PDBsum entry 2zsh

Hormone receptor

PDB id: 2zsh

Contents

Protein chains

338 a.a. *

59 a.a. *

Ligands

GA3

Waters ×216

* Residue conservation analysis

PDB id:

2zsh

Name:

Hormone receptor

Title:

Structural basis of gibberellin(ga3)-induced della recognition by the gibberellin receptor

Structure:

Probable gibberellin receptor gid1l1. Chain: a. Synonym: gid1a, gid1-like protein 1. Engineered: yes. Della protein gai. Chain: b. Fragment: della domain, unp residues 11-113. Synonym: gibberellic acid-insensitive mutant protein, restoration of growth on ammonia protein 2.

Source:

Arabidopsis thaliana. Mouse-ear cress,thale-cress. Organism_taxid: 3702. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: gai.

Resolution:

1.80Å R-factor: 0.205 R-free: 0.229

Authors:

K.Murase,Y.Hirano,T.P.Sun,T.Hakoshima

Key ref:

K.Murase et al. (2008). Gibberellin-induced DELLA recognition by the gibberellin receptor GID1. Nature, 456, 459-463. PubMed id: 19037309 DOI: 10.1038/nature07519

Date:

10-Sep-08 Release date: 25-Nov-08

Protein chain

Q9MAA7  (GID1A_ARATH) -  Gibberellin receptor GID1A from Arabidopsis thaliana

Seq: 345 a.a.

Struc: 338 a.a.

Protein chain

Q9LQT8  (GAI_ARATH) -  DELLA protein GAI from Arabidopsis thaliana

Seq: 533 a.a.

Struc: 59 a.a.

Enzyme reactions

• Enzyme class 2: Chain A: E.C.3.-.-.-
• Enzyme class 3: Chain B: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1038/nature07519

Nature 456:459-463 (2008)

PubMed id: 19037309

Gibberellin-induced DELLA recognition by the gibberellin receptor GID1.

K.Murase, Y.Hirano, T.P.Sun, T.Hakoshima.

ABSTRACT

Gibberellins control a range of growth and developmental processes in higher plants and have been widely used in the agricultural industry. By binding to a nuclear receptor, GIBBERELLIN INSENSITIVE DWARF1 (GID1), gibberellins regulate gene expression by promoting degradation of the transcriptional regulator DELLA proteins, including GIBBERELLIN INSENSITIVE (GAI). The precise manner in which GID1 discriminates and becomes activated by bioactive gibberellins for specific binding to DELLA proteins remains unclear. Here we present the crystal structure of a ternary complex of Arabidopsis thaliana GID1A, a bioactive gibberellin and the amino-terminal DELLA domain of GAI. In this complex, GID1A occludes gibberellin in a deep binding pocket covered by its N-terminal helical switch region, which in turn interacts with the DELLA domain containing DELLA, VHYNP and LExLE motifs. Our results establish a structural model of a plant hormone receptor that is distinct from the mechanism of the hormone perception and effector recognition of the known auxin receptors.

Selected figure(s)

Figure 3.
Figure 3: Recognition of GA[3] by GID1A. a, A top view of the GID1A-bound GA[3]. GID1A residues that contact GA[3] are highlighted in yellow (the core domain) or cyan (the N-terminal extension) and shown as stick models with van der Waals surfaces (dots) and hydrogen bonds (dotted lines). Omit electron density for GA[3] is shown in 3.5 contour (red). b, A side view showing nonpolar contacts between N-terminal extension helix b and the GA[3] aliphatic rings. c, A top view of the hydroxyl groups of GA[3]. d, The bound GA[3] (green) superimposes onto GA[4] (pink) with a small root mean squared deviation (0.20 Å). Water molecules are shown as blue or red spheres.

Figure 5.
Figure 5: Recognition of the DELLA domain by GID1A. a, A top view of the GID1A core domain (light blue) and the N-terminal extension (cyan) with the GAI DELLA domain (pink). The view corresponds to Fig. 2b, d. b, A close-up view of the thumb helix A hooked onto the GID1A crevice. Residues of the DELLA motif (residues D28–V38) are highlighted in green. Hydrogen bonds are indicated with dotted lines. A bridging water molecule inside the loop is shown as a red sphere. c, The LExLE motif (M43–M57). d, The VHYNP motif (T72–M87). In b–d, the residues in each motif that directly contact GID1A are highlighted in green.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 456, 459-463) copyright 2008.

Figures were selected by an automated process.