8i6t

From Proteopedia

(Difference between revisions)

Current revision

The cryo-EM structure of OsCyc1 hexamer state

Structural highlights

8i6t is a 6 chain structure with sequence from Oryza sativa Japonica Group. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.7Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CPS4_ORYSJ Catalyzes the conversion of geranylgeranyl diphosphate to the phytoalexin precursor syn-copalyl diphosphate (PubMed:15341631, PubMed:15255861, PubMed:23621683). Required for the biosynthesis of momilactones that exude from roots and act as allelochemicals against lowland weeds in paddy soil (PubMed:23621683).^[1] ^[2] ^[3]

Publication Abstract from PubMed

The large superfamily of labdane-related diterpenoids is defined by the cyclization of linear geranylgeranyl pyrophosphate (GGPP), catalyzed by copalyl diphosphate synthases (CPSs) to form the basic decalin core, the copalyl diphosphates (CPPs). Three stereochemically distinct CPPs have been found in plants, namely (+)-CPP, ent-CPP and syn-CPP. Here, we used X-ray crystallography and cryo-EM methods to describe different oligomeric structures of a syn-copalyl diphosphate synthase from Oryza sativa (OsCyc1), and provided a cryo-EM structure of OsCyc1(D367A) mutant in complex with the substrate GGPP. Further analysis showed that tetramers are the dominant form of OsCyc1 in solution and are not necessary for enzyme activity in vitro. Through rational design, we identified an OsCyc1 mutant that can generate ent-CPP in addition to syn-CPP. Our work provides a structural and mechanistic basis for comparing different CPSs and paves the way for further enzyme design to obtain diterpene derivatives with specific chirality.

Structural and functional investigations of syn-copalyl diphosphate synthase from Oryza sativa.,Ma X, Xu H, Tong Y, Luo Y, Dong Q, Jiang T Commun Chem. 2023 Nov 6;6(1):240. doi: 10.1038/s42004-023-01042-w. PMID:37932442^[4]

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

References

↑ Xu M, Hillwig ML, Prisic S, Coates RM, Peters RJ. Functional identification of rice syn-copalyl diphosphate synthase and its role in initiating biosynthesis of diterpenoid phytoalexin/allelopathic natural products. Plant J. 2004 Aug;39(3):309-18. PMID:15255861 doi:10.1111/j.1365-313X.2004.02137.x
↑ Otomo K, Kenmoku H, Oikawa H, König WA, Toshima H, Mitsuhashi W, Yamane H, Sassa T, Toyomasu T. Biological functions of ent enzymes for the branch point of gibberellin and phytoalexin biosynthesis. Plant J. 2004 Sep;39(6):886-93. PMID:15341631 doi:10.1111/j.1365-313X.2004.02175.x
↑ Toyomasu T, Usui M, Sugawara C, Otomo K, Hirose Y, Miyao A, Hirochika H, Okada K, Shimizu T, Koga J, Hasegawa M, Chuba M, Kawana Y, Kuroda M, Minami E, Mitsuhashi W, Yamane H. Reverse-genetic approach to verify physiological roles of rice phytoalexins: characterization of a knockdown mutant of OsCPS4 phytoalexin biosynthetic gene in rice. Physiol Plant. 2014 Jan;150(1):55-62. PMID:23621683 doi:10.1111/ppl.12066
↑ Ma X, Xu H, Tong Y, Luo Y, Dong Q, Jiang T. Structural and functional investigations of syn-copalyl diphosphate synthase from Oryza sativa. Commun Chem. 2023 Nov 6;6(1):240. PMID:37932442 doi:10.1038/s42004-023-01042-w

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/8i6t"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8i6t is ON HOLD  until Paper Publication
+==The cryo-EM structure of OsCyc1 hexamer state==
+<StructureSection load='8i6t' size='340' side='right'caption='[[8i6t]], [[Resolution|resolution]] 3.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8i6t]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8I6T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8I6T FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.7&#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=8i6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8i6t OCA], [https://pdbe.org/8i6t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8i6t RCSB], [https://www.ebi.ac.uk/pdbsum/8i6t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8i6t ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CPS4_ORYSJ CPS4_ORYSJ] Catalyzes the conversion of geranylgeranyl diphosphate to the phytoalexin precursor syn-copalyl diphosphate (PubMed:15341631, PubMed:15255861, PubMed:23621683). Required for the biosynthesis of momilactones that exude from roots and act as allelochemicals against lowland weeds in paddy soil (PubMed:23621683).<ref>PMID:15255861</ref> <ref>PMID:15341631</ref> <ref>PMID:23621683</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The large superfamily of labdane-related diterpenoids is defined by the cyclization of linear geranylgeranyl pyrophosphate (GGPP), catalyzed by copalyl diphosphate synthases (CPSs) to form the basic decalin core, the copalyl diphosphates (CPPs). Three stereochemically distinct CPPs have been found in plants, namely (+)-CPP, ent-CPP and syn-CPP. Here, we used X-ray crystallography and cryo-EM methods to describe different oligomeric structures of a syn-copalyl diphosphate synthase from Oryza sativa (OsCyc1), and provided a cryo-EM structure of OsCyc1(D367A) mutant in complex with the substrate GGPP. Further analysis showed that tetramers are the dominant form of OsCyc1 in solution and are not necessary for enzyme activity in vitro. Through rational design, we identified an OsCyc1 mutant that can generate ent-CPP in addition to syn-CPP. Our work provides a structural and mechanistic basis for comparing different CPSs and paves the way for further enzyme design to obtain diterpene derivatives with specific chirality.
-Authors:
+Structural and functional investigations of syn-copalyl diphosphate synthase from Oryza sativa.,Ma X, Xu H, Tong Y, Luo Y, Dong Q, Jiang T Commun Chem. 2023 Nov 6;6(1):240. doi: 10.1038/s42004-023-01042-w. PMID:37932442<ref>PMID:37932442</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 8i6t" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Oryza sativa Japonica Group]]
+[[Category: Dong QH]]
+[[Category: Jiang T]]
+[[Category: Luo YF]]
+[[Category: Ma XL]]
+[[Category: Tong YR]]
+[[Category: Xu HF]]

8i6t

From Proteopedia

Current revision

The cryo-EM structure of OsCyc1 hexamer state

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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