|
|
| (4 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| - | ==ANTHOCYANIDIN SYNTHASE FROM ARABIDOPSIS THALIANA COMPLEXED WITH NARINGENIN== | + | |
| - | <StructureSection load='2brt' size='340' side='right' caption='[[2brt]], [[Resolution|resolution]] 2.20Å' scene=''> | + | ==ANTHOCYANIDIN SYNTHASE FROM ARABIDOPSIS THALIANA COMPLEXED with naringenin== |
| | + | <StructureSection load='2brt' size='340' side='right'caption='[[2brt]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2brt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BRT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BRT FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2brt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BRT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BRT FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=NAR:NARINGENIN'>NAR</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]] 2.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1gp4|1gp4]], [[1gp5|1gp5]], [[1gp6|1gp6]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=NAR:NARINGENIN'>NAR</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Leucocyanidin_oxygenase Leucocyanidin oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.19 1.14.11.19] </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=2brt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2brt OCA], [https://pdbe.org/2brt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2brt RCSB], [https://www.ebi.ac.uk/pdbsum/2brt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2brt ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2brt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2brt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2brt RCSB], [http://www.ebi.ac.uk/pdbsum/2brt PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/LDOX_ARATH LDOX_ARATH]] Involved in anthocyanin and protoanthocyanidin biosynthesis by catalyzing the oxidation of leucoanthocyanidins into anthocyanidins. Possesses low flavonol synthase activity in vitro towards dihydrokaempferol and dihydroquercetin producing kaempferol and quercitin, respectively.<ref>PMID:12940955</ref> <ref>PMID:16153644</ref> <ref>PMID:19433090</ref> <ref>PMID:21683773</ref> <ref>PMID:16106293</ref> | + | [https://www.uniprot.org/uniprot/LDOX_ARATH LDOX_ARATH] Involved in anthocyanin and protoanthocyanidin biosynthesis by catalyzing the oxidation of leucoanthocyanidins into anthocyanidins. Possesses low flavonol synthase activity in vitro towards dihydrokaempferol and dihydroquercetin producing kaempferol and quercitin, respectively.<ref>PMID:12940955</ref> <ref>PMID:16153644</ref> <ref>PMID:19433090</ref> <ref>PMID:21683773</ref> <ref>PMID:16106293</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/br/2brt_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/br/2brt_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </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/chain_selection.php?pdb_ID=2ata 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=2brt ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| Line 28: |
Line 28: |
| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 2brt" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Dioxygenase 3D structures|Dioxygenase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| Line 33: |
Line 37: |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Arabidopsis thaliana]] | | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Leucocyanidin oxygenase]] | + | [[Category: Large Structures]] |
| - | [[Category: Clifton, I J]] | + | [[Category: Clifton IJ]] |
| - | [[Category: Schofield, C J]] | + | [[Category: Schofield CJ]] |
| - | [[Category: Turnbull, J J]] | + | [[Category: Turnbull JJ]] |
| - | [[Category: Welford, R W.D]] | + | [[Category: Welford RWD]] |
| - | [[Category: Dioxygenase]]
| + | |
| - | [[Category: Flavonoid biosynthesis]]
| + | |
| - | [[Category: Iron]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Vitamin c]]
| + | |
| Structural highlights
Function
LDOX_ARATH Involved in anthocyanin and protoanthocyanidin biosynthesis by catalyzing the oxidation of leucoanthocyanidins into anthocyanidins. Possesses low flavonol synthase activity in vitro towards dihydrokaempferol and dihydroquercetin producing kaempferol and quercitin, respectively.[1] [2] [3] [4] [5]
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 PubMed
During the biosynthesis of the tricyclic flavonoid natural products in plants, oxidative modifications to the central C-ring are catalysed by Fe(ii) and 2-oxoglutarate dependent oxygenases. The reactions catalysed by three of these enzymes; flavone synthase I, flavonol synthase and anthocyanidin synthase (ANS), are formally desaturations. In comparison, flavanone 3beta-hydroxylase catalyses hydroxylation at the C-3 pro-R position of 2S-naringenin. Incubation of ANS with the unnatural substrate (+/-)-naringenin results in predominantly C-3 hydroxylation to give cis-dihydrokaempferol as the major product; trans-dihydrokaempferol and the desaturation product, apigenin are also observed. Labelling studies have demonstrated that some of the formal desaturation reactions catalysed by ANS proceed via initial C-3 hydroxylation followed by dehydration at the active site. We describe analyses of the reaction of ANS with 2S- and 2R-naringenin substrates, including the anaerobic crystal structure of an ANS-Fe-2-oxoglutarate-naringenin complex. Together the results reveal that for the 'natural' C-2 stereochemistry of 2S-naringenin, C-3 hydroxylation predominates (>9 : 1) over desaturation, probably due to the inaccessibility of the C-2 hydrogen to the iron centre. For the 2R-naringenin substrate, desaturation is significantly increased relative to C-3 hydroxylation (ca. 1 : 1); this is probably a result of both the C-3 pro-S and C-2 hydrogen atoms being accessible to the reactive oxidising intermediate in this substrate. In contrast to the hydroxylation-elimination desaturation mechanism for some ANS substrates, the results imply that the ANS catalysed desaturation of 2R-naringenin to form apigenin proceeds with a syn-arrangement of eliminated hydrogen atoms and not via an oxygenated (gem-diol) flavonoid intermediate. Thus, by utilising flavonoid substrates with different C-2 stereochemistries, the balance between C-3 hydroxylation or C-2, C-3 desaturation mechanisms can be altered.
Structural and mechanistic studies on anthocyanidin synthase catalysed oxidation of flavanone substrates: the effect of C-2 stereochemistry on product selectivity and mechanism.,Welford RW, Clifton IJ, Turnbull JJ, Wilson SC, Schofield CJ Org Biomol Chem. 2005 Sep 7;3(17):3117-26. Epub 2005 Aug 1. PMID:16106293[6]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Abrahams S, Lee E, Walker AR, Tanner GJ, Larkin PJ, Ashton AR. The Arabidopsis TDS4 gene encodes leucoanthocyanidin dioxygenase (LDOX) and is essential for proanthocyanidin synthesis and vacuole development. Plant J. 2003 Sep;35(5):624-36. PMID:12940955
- ↑ Welford RW, Kirkpatrick JM, McNeill LA, Puri M, Oldham NJ, Schofield CJ. Incorporation of oxygen into the succinate co-product of iron(II) and 2-oxoglutarate dependent oxygenases from bacteria, plants and humans. FEBS Lett. 2005 Sep 26;579(23):5170-4. PMID:16153644 doi:10.1016/j.febslet.2005.08.033
- ↑ Preuss A, Stracke R, Weisshaar B, Hillebrecht A, Matern U, Martens S. Arabidopsis thaliana expresses a second functional flavonol synthase. FEBS Lett. 2009 Jun 18;583(12):1981-6. doi: 10.1016/j.febslet.2009.05.006. Epub, 2009 May 10. PMID:19433090 doi:10.1016/j.febslet.2009.05.006
- ↑ Appelhagen I, Jahns O, Bartelniewoehner L, Sagasser M, Weisshaar B, Stracke R. Leucoanthocyanidin Dioxygenase in Arabidopsis thaliana: characterization of mutant alleles and regulation by MYB-BHLH-TTG1 transcription factor complexes. Gene. 2011 Sep 15;484(1-2):61-8. doi: 10.1016/j.gene.2011.05.031. Epub 2011 Jun, 12. PMID:21683773 doi:10.1016/j.gene.2011.05.031
- ↑ Welford RW, Clifton IJ, Turnbull JJ, Wilson SC, Schofield CJ. Structural and mechanistic studies on anthocyanidin synthase catalysed oxidation of flavanone substrates: the effect of C-2 stereochemistry on product selectivity and mechanism. Org Biomol Chem. 2005 Sep 7;3(17):3117-26. Epub 2005 Aug 1. PMID:16106293 doi:http://dx.doi.org/10.1039/b507153d
- ↑ Welford RW, Clifton IJ, Turnbull JJ, Wilson SC, Schofield CJ. Structural and mechanistic studies on anthocyanidin synthase catalysed oxidation of flavanone substrates: the effect of C-2 stereochemistry on product selectivity and mechanism. Org Biomol Chem. 2005 Sep 7;3(17):3117-26. Epub 2005 Aug 1. PMID:16106293 doi:http://dx.doi.org/10.1039/b507153d
|
