This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5dj5

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 11:24, 25 December 2019

Crystal structure of rice DWARF14 in complex with synthetic strigolactone GR24

Structural highlights

5dj5 is a 2 chain structure with sequence from Japanese rice. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	D14, D88, HTD2, Os03g0203200, LOC_Os03g10620 (Japanese rice)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[D14_ORYSJ] Involved in strigolactone signaling pathway. May function downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form. Strigolactones are hormones that inhibit tillering and shoot branching through the MAX-dependent pathway, contribute to the regulation of shoot architectural response to phosphate-limiting conditions and function as rhizosphere signal that stimulates hyphal branching of arbuscular mycorrhizal fungi and trigger seed germination of root parasitic weeds.^[1] ^[2]

Publication Abstract from PubMed

Strigolactones (SLs) are endogenous hormones and exuded signaling molecules in plant responses to low levels of mineral nutrients. Key mediators of the SL signaling pathway in rice include the alpha/beta-fold hydrolase DWARF 14 (D14) and the F-box component DWARF 3 (D3) of the ubiquitin ligase SCF(D3) that mediate ligand-dependent degradation of downstream signaling repressors. One perplexing feature is that D14 not only functions as the SL receptor but is also an active enzyme that slowly hydrolyzes diverse natural and synthetic SLs including GR24, preventing the crystallization of a binary complex of D14 with an intact SL as well as the ternary D14/SL/D3 complex. Here we overcome these barriers to derive a structural model of D14 bound to intact GR24 and identify the interface that is required for GR24-mediated D14-D3 interaction. The mode of GR24-mediated signaling, including ligand recognition, hydrolysis by D14, and ligand-mediated D14-D3 interaction, is conserved in structurally diverse SLs. More importantly, D14 is destabilized upon the binding of ligands and D3, thus revealing an unusual mechanism of SL recognition and signaling, in which the hormone, the receptor, and the downstream effectors are systematically destabilized during the signal transduction process.

Destabilization of strigolactone receptor DWARF14 by binding of ligand and E3-ligase signaling effector DWARF3.,Zhao LH, Zhou XE, Yi W, Wu Z, Liu Y, Kang Y, Hou L, de Waal PW, Li S, Jiang Y, Scaffidi A, Flematti GR, Smith SM, Lam VQ, Griffin PR, Wang Y, Li J, Melcher K, Xu HE Cell Res. 2015 Nov;25(11):1219-36. doi: 10.1038/cr.2015.122. Epub 2015 Oct 16. PMID:26470846^[3]

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

References

↑ Arite T, Umehara M, Ishikawa S, Hanada A, Maekawa M, Yamaguchi S, Kyozuka J. d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers. Plant Cell Physiol. 2009 Aug;50(8):1416-24. doi: 10.1093/pcp/pcp091. Epub 2009, Jun 19. PMID:19542179 doi:http://dx.doi.org/10.1093/pcp/pcp091
↑ Kagiyama M, Hirano Y, Mori T, Kim SY, Kyozuka J, Seto Y, Yamaguchi S, Hakoshima T. Structures of D14 and D14L in the strigolactone and karrikin signaling pathways. Genes Cells. 2013 Jan 10. doi: 10.1111/gtc.12025. PMID:23301669 doi:10.1111/gtc.12025
↑ Zhao LH, Zhou XE, Yi W, Wu Z, Liu Y, Kang Y, Hou L, de Waal PW, Li S, Jiang Y, Scaffidi A, Flematti GR, Smith SM, Lam VQ, Griffin PR, Wang Y, Li J, Melcher K, Xu HE. Destabilization of strigolactone receptor DWARF14 by binding of ligand and E3-ligase signaling effector DWARF3. Cell Res. 2015 Nov;25(11):1219-36. doi: 10.1038/cr.2015.122. Epub 2015 Oct 16. PMID:26470846 doi:http://dx.doi.org/10.1038/cr.2015.122

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/5dj5"

@@ Line 1: / Line 1: @@
 ==Crystal structure of rice DWARF14 in complex with synthetic strigolactone GR24==
-<StructureSection load='5dj5' size='340' side='right' caption='[[5dj5]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='5dj5' size='340' side='right'caption='[[5dj5]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5dj5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DJ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DJ5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5dj5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DJ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DJ5 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GR2:(3E,3AR,8BS)-3-({[(2R)-4-METHYL-5-OXO-2,5-DIHYDROFURAN-2-YL]OXY}METHYLIDENE)-3,3A,4,8B-TETRAHYDRO-2H-INDENO[1,2-B]FURAN-2-ONE'>GR2</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">D14, D88, HTD2, Os03g0203200, LOC_Os03g10620 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</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=5dj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dj5 OCA], [http://pdbe.org/5dj5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dj5 RCSB], [http://www.ebi.ac.uk/pdbsum/5dj5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dj5 ProSAT]</span></td></tr>
 </table>
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Japanese rice]]
+[[Category: Large Structures]]
 [[Category: Hou, L]]
 [[Category: Jiang, Y]]

5dj5

From Proteopedia

Revision as of 11:24, 25 December 2019

Crystal structure of rice DWARF14 in complex with synthetic strigolactone GR24

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox