7DCA

The structure of the Arabidopsis thaliana guanosine deaminase bound by xanthosine

Summary for 7DCA

• Entry DOI: 10.2210/pdb7dca/pdb
• Descriptor: Guanosine deaminase, 2,3-dihydroxanthosine, ZINC ION, ... (4 entities in total)
• Functional Keywords: deamination, gsda, purine metabolism, hydrolase
• Biological source: Arabidopsis thaliana (Mouse-ear cress)
• Total number of polymer chains: 2
• Total formula weight: 35745.30

Authors

Xie, W.,Jia, Q.,Zeng, H. (deposition date: 2020-10-23, release date: 2021-09-29, Last modification date: 2023-11-29)

Primary citation

Jia, Q.,Zeng, H.,Li, H.,Xiao, N.,Tang, J.,Gao, S.,Zhang, J.,Xie, W.
The C-terminal loop of Arabidopsis thaliana guanosine deaminase is essential to catalysis.
Chem.Commun.(Camb.), 57:9748-9751, 2021

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 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.

PubMed: 34477187
DOI: 10.1039/d1cc03042f

Experimental method

X-RAY DIFFRACTION (2.1 Å)