1h1m: Difference between revisions
No edit summary |
No edit summary |
||
| (15 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==CRYSTAL STRUCTURE OF QUERCETIN 2,3-DIOXYGENASE ANAEROBICALLY COMPLEXED WITH THE SUBSTRATE KAEMPFEROL== | |||
<StructureSection load='1h1m' size='340' side='right'caption='[[1h1m]], [[Resolution|resolution]] 1.90Å' scene=''> | |||
== Structural highlights == | |||
<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> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> | |||
<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> | |||
<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> | |||
</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 == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h1/1h1m_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</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]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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:12486225<ref>PMID:12486225</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1h1m" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Aspergillus japonicus]] | [[Category: Aspergillus japonicus]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Dijkstra BW]] | |||
[[Category: Dijkstra | [[Category: Steiner RA]] | ||
[[Category: Steiner | |||
Latest revision as of 11:29, 6 November 2024
CRYSTAL STRUCTURE OF QUERCETIN 2,3-DIOXYGENASE ANAEROBICALLY COMPLEXED WITH THE SUBSTRATE KAEMPFEROLCRYSTAL STRUCTURE OF QUERCETIN 2,3-DIOXYGENASE ANAEROBICALLY COMPLEXED WITH THE SUBSTRATE KAEMPFEROL
Structural highlights
FunctionQDOI_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. Publication Abstract from PubMedQuercetin 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. 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:12486225[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||