6via

From Proteopedia

(Difference between revisions)

Current revision

Observing a ring-cleaving dioxygenase in action through a crystalline lens - a seven-membered lactone bound structure

Structural highlights

6via is a 1 chain structure with sequence from Cupriavidus metallidurans CH34. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.591Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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]^[1]

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Colabroy KL, Zhai H, Li T, Ge Y, Zhang Y, Liu A, Ealick SE, McLafferty FW, Begley TP. The mechanism of inactivation of 3-hydroxyanthranilate-3,4-dioxygenase by 4-chloro-3-hydroxyanthranilate. Biochemistry. 2005 May 31;44(21):7623-31. PMID:15909977 doi:http://dx.doi.org/10.1021/bi0473455
↑ Wang Y, Liu KF, Yang Y, Davis I, Liu A. Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens. Proc Natl Acad Sci U S A. 2020 Jul 30. pii: 2005327117. doi:, 10.1073/pnas.2005327117. PMID:32732435 doi:http://dx.doi.org/10.1073/pnas.2005327117

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6via"

@@ Line 3: / Line 3: @@
 <StructureSection load='6via' size='340' side='right'caption='[[6via]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6via]] 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=6VIA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VIA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6via]] 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=6VIA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VIA FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EAY:(2R,3E)-2-hydroxy-3-imino-2,3-dihydrooxepine-4-carboxylic+acid'>EAY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.591&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EAY:(2R,3E)-2-hydroxy-3-imino-2,3-dihydrooxepine-4-carboxylic+acid'>EAY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=6via FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6via OCA], [https://pdbe.org/6via PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6via RCSB], [https://www.ebi.ac.uk/pdbsum/6via PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6via 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>
+[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 ==
@@ Line 27: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: 3-hydroxyanthranilate 3,4-dioxygenase]]
+[[Category: Cupriavidus metallidurans CH34]]
-[[Category: Cupmc]]
 [[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]]

6via

From Proteopedia

Current revision

Observing a ring-cleaving dioxygenase in action through a crystalline lens - a seven-membered lactone bound structure

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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