This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
6vi5
From Proteopedia
(Difference between revisions)
| Line 1: | Line 1: | ||
==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]] | ||
Revision as of 05:47, 6 October 2021
Observing a ring-cleaving dioxygenase in action through a crystalline lens - a resting state structure
| |||||||||||
