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7kov
From Proteopedia
(Difference between revisions)
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==Crystal structure of Azotobacter vinelandii 3-mercaptopropionic acid dioxygenase in complex with thiocyanate== | ==Crystal structure of Azotobacter vinelandii 3-mercaptopropionic acid dioxygenase in complex with thiocyanate== | ||
| - | <StructureSection load='7kov' size='340' side='right'caption='[[7kov]]' scene=''> | + | <StructureSection load='7kov' size='340' side='right'caption='[[7kov]], [[Resolution|resolution]] 2.95Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KOV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KOV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7kov]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_478 Atcc 478]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KOV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KOV FirstGlance]. <br> |
| - | </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=7kov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kov OCA], [https://pdbe.org/7kov PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kov RCSB], [https://www.ebi.ac.uk/pdbsum/7kov PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kov ProSAT]</span></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr> |
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6xb9|6xb9]]</div></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=7kov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kov OCA], [https://pdbe.org/7kov PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kov RCSB], [https://www.ebi.ac.uk/pdbsum/7kov PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kov ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Thiol dioxygenases are a subset of non-heme iron oxygenases that catalyze the formation of sulfinic acids from sulfhydryl-containing substrates and dioxygen. Among this class, cysteine dioxygenases (CDOs) and 3-mercaptopropionic acid dioxygenases (3MDOs) are the best characterized, and the mode of substrate binding for CDOs is well understood. However, the manner in which 3-mercaptopropionic acid (3MPA) coordinates to the non-heme iron site in 3MDO remains matters of debate. A model for bidentate 3MPA-coordination at the 3MDO Fe-site has been proposed on the basis of computational docking, whereas steady-state kinetics and EPR spectroscopic measurements suggest a thiolate-only coordination of the substrate. To address this gap in knowledge, we determined the structure of Azobacter vinelandii 3MDO (Av3MDO) in complex with the substrate analog and competitive inhibitor, 3-hydroxypropionic acid (3HPA). The structure together with DFT computational modeling demonstrate that 3HPA (and 3MPA) associate with iron as chelate complexes with the substrate-carboxylate group forming an additional interaction with Arg168 and the thiol bound at the same position as in CDO. A chloride ligand was bound to iron in the coordination site assigned as the O2-binding site. Supporting HYSCORE spectroscopic experiments were performed on the (3MPA/NO)-bound Av3MDO iron nitrosyl (S = 3/2) site. In combination with spectroscopic simulations and optimized DFT models, this work provides an experimentally verified model of the Av3MDO enzyme-substrate complex, effectively resolving a debate in the literature regarding the preferred substrate-binding denticity. These results elegantly explain the observed 3MDO substrate-specificity, but leave unanswered questions regarding the mechanism of substrate-gated reactivity with dioxygen. | ||
| + | |||
| + | Structure of 3-mercaptopropionic acid dioxygenase with a substrate analog reveals bidentate substrate binding at the iron center.,York NJ, Lockart MM, Sardar S, Khadka N, Shi W, Stenkamp RE, Zhang J, Kiser PD, Pierce BS J Biol Chem. 2021 Mar 1:100492. doi: 10.1016/j.jbc.2021.100492. PMID:33662397<ref>PMID:33662397</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7kov" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Atcc 478]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Kiser | + | [[Category: Kiser, P D]] |
| + | [[Category: Facial triad]] | ||
| + | [[Category: Non-heme iron]] | ||
| + | [[Category: Oxidoreductase]] | ||
| + | [[Category: Thiocyanate]] | ||
Revision as of 07:00, 17 March 2021
Crystal structure of Azotobacter vinelandii 3-mercaptopropionic acid dioxygenase in complex with thiocyanate
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