6O5J

Crystal Structure of DAD2 bound to quinazolinone derivative

PDB DOI: 10.2210/pdb6O5J/pdb

Classification: HORMONE
Organism(s): Petunia x hybrida
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-03-03 Released: 2019-06-26
Deposition Author(s): Hamiaux, C.
Funding Organization(s): Royal Society of New Zealand

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.182
R-Value Work: 0.144
R-Value Observed: 0.146

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Chemical synthesis and characterization of a new quinazolinedione competitive antagonist for strigolactone receptors with an unexpected binding mode.

Hamiaux, C., Larsen, L., Lee, H.W., Luo, Z., Sharma, P., Hawkins, B.C., Perry, N.B., Snowden, K.C.

(2019) Biochem J 476: 1843-1856

PubMed: 31186286 Search on PubMed
DOI: 10.1042/BCJ20190288
Primary Citation of Related Structures:
6O5J

PubMed Abstract:

Strigolactones (SLs) are multifunctional plant hormones regulating essential physiological processes affecting growth and development. In vascular plants, SLs are recognized by α/β hydrolase-fold proteins from the D14/DAD2 (Dwarf14/Decreased Apical Dominance 2) family in the initial step of the signaling pathway. We have previously discovered that N -phenylanthranilic acid derivatives (e.g. tolfenamic acid) are potent antagonists of SL receptors, prompting us to design quinazolinone and quinazolinedione derivatives (QADs and QADDs, respectively) as second-generation antagonists. Initial in silico docking studies suggested that these compounds would bind to DAD2, the petunia SL receptor, with higher affinity than the first-generation compounds. However, only one of the QADs/QADDs tested in in vitro assays acted as a competitive antagonist of SL receptors, with reduced affinity and potency compared with its N -phenylanthranilic acid 'parent'. X-ray crystal structure analysis revealed that the binding mode of the active QADD inside DAD2's cavity was not that predicted in silico , highlighting a novel inhibition mechanism for SL receptors. Despite a ∼10-fold difference in potency in vitro , the QADD and tolfenamic acid had comparable activity in planta , suggesting that the QADD compensates for lower potency with increased bioavailability. Altogether, our results establish this QADD as a novel lead compound towards the development of potent and bioavailable antagonists of SL receptors.

Related Citations:

Inhibition of strigolactone receptors by N-phenylanthranilic acid derivatives: Structural and functional insights
Hamiaux, C., Drummond, R.S.M., Luo, Z., Lee, H.W., Sharma, P., Janssen, B.J., Perry, N.B., Denny, W.A., Snowden, K.C.
(2018) J Biol Chem 293: 6530

DAD2 is an a/b hydrolase likely to be involved in the perception of the plant branching hormone, strigolactone
Hamiaux, C., Drummond, R.S., Janssen, B.J., Ledger, S.E., Cooney, J.M., Newcomb, R.D., Snowden, K.C.
(2012) Curr Biol 22: 2032

Organizational Affiliation:

The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable strigolactone esterase DAD2	A, B	264	Petunia x hybrida	Mutation(s): 1 Gene Names: DAD2 EC: 3.1
UniProt
Find proteins for J9U5U9 (Petunia hybrida) Explore J9U5U9 Go to UniProtKB: J9U5U9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	J9U5U9
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LM7 Query on LM7 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	1-(4-hydroxy-3-nitrophenyl)quinazoline-2,4(1H,3H)-dione C₁₄ H₉ N₃ O₅ YVQCKIRAVMSRGN-UHFFFAOYSA-N		Ligand Interaction
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B]	G [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B]	D [auth A], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction