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| | ==Crystal Structure of the Lipocalin domain of Violaxanthin de-epoxidase (VDE) at pH7== | | ==Crystal Structure of the Lipocalin domain of Violaxanthin de-epoxidase (VDE) at pH7== |
| - | <StructureSection load='3cqn' size='340' side='right' caption='[[3cqn]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='3cqn' size='340' side='right'caption='[[3cqn]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3cqn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CQN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CQN FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3cqn]] is a 2 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=3CQN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CQN FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3cqr|3cqr]]</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]] 2Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VDE1, AVDE1, NPQ1, VXDE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=3cqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cqn OCA], [https://pdbe.org/3cqn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cqn RCSB], [https://www.ebi.ac.uk/pdbsum/3cqn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cqn ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Violaxanthin_de-epoxidase Violaxanthin de-epoxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.23.5.1 1.23.5.1] </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=3cqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cqn OCA], [http://pdbe.org/3cqn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cqn RCSB], [http://www.ebi.ac.uk/pdbsum/3cqn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3cqn ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/VDE_ARATH VDE_ARATH]] Part of the xanthophyll (or violaxanthin) cycle for controlling the concentration of zeaxanthin in chloroplasts. Catalyzes the two-step mono de-epoxidation reaction. Stereospecific for all-trans xanthophylls. Zeaxanthin induces the dissipation of excitation energy in the chlorophyll of the light-harvesting protein complex of photosystem II.<ref>PMID:10982442</ref> <ref>PMID:11855651</ref> <ref>PMID:9668132</ref> | + | [https://www.uniprot.org/uniprot/VDE_ARATH VDE_ARATH] Part of the xanthophyll (or violaxanthin) cycle for controlling the concentration of zeaxanthin in chloroplasts. Catalyzes the two-step mono de-epoxidation reaction. Stereospecific for all-trans xanthophylls. Zeaxanthin induces the dissipation of excitation energy in the chlorophyll of the light-harvesting protein complex of photosystem II.<ref>PMID:10982442</ref> <ref>PMID:11855651</ref> <ref>PMID:9668132</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cq/3cqn_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cq/3cqn_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arath]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Violaxanthin de-epoxidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Arnoux, P]] | + | [[Category: Arnoux P]] |
| - | [[Category: Morosinotto, T]] | + | [[Category: Morosinotto T]] |
| - | [[Category: Pignol, D]] | + | [[Category: Pignol D]] |
| - | [[Category: Antheraxanthin]]
| + | |
| - | [[Category: Chloroplast]]
| + | |
| - | [[Category: De-epoxidase]]
| + | |
| - | [[Category: Enzyme]]
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| - | [[Category: Lipocalin]]
| + | |
| - | [[Category: Membrane]]
| + | |
| - | [[Category: Non photochemical quenching]]
| + | |
| - | [[Category: Npq]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Ph dependant transition]]
| + | |
| - | [[Category: Thylakoid]]
| + | |
| - | [[Category: Transit peptide]]
| + | |
| - | [[Category: Violaxanthin]]
| + | |
| - | [[Category: Xanthophyll cycle]]
| + | |
| - | [[Category: Zeaxanthin]]
| + | |
| Structural highlights
Function
VDE_ARATH Part of the xanthophyll (or violaxanthin) cycle for controlling the concentration of zeaxanthin in chloroplasts. Catalyzes the two-step mono de-epoxidation reaction. Stereospecific for all-trans xanthophylls. Zeaxanthin induces the dissipation of excitation energy in the chlorophyll of the light-harvesting protein complex of photosystem II.[1] [2] [3]
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
Plants adjust their photosynthetic activity to changing light conditions. A central regulation of photosynthesis depends on the xanthophyll cycle, in which the carotenoid violaxanthin is converted into zeaxanthin in strong light, thus activating the dissipation of the excess absorbed energy as heat and the scavenging of reactive oxygen species. Violaxanthin deepoxidase (VDE), the enzyme responsible for zeaxanthin synthesis, is activated by the acidification of the thylakoid lumen when photosynthetic electron transport exceeds the capacity of assimilatory reactions: at neutral pH, VDE is a soluble and inactive enzyme, whereas at acidic pH, it attaches to the thylakoid membrane where it binds its violaxanthin substrate. VDE also uses ascorbate as a cosubstrate with a pH-dependent Km that may reflect a preference for ascorbic acid. We determined the structures of the central lipocalin domain of VDE (VDEcd) at acidic and neutral pH. At neutral pH, VDEcd is monomeric with its active site occluded within a lipocalin barrel. Upon acidification, the barrel opens up and the enzyme appears as a dimer. A channel linking the two active sites of the dimer can harbor the entire carotenoid substrate and thus may permit the parallel deepoxidation of the two violaxanthin beta-ionone rings, making VDE an elegant example of the adaptation of an asymmetric enzyme to its symmetric substrate.
A structural basis for the pH-dependent xanthophyll cycle in Arabidopsis thaliana.,Arnoux P, Morosinotto T, Saga G, Bassi R, Pignol D Plant Cell. 2009 Jul;21(7):2036-44. Epub 2009 Jul 28. PMID:19638474[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Havaux M, Bonfils JP, Lutz C, Niyogi KK. Photodamage of the photosynthetic apparatus and its dependence on the leaf developmental stage in the npq1 Arabidopsis mutant deficient in the xanthophyll cycle enzyme violaxanthin de-epoxidase. Plant Physiol. 2000 Sep;124(1):273-84. PMID:10982442
- ↑ Hieber AD, Bugos RC, Verhoeven AS, Yamamoto HY. Overexpression of violaxanthin de-epoxidase: properties of C-terminal deletions on activity and pH-dependent lipid binding. Planta. 2002 Jan;214(3):476-83. PMID:11855651
- ↑ Niyogi KK, Grossman AR, Bjorkman O. Arabidopsis mutants define a central role for the xanthophyll cycle in the regulation of photosynthetic energy conversion. Plant Cell. 1998 Jul;10(7):1121-34. PMID:9668132
- ↑ Arnoux P, Morosinotto T, Saga G, Bassi R, Pignol D. A structural basis for the pH-dependent xanthophyll cycle in Arabidopsis thaliana. Plant Cell. 2009 Jul;21(7):2036-44. Epub 2009 Jul 28. PMID:19638474 doi:http://dx.doi.org/10.1105/tpc.109.068007
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