4whr: Difference between revisions
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==Anhydride reaction intermediate trapped in Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5== | ==Anhydride reaction intermediate trapped in Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5== | ||
<StructureSection load='4whr' size='340' side='right' caption='[[4whr]], [[Resolution|resolution]] 1.58Å' scene=''> | <StructureSection load='4whr' size='340' side='right'caption='[[4whr]], [[Resolution|resolution]] 1.58Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4whr]] is a 6 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4whr]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WHR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WHR FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3N8:4-FLUOROBENZENE-1,2-DIOL'>3N8</scene>, <scene name='pdbligand=3NJ:4-FLUOROOXEPINE-2,7-DIONE'>3NJ</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand= | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.58Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3N8:4-FLUOROBENZENE-1,2-DIOL'>3N8</scene>, <scene name='pdbligand=3NJ:4-FLUOROOXEPINE-2,7-DIONE'>3NJ</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MHO:S-OXYMETHIONINE'>MHO</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=4whr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4whr OCA], [https://pdbe.org/4whr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4whr RCSB], [https://www.ebi.ac.uk/pdbsum/4whr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4whr ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/PCXA_PSEPU PCXA_PSEPU] Plays an essential role in the utilization of numerous aromatic and hydroaromatic compounds via the beta-ketoadipate pathway. | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 22: | Line 19: | ||
</div> | </div> | ||
<div class="pdbe-citations 4whr" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 4whr" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Pseudomonas putida]] | ||
[[Category: Knoot | [[Category: Knoot CJ]] | ||
[[Category: Lipscomb | [[Category: Lipscomb JD]] | ||
Latest revision as of 10:31, 27 September 2023
Anhydride reaction intermediate trapped in Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5Anhydride reaction intermediate trapped in Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5
Structural highlights
FunctionPCXA_PSEPU Plays an essential role in the utilization of numerous aromatic and hydroaromatic compounds via the beta-ketoadipate pathway. Publication Abstract from PubMedIntradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe3+ to activate O2 and catecholic substrates for reaction. The inability of Fe3+ to directly bind O2 presents a mechanistic conundrum. The reaction mechanism of protocatechuate 3,4-dioxygenase is investigated here using the alternative substrate 4-fluorocatechol. This substrate is found to slow the reaction at several steps throughout the mechanistic cycle, allowing the intermediates to be detected in solution studies. When the reaction was initiated in an enzyme crystal, it was found to halt at one of two intermediates depending on the pH of the surrounding solution. The X-ray crystal structure of the intermediate at pH 6.5 revealed the key alkylperoxo-Fe3+ species, and the anhydride-Fe3+ intermediate was found for a crystal reacted at pH 8.5. Intermediates of these types have not been structurally characterized for intradiol dioxygenases, and they validate four decades of spectroscopic, kinetic, and computational studies. In contrast to our similar in crystallo crystallographic studies of an Fe2+-containing extradiol dioxygenase, no evidence for a superoxo or peroxo intermediate preceding the alkylperoxo was found. This observation and the lack of spectroscopic evidence for an Fe2+ intermediate that could bind O2 are consistent with concerted formation of the alkylperoxo followed by Criegee rearrangement to yield the anhydride and ultimately ring-opened product. Structural comparison of the alkylperoxo intermediates from the intra- and extradiol dioxygenases provides a rationale for site specificity of ring cleavage. Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase.,Knoot CJ, Purpero VM, Lipscomb JD Proc Natl Acad Sci U S A. 2014 Dec 29. pii: 201419118. PMID:25548185[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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