5UK3

Crystal structure of cyanase from T. urticae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.1021/acs.jafc.7b01333
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of South Carolina , Columbia, South Carolina 29208, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
176Tetranychus urticaeMutation(s): 0 
UniProt
Find proteins for T1KZQ3 (Tetranychus urticae)
Explore T1KZQ3 
Go to UniProtKB:  T1KZQ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT1KZQ3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.074α = 90
b = 81.611β = 100.37
c = 136.466γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
MOLREPphasing
HKL-3000phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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