1h1m

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[[Image:1h1m.gif|left|200px]]<br /><applet load="1h1m" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1h1m, resolution 1.90&Aring;" />
 
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'''CRYSTAL STRUCTURE OF QUERCETIN 2,3-DIOXYGENASE ANAEROBICALLY COMPLEXED WITH THE SUBSTRATE KAEMPFEROL'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF QUERCETIN 2,3-DIOXYGENASE ANAEROBICALLY COMPLEXED WITH THE SUBSTRATE KAEMPFEROL==
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Quercetin 2,3-dioxygenase (2,3QD) is the only firmly established copper, dioxygenase known so far. Depending solely on a mononuclear Cu center, it, catalyzes the breakage of the O-heterocycle of flavonols, producing more, easily degradable phenolic carboxylic acid ester derivatives. In the, enzymatic process, two CC bonds are broken and concomitantly carbon, monoxide is released. The x-ray structures of Aspergillus japonicus 2,3QD, anaerobically complexed with the substrate kaempferol and the natural, substrate quercetin have been determined at 1.90- and 1.75-A resolution, respectively. Flavonols coordinate to the copper ion as monodentate, ligands through their 3OH group. They occupy a shallow and overall, hydrophobic cavity proximal to the metal center. As a result of a van der, Waals contact between the most outward flavonol A-ring and Pro(164), a, flexible loop in front of the active site becomes partly ordered., Interestingly, flavonols bound to 2,3QD are bent at the C2 atom, which is, pyramidalized. The increased local sp(3) character at this atom may, stabilize a carbon-centered radical activated for dioxygen attack. Glu(73), coordinates the copper through its O epsilon 1 atom. The short distance of, about 2.55 A between its O epsilon 2 atom and the flavonol O3 atom, suggests that a hydrogen bond exists between the two atoms, indicating, that Glu(73) can act as a base in flavonol deprotonation and that it, retains the proton. Structure-based geometric considerations indicate O(2), binding to the flavonol C2 atom as the preferred route for flavonol, dioxygenation.
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<StructureSection load='1h1m' size='340' side='right'caption='[[1h1m]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1h1m]] 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=1H1M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1H1M FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=KMP:3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENYL)-4H-CHROMEN-4-ONE'>KMP</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1h1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h1m OCA], [https://pdbe.org/1h1m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h1m RCSB], [https://www.ebi.ac.uk/pdbsum/1h1m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h1m ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h1/1h1m_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1h1m ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1H1M is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_japonicus Aspergillus japonicus] with <scene name='pdbligand=NAG:'>NAG</scene>, <scene name='pdbligand=CU:'>CU</scene>, <scene name='pdbligand=KMP:'>KMP</scene> and <scene name='pdbligand=MPD:'>MPD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Quercetin_2,3-dioxygenase Quercetin 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.24 1.13.11.24] Known structural/functional Site: <scene name='pdbsite=CUA:Cu+Binding+Site+For+Chain+D'>CUA</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H1M OCA].
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*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Anaerobic enzyme.substrate structures provide insight into the reaction mechanism of the copper-dependent quercetin 2,3-dioxygenase., Steiner RA, Kalk KH, Dijkstra BW, Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16625-30. Epub 2002 Dec 16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12486225 12486225]
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[[Category: Aspergillus japonicus]]
[[Category: Aspergillus japonicus]]
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[[Category: Quercetin 2,3-dioxygenase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Dijkstra BW]]
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[[Category: Dijkstra, B.W.]]
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[[Category: Steiner RA]]
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[[Category: Steiner, R.A.]]
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[[Category: CU]]
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[[Category: KMP]]
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[[Category: MPD]]
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[[Category: NAG]]
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[[Category: copper]]
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[[Category: dioxygenase]]
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[[Category: flavonol]]
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[[Category: oxidoreductase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 09:45:10 2008''
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Current revision

CRYSTAL STRUCTURE OF QUERCETIN 2,3-DIOXYGENASE ANAEROBICALLY COMPLEXED WITH THE SUBSTRATE KAEMPFEROL

PDB ID 1h1m

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