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5DJ5

Crystal structure of rice DWARF14 in complex with synthetic strigolactone GR24

Summary for 5DJ5
Entry DOI10.2210/pdb5dj5/pdb
DescriptorProbable strigolactone esterase D14, (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 (3 entities in total)
Functional Keywordsalpha/beta, hydrolase
Biological sourceOryza sativa subsp. japonica (Rice)
Total number of polymer chains2
Total formula weight58803.48
Authors
Zhou, X.E.,Zhao, L.-H.,Yi, W.,Wu, Z.-S.,Liu, Y.,Kang, Y.,Hou, L.,de Waal, P.W.,Li, S.,Jiang, Y.,Melcher, K.,Xu, H.E. (deposition date: 2015-09-01, release date: 2015-10-28, Last modification date: 2023-09-27)
Primary citationZhao, L.H.,Zhou, X.E.,Yi, W.,Wu, Z.,Liu, Y.,Kang, Y.,Hou, L.,de Waal, P.W.,Li, S.,Jiang, Y.,Scaffidi, A.,Flematti, G.R.,Smith, S.M.,Lam, V.Q.,Griffin, P.R.,Wang, Y.,Li, J.,Melcher, K.,Xu, H.E.
Destabilization of strigolactone receptor DWARF14 by binding of ligand and E3-ligase signaling effector DWARF3.
Cell Res., 25:1219-1236, 2015
Cited by
PubMed Abstract: 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 α/β-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.
PubMed: 26470846
DOI: 10.1038/cr.2015.122
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.4 Å)
Structure validation

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