7DC9

The structure of the Arabidopsis thaliana guanosine deaminase mutant E82Q complex with guanosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The C-terminal loop of Arabidopsis thaliana guanosine deaminase is essential to catalysis.

Jia, Q.Zeng, H.Li, H.Xiao, N.Tang, J.Gao, S.Zhang, J.Xie, W.

(2021) Chem Commun (Camb) 57: 9748-9751

  • DOI: https://doi.org/10.1039/d1cc03042f
  • Primary Citation of Related Structures:  
    7DBF, 7DC9, 7DCA

  • PubMed Abstract: 

    Guanosine deaminase (GSDA) in plants specifically deaminates (de)guanosine to produce xanthosine with high specificity, which is further converted to xanthine, a key intermediate in purine metabolism and nitrogen recycling. We solved GSDA's structures from Arabidopsis thaliana in the free and ligand-bound forms at high resolutions. Unlike GDA, the enzyme employs a single-proton shuttle mechanism for catalysis and both the substrate and enzyme undergo structural rearrangements. The last fragment of the enzyme loops back and seals the active site, and the substrate rotates during the reaction, both essential to deamination. We further identified more substrates that could be employed by the enzyme and compare it with other deaminases to reveal the recognition differences of specific substrates. Our studies provide insight into this important enzyme involved in purine metabolism and will potentially aid in the development of deaminase-based gene-editing tools.


  • Organizational Affiliation

    MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, 510006, People's Republic of China. xiewei6@mail.sysu.edu.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanosine deaminaseA,
B [auth D]
161Arabidopsis thalianaMutation(s): 1 
Gene Names: GSDATAD4At5g28050
EC: 3.5.4.15
UniProt
Find proteins for Q94BU8 (Arabidopsis thaliana)
Explore Q94BU8 
Go to UniProtKB:  Q94BU8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94BU8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.812α = 90
b = 119.812β = 90
c = 39.884γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31870782

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description