6vi5: Difference between revisions
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==Observing a ring-cleaving dioxygenase in action through a crystalline lens - a resting state structure== | ==Observing a ring-cleaving dioxygenase in action through a crystalline lens - a resting state structure== | ||
<StructureSection load='6vi5' size='340' side='right'caption='[[6vi5]]' scene=''> | <StructureSection load='6vi5' size='340' side='right'caption='[[6vi5]], [[Resolution|resolution]] 1.60Å' 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=6VI5 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6vi5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cupmc Cupmc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VI5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VI5 FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | </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=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nbaC, Rmet_5193 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266264 CUPMC])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3-hydroxyanthranilate_3,4-dioxygenase 3-hydroxyanthranilate 3,4-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.6 1.13.11.6] </span></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=6vi5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vi5 OCA], [https://pdbe.org/6vi5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vi5 RCSB], [https://www.ebi.ac.uk/pdbsum/6vi5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vi5 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[[https://www.uniprot.org/uniprot/3HAO_CUPMC 3HAO_CUPMC]] Catalyzes the oxidative ring opening of 3-hydroxyanthranilate to 2-amino-3-carboxymuconate semialdehyde, which spontaneously cyclizes to quinolinate.[HAMAP-Rule:MF_00825]<ref>PMID:15909977</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The synthesis of quinolinic acid from tryptophan is a critical step in the de novo biosynthesis of nicotinamide adenine dinucleotide (NAD(+)) in mammals. Herein, the nonheme iron-based 3-hydroxyanthranilate-3,4-dioxygenase responsible for quinolinic acid production was studied by performing time-resolved in crystallo reactions monitored by UV-vis microspectroscopy, electron paramagnetic resonance (EPR) spectroscopy, and X-ray crystallography. Seven catalytic intermediates were kinetically and structurally resolved in the crystalline state, and each accompanies protein conformational changes at the active site. Among them, a monooxygenated, seven-membered lactone intermediate as a monodentate ligand of the iron center at 1.59-A resolution was captured, which presumably corresponds to a substrate-based radical species observed by EPR using a slurry of small-sized single crystals. Other structural snapshots determined at around 2.0-A resolution include monodentate and subsequently bidentate coordinated substrate, superoxo, alkylperoxo, and two metal-bound enol tautomers of the unstable dioxygenase product. These results reveal a detailed stepwise O-atom transfer dioxygenase mechanism along with potential isomerization activity that fine-tunes product profiling and affects the production of quinolinic acid at a junction of the metabolic pathway. | |||
Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens.,Wang Y, Liu KF, Yang Y, Davis I, Liu A Proc Natl Acad Sci U S A. 2020 Jul 30. pii: 2005327117. doi:, 10.1073/pnas.2005327117. PMID:32732435<ref>PMID:32732435</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6vi5" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: 3-hydroxyanthranilate 3,4-dioxygenase]] | |||
[[Category: Cupmc]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Liu A]] | [[Category: Liu, A]] | ||
[[Category: Liu F]] | [[Category: Liu, F]] | ||
[[Category: Wang Y]] | [[Category: Wang, Y]] | ||
[[Category: Yang Y]] | [[Category: Yang, Y]] | ||
[[Category: Extradiol dioxygenase]] | |||
[[Category: In crystallo reaction]] | |||
[[Category: Intermediate]] | |||
[[Category: Nad+ biosynthesis]] | |||
[[Category: Oxidoreductase]] | |||