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| | ==Crystal structure of ent-copalyl diphosphate synthase from Arabidopsis thaliana in complex with (S)-15-aza-14,15-dihydrogeranylgeranyl thiolodiphosphate at 1.55 A resolution== | | ==Crystal structure of ent-copalyl diphosphate synthase from Arabidopsis thaliana in complex with (S)-15-aza-14,15-dihydrogeranylgeranyl thiolodiphosphate at 1.55 A resolution== |
| - | <StructureSection load='4lix' size='340' side='right' caption='[[4lix]], [[Resolution|resolution]] 1.55Å' scene=''> | + | <StructureSection load='4lix' size='340' side='right'caption='[[4lix]], [[Resolution|resolution]] 1.55Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4lix]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ochroconis_lascauxensis Ochroconis lascauxensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LIX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LIX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4lix]] 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=4LIX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LIX FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AG8:S-[(2E,6E,10E)-14-(DIMETHYLAMINO)-3,7,11-TRIMETHYLTETRADECA-2,6,10-TRIEN-1-YL]+TRIHYDROGEN+THIODIPHOSPHATE'>AG8</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.548Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG8:S-[(2E,6E,10E)-14-(DIMETHYLAMINO)-3,7,11-TRIMETHYLTETRADECA-2,6,10-TRIEN-1-YL]+TRIHYDROGEN+THIODIPHOSPHATE'>AG8</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3pya|3pya]], [[3pyb|3pyb]]</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=4lix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lix OCA], [https://pdbe.org/4lix PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lix RCSB], [https://www.ebi.ac.uk/pdbsum/4lix PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lix ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ABC33, At4g02780, CPS, CPS1, GA1, T5J8.9, TPSGA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=994323 Ochroconis lascauxensis])</td></tr>
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| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ent-copalyl_diphosphate_synthase Ent-copalyl diphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.5.1.13 5.5.1.13] </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=4lix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lix OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lix RCSB], [http://www.ebi.ac.uk/pdbsum/4lix PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/KSA_ARATH KSA_ARATH]] Catalyzes the conversion of geranylgeranyl diphosphate to the gibberellin precursor ent-copalyl diphosphate.<ref>PMID:17457817</ref> <ref>PMID:20430888</ref> | + | [https://www.uniprot.org/uniprot/KSA_ARATH KSA_ARATH] Catalyzes the conversion of geranylgeranyl diphosphate to the gibberellin precursor ent-copalyl diphosphate.<ref>PMID:17457817</ref> <ref>PMID:20430888</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | 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 4lix" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ent-copalyl diphosphate synthase]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Ochroconis lascauxensis]] | + | [[Category: Large Structures]] |
| - | [[Category: Christianson, D W]] | + | [[Category: Christianson DW]] |
| - | [[Category: Koksal, M]] | + | [[Category: Koksal M]] |
| - | [[Category: Biosynthesis of ent-copalyl diphosphate]]
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| - | [[Category: Class i and ii terpene cyclase fold]]
| + | |
| - | [[Category: Class ii diterpene cyclase]]
| + | |
| - | [[Category: Dxdd motif]]
| + | |
| - | [[Category: Gibberellin biosynthesis]]
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| - | [[Category: Isomerase]]
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| Structural highlights
Function
KSA_ARATH Catalyzes the conversion of geranylgeranyl diphosphate to the gibberellin precursor ent-copalyl diphosphate.[1] [2]
Publication Abstract from PubMed
BACKGROUND: The diterpene cyclase ent-copalyl diphosphate synthase (CPS) catalyzes the first committed step in the biosynthesis of gibberellins. The previously reported 2.25A resolution crystal structure of CPS complexed with (S)-15-aza-14,15-dihydrogeranylgeranyl thiolodiphosphate (1) established the alphabetagamma domain architecture, but ambiguities regarding substrate analog binding remained. METHOD: Use of crystallization additives yielded CPS crystals diffracting to 1.55A resolution. Additionally, active site residues that hydrogen bond with D379, either directly or through hydrogen bonded water molecules, were probed by mutagenesis. RESULTS: This work clarifies structure-function relationships that were ambiguous in the lower resolution structure. Well-defined positions for the diphosphate group and tertiary ammonium cation of 1, as well as extensive solvent structure, are observed. CONCLUSIONS: Two channels involving hydrogen bonded solvent and protein residues lead to the active site, forming hydrogen bonded "proton wires" that link general acid D379 with bulk solvent. These proton wires may facilitate proton transfer with the general acid during catalysis. Activity measurements made with mutant enzymes indicate that N425, which donates a hydrogen bond directly to D379, and T421, which hydrogen bonds with D379 through an intervening solvent molecule, help orient D379 for catalysis. Residues involved in hydrogen bonds with the proton wire, R340 and D503, are also important. Finally, conserved residue E211, which is located near the diphosphate group of 1, is proposed to be a ligand to Mg2+ required for optimal catalytic activity. GENERAL SIGNIFICANCE: This work establishes structure-function relationships for class II terpenoid cyclases.
1.55A-resolution structure of ent-copalyl diphosphate synthase and exploration of general acid function by site-directed mutagenesis.,Koksal M, Potter K, Peters RJ, Christianson DW Biochim Biophys Acta. 2013 Sep 12. pii: S0304-4165(13)00379-6. doi:, 10.1016/j.bbagen.2013.09.004. PMID:24036329[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Prisic S, Xu J, Coates RM, Peters RJ. Probing the role of the DXDD motif in Class II diterpene cyclases. Chembiochem. 2007 May 25;8(8):869-74. PMID:17457817 doi:10.1002/cbic.200700045
- ↑ Mann FM, Prisic S, Davenport EK, Determan MK, Coates RM, Peters RJ. A single residue switch for Mg(2+)-dependent inhibition characterizes plant class II diterpene cyclases from primary and secondary metabolism. J Biol Chem. 2010 Jul 2;285(27):20558-63. doi: 10.1074/jbc.M110.123307. Epub 2010, Apr 29. PMID:20430888 doi:10.1074/jbc.M110.123307
- ↑ Koksal M, Potter K, Peters RJ, Christianson DW. 1.55A-resolution structure of ent-copalyl diphosphate synthase and exploration of general acid function by site-directed mutagenesis. Biochim Biophys Acta. 2013 Sep 12. pii: S0304-4165(13)00379-6. doi:, 10.1016/j.bbagen.2013.09.004. PMID:24036329 doi:10.1016/j.bbagen.2013.09.004
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