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6vib
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 6vib is ON HOLD until Paper Publication Authors: Wang, Y., Liu, F., Yang, Y., Liu, A. Description: Probing Extradiol Dioxygenase Mechanism in NAD+ ...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Observing a ring-cleaving dioxygenase in action through a crystalline lens - enol tautomers of ACMS bidentately bound structure== | |
| + | <StructureSection load='6vib' size='340' side='right'caption='[[6vib]], [[Resolution|resolution]] 1.84Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6vib]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cupriavidus_metallidurans_CH34 Cupriavidus metallidurans CH34]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VIB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VIB 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]] 1.84Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2FO:(2Z,3Z)-2-[(2Z)-3-hydroxyprop-2-en-1-ylidene]-3-iminobutanedioic+acid'>2FO</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6vib FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vib OCA], [https://pdbe.org/6vib PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vib RCSB], [https://www.ebi.ac.uk/pdbsum/6vib PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vib ProSAT]</span></td></tr> | ||
| + | </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> |
| - | [[Category: | + | <div class="pdbe-citations 6vib" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | |
| - | [[Category: Liu | + | ==See Also== |
| - | [[Category: Liu | + | *[[Dioxygenase 3D structures|Dioxygenase 3D structures]] |
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Cupriavidus metallidurans CH34]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Liu A]] | ||
| + | [[Category: Liu F]] | ||
| + | [[Category: Wang Y]] | ||
| + | [[Category: Yang Y]] | ||
Current revision
Observing a ring-cleaving dioxygenase in action through a crystalline lens - enol tautomers of ACMS bidentately bound structure
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