3s9v: Difference between revisions

Latest revision as of 09:48, 1 March 2024

abietadiene synthase from Abies grandis

Structural highlights

3s9v is a 4 chain structure with sequence from Abies grandis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TPSDV_ABIGR Involved in defensive oleoresin formation in conifers in response to insect attack or other injury. Involved in diterpene (C20) olefins biosynthesis. Bifunctional enzyme that catalyzes two sequential cyclizations of geranylgeranyl diphosphate (GGPP) to abietadiene. The copalyl diphosphate (CPP) intermediate diffuses freely between the 2 active sites in the enzyme. Changes in reaction pH, but not salt concentration, influence the relative proportion of the major products of the enzyme, abitadiene, levopimaradiene and neoabitadiene.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

References

↑ Bohlmann J, Meyer-Gauen G, Croteau R. Plant terpenoid synthases: molecular biology and phylogenetic analysis. Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4126-33. PMID:9539701
↑ Peters RJ, Flory JE, Jetter R, Ravn MM, Lee HJ, Coates RM, Croteau RB. Abietadiene synthase from grand fir (Abies grandis): characterization and mechanism of action of the "pseudomature" recombinant enzyme. Biochemistry. 2000 Dec 19;39(50):15592-602. PMID:11112547
↑ Ravn MM, Coates RM, Flory JE, Peters RJ, Croteau R. Stereochemistry of the cyclization-rearrangement of (+)-copalyl diphosphate to (-)-abietadiene catalyzed by recombinant abietadiene synthase from Abies grandis. Org Lett. 2000 Mar 9;2(5):573-6. PMID:10814381
↑ Peters RJ, Croteau RB. Abietadiene synthase catalysis: conserved residues involved in protonation-initiated cyclization of geranylgeranyl diphosphate to (+)-copalyl diphosphate. Biochemistry. 2002 Feb 12;41(6):1836-42. PMID:11827528
↑ Peters RJ, Carter OA, Zhang Y, Matthews BW, Croteau RB. Bifunctional abietadiene synthase: mutual structural dependence of the active sites for protonation-initiated and ionization-initiated cyclizations. Biochemistry. 2003 Mar 11;42(9):2700-7. PMID:12614165 doi:https://dx.doi.org/10.1021/bi020492n
↑ Wilderman PR, Peters RJ. A single residue switch converts abietadiene synthase into a pimaradiene specific cyclase. J Am Chem Soc. 2007 Dec 26;129(51):15736-7. Epub 2007 Dec 1. PMID:18052062 doi:https://dx.doi.org/10.1021/ja074977g
↑ 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

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OCA

[1] Bohlmann J, Meyer-Gauen G, Croteau R. Plant terpenoid synthases: molecular biology and phylogenetic analysis. Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4126-33. PMID:9539701

[2] Peters RJ, Flory JE, Jetter R, Ravn MM, Lee HJ, Coates RM, Croteau RB. Abietadiene synthase from grand fir (Abies grandis): characterization and mechanism of action of the "pseudomature" recombinant enzyme. Biochemistry. 2000 Dec 19;39(50):15592-602. PMID:11112547

[3] Ravn MM, Coates RM, Flory JE, Peters RJ, Croteau R. Stereochemistry of the cyclization-rearrangement of (+)-copalyl diphosphate to (-)-abietadiene catalyzed by recombinant abietadiene synthase from Abies grandis. Org Lett. 2000 Mar 9;2(5):573-6. PMID:10814381

[4] Peters RJ, Croteau RB. Abietadiene synthase catalysis: conserved residues involved in protonation-initiated cyclization of geranylgeranyl diphosphate to (+)-copalyl diphosphate. Biochemistry. 2002 Feb 12;41(6):1836-42. PMID:11827528

[5] Peters RJ, Carter OA, Zhang Y, Matthews BW, Croteau RB. Bifunctional abietadiene synthase: mutual structural dependence of the active sites for protonation-initiated and ionization-initiated cyclizations. Biochemistry. 2003 Mar 11;42(9):2700-7. PMID:12614165 doi:https://dx.doi.org/10.1021/bi020492n

[6] Wilderman PR, Peters RJ. A single residue switch converts abietadiene synthase into a pimaradiene specific cyclase. J Am Chem Soc. 2007 Dec 26;129(51):15736-7. Epub 2007 Dec 1. PMID:18052062 doi:https://dx.doi.org/10.1021/ja074977g

[7] 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

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[2]

[3]

[4]

[5]

[6]

[7]

@@ Line 3: / Line 3: @@
 <StructureSection load='3s9v' size='340' side='right'caption='[[3s9v]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3s9v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Abigr Abigr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S9V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S9V FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3s9v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Abies_grandis Abies grandis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S9V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S9V FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ag22, ac22 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=46611 ABIGR])</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]] 2.3&#8491;</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=3s9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s9v OCA], [https://pdbe.org/3s9v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s9v RCSB], [https://www.ebi.ac.uk/pdbsum/3s9v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s9v ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/TPSDV_ABIGR TPSDV_ABIGR]] Involved in defensive oleoresin formation in conifers in response to insect attack or other injury. Involved in diterpene (C20) olefins biosynthesis. Bifunctional enzyme that catalyzes two sequential cyclizations of geranylgeranyl diphosphate (GGPP) to abietadiene. The copalyl diphosphate (CPP) intermediate diffuses freely between the 2 active sites in the enzyme. Changes in reaction pH, but not salt concentration, influence the relative proportion of the major products of the enzyme, abitadiene, levopimaradiene and neoabitadiene.<ref>PMID:9539701</ref> <ref>PMID:11112547</ref> <ref>PMID:10814381</ref> <ref>PMID:11827528</ref> <ref>PMID:12614165</ref> <ref>PMID:18052062</ref> <ref>PMID:20430888</ref>
+[https://www.uniprot.org/uniprot/TPSDV_ABIGR TPSDV_ABIGR] Involved in defensive oleoresin formation in conifers in response to insect attack or other injury. Involved in diterpene (C20) olefins biosynthesis. Bifunctional enzyme that catalyzes two sequential cyclizations of geranylgeranyl diphosphate (GGPP) to abietadiene. The copalyl diphosphate (CPP) intermediate diffuses freely between the 2 active sites in the enzyme. Changes in reaction pH, but not salt concentration, influence the relative proportion of the major products of the enzyme, abitadiene, levopimaradiene and neoabitadiene.<ref>PMID:9539701</ref> <ref>PMID:11112547</ref> <ref>PMID:10814381</ref> <ref>PMID:11827528</ref> <ref>PMID:12614165</ref> <ref>PMID:18052062</ref> <ref>PMID:20430888</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Abietadiene synthase from Abies grandis (AgAS) is a model system for diterpene synthase activity, catalyzing class I (ionization-initiated) and class II (protonation-initiated) cyclization reactions. Reported here is the crystal structure of AgAS at 2.3 A resolution and molecular dynamics simulations of that structure with and without active site ligands. AgAS has three domains (alpha, beta, and gamma). The class I active site is within the C-terminal alpha domain, and the class II active site is between the N-terminal gamma and beta domains. The domain organization resembles that of monofunctional diterpene synthases and is consistent with proposed evolutionary origins of terpene synthases. Molecular dynamics simulations were carried out to determine the effect of substrate binding on enzymatic structure. Although such studies of the class I active site do lead to an enclosed substrate-Mg(2+) complex similar to that observed in crystal structures of related plant enzymes, it does not enforce a single substrate conformation consistent with the known product stereochemistry. Simulations of the class II active site were more informative, with observation of a well ordered external loop migration. This "loop-in" conformation not only limits solvent access but also greatly increases the number of conformational states accessible to the substrate while destabilizing the nonproductive substrate conformation present in the "loop-out" conformation. Moreover, these conformational changes at the class II active site drive the substrate toward the proposed transition state. Docked substrate complexes were further assessed with regard to the effects of site-directed mutations on class I and II activities.
-Insights into diterpene cyclization from structure of bifunctional abietadiene synthase from Abies grandis.,Zhou K, Gao Y, Hoy JA, Mann FM, Honzatko RB, Peters RJ J Biol Chem. 2012 Feb 24;287(9):6840-50. Epub 2012 Jan 4. PMID:22219188<ref>PMID:22219188</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3s9v" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Abigr]]
+[[Category: Abies grandis]]
 [[Category: Large Structures]]
-[[Category: Honzatko, R B]]
+[[Category: Honzatko RB]]
-[[Category: Hoy, J A]]
+[[Category: Hoy JA]]
-[[Category: Mann, F M]]
+[[Category: Mann FM]]
-[[Category: Peters, R J]]
+[[Category: Peters RJ]]
-[[Category: Zhou, K]]
+[[Category: Zhou K]]
-[[Category: Alpha bundle/barrel]]
-[[Category: Isomerase]]
-[[Category: Lyase]]

3s9v: Difference between revisions

Latest revision as of 09:48, 1 March 2024

abietadiene synthase from Abies grandis

Structural highlights

Function

References

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