5mog

From Proteopedia

(Difference between revisions)

Current revision

Oryza sativa phytoene desaturase inhibited by norflurazon

Structural highlights

5mog is a 5 chain structure with sequence from Oryza sativa Indica Group. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.77Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PDS_ORYSI Converts phytoene into zeta-carotene via the intermediary of phytofluene by the symmetrical introduction of two double bonds at the C-11 and C-11' positions of phytoene with a concomitant isomerization of two neighboring double bonds at the C9 and C9' positions from trans to cis. Active with decylplastoquinone (DPQ) as substrate (PubMed:26147209, PubMed:29176862). Also active with other benzoquinones, which are strongly preferred over naphthoquinones as substrates (PubMed:26147209).^[1] ^[2]

Publication Abstract from PubMed

Cyanobacteria and plants synthesize carotenoids via a poly-cis pathway starting with phytoene, a membrane-bound C40 hydrocarbon. Phytoene desaturase (PDS) introduces two double bonds and concomitantly isomerizes two neighboring double bonds from trans to cis. PDS assembles into homo-tetramers that interact monotopically with membranes. A long hydrophobic tunnel is proposed to function in the sequential binding of phytoene and the electron acceptor plastoquinone. The herbicidal inhibitor norflurazon binds at a plastoquinone site thereby blocking reoxidation of FADred. Comparison with the sequence-dissimilar bacterial carotene desaturase CRTI reveals substantial similarities in the overall protein fold, defining both as members of the GR2 family of flavoproteins. However, the PDS active center architecture is unprecedented: no functional groups are found in the immediate flavin vicinity that might participate in dehydrogenation and isomerization. This suggests that the isoalloxazine moiety is sufficient for catalysis. Despite mechanistic differences, an ancient evolutionary relation of PDS and CRTI is apparent.

Structure of Phytoene Desaturase Provides Insights into Herbicide Binding and Reaction Mechanisms Involved in Carotene Desaturation.,Brausemann A, Gemmecker S, Koschmieder J, Ghisla S, Beyer P, Einsle O Structure. 2017 Aug 1;25(8):1222-1232.e3. doi: 10.1016/j.str.2017.06.002. Epub, 2017 Jun 29. PMID:28669634^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Gemmecker S, Schaub P, Koschmieder J, Brausemann A, Drepper F, Rodriguez-Franco M, Ghisla S, Warscheid B, Einsle O, Beyer P. Phytoene Desaturase from Oryza sativa: Oligomeric Assembly, Membrane Association and Preliminary 3D-Analysis. PLoS One. 2015 Jul 6;10(7):e0131717. PMID:26147209 doi:10.1371/journal.pone.0131717
↑ Koschmieder J, Fehling-Kaschek M, Schaub P, Ghisla S, Brausemann A, Timmer J, Beyer P. Plant-type phytoene desaturase: Functional evaluation of structural implications. PLoS One. 2017 Nov 27;12(11):e0187628. PMID:29176862 doi:10.1371/journal.pone.0187628
↑ Brausemann A, Gemmecker S, Koschmieder J, Ghisla S, Beyer P, Einsle O. Structure of Phytoene Desaturase Provides Insights into Herbicide Binding and Reaction Mechanisms Involved in Carotene Desaturation. Structure. 2017 Aug 1;25(8):1222-1232.e3. doi: 10.1016/j.str.2017.06.002. Epub, 2017 Jun 29. PMID:28669634 doi:http://dx.doi.org/10.1016/j.str.2017.06.002

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5mog"

@@ Line 3: / Line 3: @@
 <StructureSection load='5mog' size='340' side='right'caption='[[5mog]], [[Resolution|resolution]] 2.77&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5mog]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MOG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5MOG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5mog]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Indica_Group Oryza sativa Indica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MOG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MOG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=NRF:Norflurazon'>NRF</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 2.77&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5mog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mog OCA], [http://pdbe.org/5mog PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mog RCSB], [http://www.ebi.ac.uk/pdbsum/5mog PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mog ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=NRF:Norflurazon'>NRF</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=5mog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mog OCA], [https://pdbe.org/5mog PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mog RCSB], [https://www.ebi.ac.uk/pdbsum/5mog PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mog ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CRTI_ORYSI CRTI_ORYSI]] This enzyme converts phytoene into zeta-carotene via the intermediary of phytofluene by the symmetrical introduction of two double bonds at the C-11 and C-11' positions of phytoene.
+[https://www.uniprot.org/uniprot/PDS_ORYSI PDS_ORYSI] Converts phytoene into zeta-carotene via the intermediary of phytofluene by the symmetrical introduction of two double bonds at the C-11 and C-11' positions of phytoene with a concomitant isomerization of two neighboring double bonds at the C9 and C9' positions from trans to cis. Active with decylplastoquinone (DPQ) as substrate (PubMed:26147209, PubMed:29176862). Also active with other benzoquinones, which are strongly preferred over naphthoquinones as substrates (PubMed:26147209).<ref>PMID:26147209</ref> <ref>PMID:29176862</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Beyer, P]]
+[[Category: Oryza sativa Indica Group]]
-[[Category: Brausemann, A]]
+[[Category: Beyer P]]
-[[Category: Einsle, O]]
+[[Category: Brausemann A]]
-[[Category: Gemmecker, S]]
+[[Category: Einsle O]]
-[[Category: Koschmieder, J]]
+[[Category: Gemmecker S]]
-[[Category: Carotenoid biosynthesis]]
+[[Category: Koschmieder J]]
-[[Category: Inhibitor]]
-[[Category: Isomerase]]
-[[Category: Oxidoreductase]]

5mog

From Proteopedia

Current revision

Oryza sativa phytoene desaturase inhibited by norflurazon

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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