5UK3 | pdb_00005uk3

Crystal structure of cyanase from T. urticae

• PDB DOI: https://doi.org/10.2210/pdb5UK3/pdb

• Classification: LYASE
• Organism(s): Tetranychus urticae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-01-19 Released: 2017-06-21 
• Deposition Author(s): Schlachter, C.R., Chruszcz, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.240 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Structural Characterization of a Eukaryotic Cyanase from Tetranychus urticae.

Schlachter, C.R., Klapper, V., Wybouw, N., Radford, T., Van Leeuwen, T., Grbic, M., Chruszcz, M.

(2017) J Agric Food Chem 65: 5453-5462

• PubMed: 28613863 
• DOI: https://doi.org/10.1021/acs.jafc.7b01333
• Primary Citation Related Structures: 
  5UK3


• PubMed Abstract: 
  

  The two-spotted spider mite Tetranychus urticae is a polyphagous agricultural pest and poses a high risk to global crop production as it is rapidly developing pesticide resistance. Genomic and transcriptomic analysis has revealed the presence of a remarkable cyanase gene in T. urticae and related mite species within the Acariformes lineage. Cyanase catalyzes the detoxification of cyanate and is potentially an attractive protein target for the development of new acaricides. Phylogenetic analysis indicates that within the Acariformes, the cyanase gene originates from a single horizontal gene transfer event, which precedes subsequent speciation. Our structural studies presented here compare and contrast prokaryotic cyanases to T. urticae cyanase, which all form homodecamers and have conserved active site residues, but display different surface areas between homodimers in the overall decameric structure.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of South Carolina , Columbia, South Carolina 29208, United States.
Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands.
Department of Crop Protection, Ghent University , Ghent B-9000, Belgium.
Department of Biology, Western University , London, Ontario N6A 5B7, Canada.
University of La Rioja , Logrono 26006, Spain.

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

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

Macromolecule Content 

• Total Structure Weight: 202.41 kDa 
• Atom Count: 10,811 
• Modeled Residue Count: 1,378 
• Deposited Residue Count: 1,760 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D, E, F, G, H, I, J	176	Tetranychus urticae	Mutation(s): 0
UniProt
Find proteins for T1KZQ3 (Tetranychus urticae) Explore T1KZQ3  Go to UniProtKB:  T1KZQ3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.240 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35uk3

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.074	α = 90
b = 81.611	β = 100.37
c = 136.466	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
MOLREP	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Schlachter, C.R., Chruszcz, M.

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release
  
• Version 1.1: 2017-06-28
  Changes: Database references
• Version 1.2: 2017-07-26
  Changes: Database references
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description