PDBsum entry 3c6o

Signaling protein

PDB id: 3c6o

Contents

Protein chains

76 a.a. *

567 a.a. *

Ligands

IHP

2S2

Waters ×226

* Residue conservation analysis

PDB id:

3c6o

Name:

Signaling protein

Title:

Small molecule agonists and antagonists of f-box protein-substrate interactions in auxin perception and signaling

Structure:

Skp1-like protein 1a. Chain: a. Synonym: skp1-like 1, ufo-binding protein 1. Engineered: yes. Transport inhibitor response 1. Chain: b. Synonym: f-box/lrr-repeat protein 1. Engineered: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: skp1a, ask1, skp1, uip1. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Gene: tir1, fbl1, wei1. Expression_system_taxid: 7108

Resolution:

2.70Å R-factor: 0.187 R-free: 0.272

Authors:

X.Tan

Key ref:

K.Hayashi et al. (2008). Small-molecule agonists and antagonists of F-box protein-substrate interactions in auxin perception and signaling. Proc Natl Acad Sci U S A, 105, 5632-5637. PubMed id: 18391211 DOI: 10.1073/pnas.0711146105

Date:

04-Feb-08 Release date: 22-Apr-08

Protein chain

Q39255  (SKP1A_ARATH) -  SKP1-like protein 1A from Arabidopsis thaliana

Seq: 160 a.a.

Struc: 76 a.a.*

Protein chain

Q570C0  (TIR1_ARATH) -  Protein TRANSPORT INHIBITOR RESPONSE 1 from Arabidopsis thaliana

Seq: 594 a.a.

Struc: 567 a.a.

* PDB and UniProt seqs differ at 14 residue positions (black crosses)

DOI no: 10.1073/pnas.0711146105

Proc Natl Acad Sci U S A 105:5632-5637 (2008)

PubMed id: 18391211

Small-molecule agonists and antagonists of F-box protein-substrate interactions in auxin perception and signaling.

K.Hayashi, X.Tan, N.Zheng, T.Hatate, Y.Kimura, S.Kepinski, H.Nozaki.

ABSTRACT

The regulation of gene expression by the hormone auxin is a crucial mechanism in plant development. We have shown that the Arabidopsis F-box protein TIR1 is a receptor for auxin, and our recent structural work has revealed the molecular mechanism of auxin perception. TIR1 is the substrate receptor of the ubiquitin-ligase complex SCF(TIR1). Auxin binding enhances the interaction between TIR1 and its substrates, the Aux/IAA repressors, thereby promoting the ubiquitination and degradation of Aux/IAAs, altering the expression of hundreds of genes. TIR1 is the prototype of a new class of hormone receptor and the first example of an SCF ubiquitin-ligase modulated by a small molecule. Here, we describe the design, synthesis, and characterization of a series of auxin agonists and antagonists. We show these molecules are specific to TIR1-mediated events in Arabidopsis, and their mode of action in binding to TIR1 is confirmed by x-ray crystallographic analysis. Further, we demonstrate the utility of these probes for the analysis of TIR1-mediated auxin signaling in the moss Physcomitrella patens. Our work not only provides a useful tool for plant chemical biology but also demonstrates an example of a specific small-molecule inhibitor of F-box protein-substrate recruitment. Substrate recognition and subsequent ubiquitination by SCF-type ubiquitin ligases are central to many cellular processes in eukaryotes, and ubiquitin-ligase function is affected in several human diseases. Our work supports the idea that it may be possible to design small-molecule agents to modulate ubiquitin-ligase function therapeutically.

Selected figure(s)

Figure 5.
Crystal structure and molecular docking analysis of TIR1–probe complexes. (A and B) Crystal structure of TIR1–probe complexes. TIR1 is shown as silver ribbon. Probes 3, 4, and 8 are shown as blue, yellow, and green, respectively. IAA7 degron peptide (pink, surface-filled model) and IAA (red) were superimposed on the coordinates in the crystal structure of the TIR1-IAA-IAA7 complex. (C) Molecular docking of TIR1 probe. Predicted binding conformers of 3 (blue) and 4 (yellow) to TIR1 auxin-binding site. Fifty possible binding conformers were predicted by the program AutoDock. Ten representative conformers were shown based on rmsd values to the coordinates of IAA moiety in 3 and 4 in crystal structure.

Figure 6.
The TIR1/AFB specific probe 8 blocks auxin responses of moss P. patens. (A) Effects of 8 on NAA-induced elongation of P. patens gametophores. The juvenile gametophore was incubated for 60 h with chemicals (2 μM NAA and/or 20 μM 8). Arrows indicate the elongation zone in response to NAA. (Scale bar, 10 mm.) (B) Effects of 8 and NAA on the development of chloronemata. Chloronema cells were cultured on a BCDATG medium for 10 days in the presence of 0.5 μM NAA and/or 10 μM 8. Arrows indicate caulonemata.

Figures were selected by an automated process.