to ammonia, have made a detailed understanding of the FeMo cofactor (FeMoco) active site electronic structure an ongo-ing challenge. Selective substitution of sulfur by selenium in FeMoco affords a unique probe wherein local Fe-Se in-teractions can be directly interrogated via high-energy resolution fluorescence detected X-ray absorption spectroscop-ic (HERFD XAS) and extended X-ray absorption fine structure (EXAFS) studies. These studies reveal a significant asymmetry in the electronic distribution of the FeMoco, suggesting a more localized electronic structure picture than is typically assumed for iron-sulfur clusters. Supported by experimental small molecule model data in combination with time dependent density functional theory (TDDFT) calculations, the HERFD XAS data is consistent with an assign-ment of Fe2/Fe6 as an antiferromagnetically coupled diferric pair. HERFD XAS and EXAFS have also been applied to Se-substituted CO-inhibited MoFe protein, demonstrating the ability of these methods to reveal electronic and struc-tural changes that occur upon substrate binding. These results emphasize the utility of Se HERFD XAS and EXAFS for selectively probing the local electronic and geometric structure of FeMoco. Localized Electronic Structure of Nitrogenase FeMoco Re-vealed by Selenium K-edge High Resolution X-ray Absorption Spectroscopy.,Henthorn JT, Arias RJ, Koroidov S, Kroll T, Sokaras D, Bergmann U, Rees DC, DeBeer S J Am Chem Soc. 2019 Jul 29. doi: 10.1021/jacs.9b06988. PMID:31356071[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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