7TVW | pdb_00007tvw

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 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

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 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.
Chemical Biology Research Group RIKEN Centre for Sustainable Resource Science Wako Saitama Japan.
Bioprobe Application Research Unit RIKEN Centre for Sustainable Resource Science Wako Saitama Japan.
Howard Hughes Medical Institute 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 
• Modeled 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 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

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