View source for 7ojm


==CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) CATALYTICALLY INACTIVE H251A VARIANT COMPLEXED WITH 2-METHYL-QUINOLIN-4(1H)-ONE UNDER NORMOXIC CONDITIONS==
<StructureSection load='7ojm' size='340' side='right'caption='[[7ojm]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7ojm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenarthrobacter_nitroguajacolicus Paenarthrobacter nitroguajacolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OJM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OJM FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.001&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SRT:S,R+MESO-TARTARIC+ACID'>SRT</scene>, <scene name='pdbligand=VFH:2-methyl-1~{H}-quinolin-4-one'>VFH</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=7ojm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ojm OCA], [https://pdbe.org/7ojm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ojm RCSB], [https://www.ebi.ac.uk/pdbsum/7ojm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ojm ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/HOD_PAENT HOD_PAENT] Ring-cleaving dioxygenase involved in quinaldine degradation and utilization.<ref>PMID:10746195</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Protein fold adaptation to novel enzymatic reactions is a fundamental evolutionary process. Cofactor-independent oxygenases degrading N-heteroaromatic substrates belong to the alpha/beta-hydrolase (ABH) fold superfamily that typically does not catalyze oxygenation reactions. Here, we have integrated crystallographic analyses under normoxic and hyperoxic conditions with molecular dynamics and quantum mechanical calculations to investigate its prototypic 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (HOD) member. O(2) localization to the "oxyanion hole", where catalysis occurs, is an unfavorable event and the direct competition between dioxygen and water for this site is modulated by the "nucleophilic elbow" residue. A hydrophobic pocket that overlaps with the organic substrate binding site can act as a proximal dioxygen reservoir. Freeze-trap pressurization allowed the structure of the ternary complex with a substrate analogue and O(2) bound at the oxyanion hole to be determined. Theoretical calculations reveal that O(2) orientation is coupled to the charge of the bound organic ligand. When 1-H-3-hydroxy-4-oxoquinaldine is uncharged, O(2) binds with its molecular axis along the ligand's C2-C4 direction in full agreement with the crystal structure. Substrate activation triggered by deprotonation of its 3-OH group by the His-Asp dyad, rotates O(2) by approximately 60 degrees . This geometry maximizes the charge transfer between the substrate and O(2), thus weakening the double bond of the latter. Electron density transfer to the O(2)(pi*) orbital promotes the formation of the peroxide intermediate via intersystem crossing that is rate-determining. Our work provides a detailed picture of how evolution has repurposed the ABH-fold architecture and its simple catalytic machinery to accomplish metal-independent oxygenation.

Evolutionary adaptation from hydrolytic to oxygenolytic catalysis at the alpha/beta-hydrolase fold.,Bui S, Gil-Guerrero S, van der Linden P, Carpentier P, Ceccarelli M, Jambrina PG, Steiner RA Chem Sci. 2023 Sep 18;14(38):10547-10560. doi: 10.1039/d3sc03044j. eCollection , 2023 Oct 4. PMID:37799987<ref>PMID:37799987</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7ojm" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Paenarthrobacter nitroguajacolicus]]
[[Category: Bui S]]
[[Category: Steiner RA]]