1gqh: Difference between revisions

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<StructureSection load='1gqh' size='340' side='right'caption='[[1gqh]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
<StructureSection load='1gqh' size='340' side='right'caption='[[1gqh]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1gqh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspja Aspja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GQH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GQH FirstGlance]. <br>
<table><tr><td colspan='2'>[[1gqh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_japonicus Aspergillus japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GQH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GQH FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=KOJ:5-HYDROXY-2-(HYDROXYMETHYL)-4H-PYRAN-4-ONE'>KOJ</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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]] 2.15&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1juh|1juh]], [[1gqg|1gqg]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=KOJ:5-HYDROXY-2-(HYDROXYMETHYL)-4H-PYRAN-4-ONE'>KOJ</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Quercetin_2,3-dioxygenase Quercetin 2,3-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.24 1.13.11.24] </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=1gqh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gqh OCA], [https://pdbe.org/1gqh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gqh RCSB], [https://www.ebi.ac.uk/pdbsum/1gqh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gqh ProSAT]</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=1gqh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gqh OCA], [https://pdbe.org/1gqh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gqh RCSB], [https://www.ebi.ac.uk/pdbsum/1gqh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gqh ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/QDOI_ASPJA QDOI_ASPJA] Performs the first step in the degradation of the flavonoid quercetin by a dioxygenase reaction. The enzyme catalyzes the cleavage of the O-heteroaromatic ring of the flavonol quercetin yielding the depside 2-protocatechuoyl-phloroglucinol carboxylic acid and carbon monoxide. This involves the remarkable dioxygenolytic cleavage of two carbon-carbon bonds.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gqh ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gqh ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structures of the copper-dependent Aspergillus japonicus quercetin 2,3-dioxygenase (2,3QD) complexed with the inhibitors diethyldithiocarbamate (DDC) and kojic acid (KOJ) are reported at 1.70 and 2.15 A resolution, respectively. Both inhibitors asymmetrically chelate the metal center and assume a common orientation in the active site cleft. Their molecular plane blocks access to the inner portion of the cavity which is lined by the side chains of residues Met51, Thr53, Phe75, Phe114, and Met123 and which is believed to bind the flavonol B-ring of the natural substrate. The binding of the inhibitors brings order into the mixed coordination observed in the native enzyme. DDC and KOJ induce a single conformation of the Glu73 side chain, although in different ways. In the presence of DDC, Glu73 is detached from the copper ion with its carboxylate moiety pointing away from the active site cavity. In contrast, when KOJ is bound, Glu73 ligates the Cu ion through its O(epsilon)(1) atom with a monodentate geometry. Compared to the native coordinating conformation, this conformation is approximately 90 degrees rotated about the chi(3) angle. This latter Glu73 conformation is compatible with the presence of a bound substrate.
Functional analysis of the copper-dependent quercetin 2,3-dioxygenase. 1. Ligand-induced coordination changes probed by X-ray crystallography: inhibition, ordering effect, and mechanistic insights.,Steiner RA, Kooter IM, Dijkstra BW Biochemistry. 2002 Jun 25;41(25):7955-62. PMID:12069585<ref>PMID:12069585</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1gqh" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Aspja]]
[[Category: Aspergillus japonicus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Quercetin 2,3-dioxygenase]]
[[Category: Dijkstra BW]]
[[Category: Dijkstra, B W]]
[[Category: Steiner RA]]
[[Category: Steiner, R A]]
[[Category: Dioxygenase]]
[[Category: Oxidoreductase]]

Latest revision as of 14:23, 27 March 2024

Quercetin 2,3-dioxygenase in complex with the inhibitor kojic acidQuercetin 2,3-dioxygenase in complex with the inhibitor kojic acid

Structural highlights

1gqh is a 4 chain structure with sequence from Aspergillus japonicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.15Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

QDOI_ASPJA Performs the first step in the degradation of the flavonoid quercetin by a dioxygenase reaction. The enzyme catalyzes the cleavage of the O-heteroaromatic ring of the flavonol quercetin yielding the depside 2-protocatechuoyl-phloroglucinol carboxylic acid and carbon monoxide. This involves the remarkable dioxygenolytic cleavage of two carbon-carbon bonds.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1gqh, resolution 2.15Å

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