7BV5

Crystal structure of the yeast heterodimeric ADAT2/3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of the yeast heterodimeric ADAT2/3 deaminase.

Liu, X., Chen, R., Sun, Y., Chen, R., Zhou, J., Tian, Q., Tao, X., Zhang, Z., Luo, G.Z., Xie, W.

(2020) BMC Biol 18: 189-189

  • DOI: https://doi.org/10.1186/s12915-020-00920-2
  • Primary Citation of Related Structures:  
    7BV5

  • PubMed Abstract: 

    The adenosine-to-inosine (A-to-I) editing in anticodons of tRNAs is critical for wobble base-pairing during translation. This modification is produced via deamination on A34 and catalyzed by the adenosine deaminase acting on tRNA (ADAT) enzyme. Eukaryotic ADATs are heterodimers composed of the catalytic subunit ADAT2 and the structural subunit ADAT3, but their molecular assemblies and catalytic mechanisms are largely unclear.

    • Organizational Affiliation: 

    MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou, 510275, Guangdong, People's Republic of China.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-specific adenosine deaminase subunit TAD2
A, B
253Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TAD2, YJL035C, J1246
EC: 3.5.4.33
UniProt
Find proteins for P47058 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47058 
Go to UniProtKB:  P47058
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47058
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-specific adenosine deaminase subunit TAD3
C, D
328Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TAD3, YLR316C
UniProt
Find proteins for Q9URQ3 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q9URQ3 
Go to UniProtKB:  Q9URQ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9URQ3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.591α = 90
b = 118.543β = 90
c = 91.142γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31700657

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description