4PUT | pdb_00004put

Crystal structure of the Arabidopsis thaliana TOP2 oligopeptidase

• PDB DOI: https://doi.org/10.2210/pdb4PUT/pdb

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


• Deposited: 2014-03-13 Released: 2014-05-14 
• Deposition Author(s): Wang, R., Rajagopalan, K., Tong, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.247 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

Structure of the Arabidopsis thaliana TOP2 oligopeptidase.

Wang, R., Rajagopalan, K., Sadre-Bazzaz, K., Moreau, M., Klessig, D.F., Tong, L.

(2014) Acta Crystallogr Sect F Struct Biol Cryst Commun 70: 555-559

• PubMed: 24817709 
• DOI: https://doi.org/10.1107/S2053230X14006128
• Primary Citation Related Structures: 
  4PUT


• PubMed Abstract: 
  

  Thimet oligopeptidase (TOP) is a zinc-dependent metallopeptidase. Recent studies suggest that Arabidopsis thaliana TOP1 and TOP2 are targets for salicylic acid (SA) binding and participate in SA-mediated plant innate immunity. The crystal structure of A. thaliana TOP2 has been determined at 3.0 Å resolution. Comparisons to the structure of human TOP revealed good overall structural conservation, especially in the active-site region, despite their weak sequence conservation. The protein sample was incubated with the photo-activated SA analog 4-azido-SA and exposed to UV irradiation before crystallization. However, there was no conclusive evidence for the binding of SA based on the X-ray diffraction data. Further studies are needed to elucidate the molecular mechanism of how SA regulates the activity of A. thaliana TOP1 and TOP2.

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Organizational Affiliation: 
• Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
The Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14850, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 81.42 kDa 
• Atom Count: 5,519 
• Modeled Residue Count: 692 
• Deposited Residue Count: 721 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosolic oligopeptidase A	A	721	Arabidopsis thaliana	Mutation(s): 0  Gene Names: CYOP, TOP2, At5g10540, F12B17.110 EC: 3.4.24.70
UniProt
Find proteins for Q949P2 (Arabidopsis thaliana) Explore Q949P2  Go to UniProtKB:  Q949P2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.247 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.74	α = 90
b = 168.74	β = 90
c = 175.59	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PRIME-X	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-14 
Deposition Author(s): Wang, R., Rajagopalan, K., Tong, L.

Revision History  

• Version 1.0: 2014-05-14
  Type: Initial release
  
• Version 1.1: 2014-06-25
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Refinement description