7TVW

Crystal structure of Arabidopsis thaliana DLK2

• PDB DOI: https://doi.org/10.2210/pdb7TVW/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-02-06 Released: 2022-09-28 
• Deposition Author(s): Burger, M., Chory, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.188 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 

Literature

Crystal structure of Arabidopsis DWARF14-LIKE2 (DLK2) reveals a distinct substrate binding pocket architecture.

Burger, M., Honda, K., Kondoh, Y., Hong, S., Watanabe, N., Osada, H., Chory, J.

(2022) Plant Direct 6: e446-e446

• PubMed: 36172078 
• DOI: https://doi.org/10.1002/pld3.446
• Primary Citation of Related Structures:  
  7TVW


• PubMed Abstract: 
  

  In Arabidopsis thaliana , the Sigma factor B regulator RsbQ-like family of α/β hydrolases contains the strigolactone (SL) receptor DWARF14 (AtD14), the karrikin receptor KARRIKIN INSENSITIVE2 (AtKAI2), and DWARF14-LIKE2 (AtDLK2), a protein of unknown function. Despite very similar protein folds, AtD14 and AtKAI2 differ in size and architecture of their ligand binding pockets, influencing their substrate specificity. We present the 1.5 Å crystal structure of AtDLK2, revealing the smallest ligand binding pocket in the protein family, bordered by two unique glycine residues. We identified a gatekeeper residue in the protein's lid domain and present a pyrrolo-quinoline-dione compound that inhibits AtDLK2's enzymatic activity.

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Organizational Affiliation: 

Plant Biology Laboratory Salk Institute for Biological Studies La Jolla California USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 30.21 kDa 
• Atom Count: 2,411 
• Modelled Residue Count: 265 
• Deposited Residue Count: 275 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha/beta-Hydrolases superfamily protein	A	275	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At3g24420
UniProt
Find proteins for Q9LK01 (Arabidopsis thaliana) Explore Q9LK01  Go to UniProtKB:  Q9LK01

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.188 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.56	α = 90
b = 84.59	β = 90
c = 76.88	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-28 
Deposition Author(s): Burger, M., Chory, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-09-28
  Type: Initial release
  
• Version 1.1: 2022-10-12
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description