3W06
Crystal structure of Arabidopsis thaliana DWARF14 Like (AtD14L)
Summary for 3W06
| Entry DOI | 10.2210/pdb3w06/pdb |
| Related | 3W04 3W05 |
| Descriptor | Hydrolase, alpha/beta fold family protein, 1,2-ETHANEDIOL (3 entities in total) |
| Functional Keywords | karrikin signaling, alpha/beta hydrolase, karrikin binding, hydrolase |
| Biological source | Arabidopsis thaliana (mouse-ear cress,thale-cress) |
| Total number of polymer chains | 1 |
| Total formula weight | 30342.48 |
| Authors | Kagiyama, M.,Hirano, Y.,Mori, T.,Kim, S.Y.,Kyozuka, J.,Seto, Y.,Yamaguchi, S.,Hakoshima, T. (deposition date: 2012-10-19, release date: 2013-01-23, Last modification date: 2023-11-08) |
| Primary citation | Kagiyama, M.,Hirano, Y.,Mori, T.,Kim, S.Y.,Kyozuka, J.,Seto, Y.,Yamaguchi, S.,Hakoshima, T. Structures of D14 and D14L in the strigolactone and karrikin signaling pathways Genes Cells, 18:147-160, 2013 Cited by PubMed Abstract: Strigolactones (SLs) are plant hormones that inhibit shoot branching. DWARF14 (D14) inhibits rice tillering and is an SL receptor candidate in the branching inhibition pathway, whereas the close homologue DWARF14-LIKE (D14L) participates in the signaling pathway of karrikins (KARs), which are derived from burnt vegetation as smoke stimulants of seed germination. We provide the first evidence for direct binding of the bioactive SL analogue GR24 to D14. Isothermal titration calorimetry measurements show a D14-GR24 binding affinity in the sub-micromolar range. Similarly, bioactive KAR1 directly binds D14L in the micromolar range. The crystal structure of rice D14 shows a compact α-/β-fold hydrolase domain forming a deep ligand-binding pocket capable of accommodating GR24. Insertion of four α-helices between β6 strand and αD helix forms the helical cap of the pocket, although the pocket is open to the solvent. The pocket contains the conserved catalytic triad Ser-His-Asp aligned with the oxyanion hole, suggesting hydrolase activity. Although these structural characteristics are conserved in D14L, the D14L pocket is smaller than that of D14. The KAR-insensitive mutation kai2-1 is located at the prominent long β6-αD1 loop, which is characteristic in D14 and D14L, but not in related α-/β-fold hydrolases. PubMed: 23301669DOI: 10.1111/gtc.12025 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.15 Å) |
Structure validation
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