6IJM
Apo structure of the N6-methyl-AMP Deaminase from Arabidopsis thaliana
Summary for 6IJM
| Entry DOI | 10.2210/pdb6ijm/pdb |
| Descriptor | Adenosine/AMP deaminase family protein, ZINC ION (3 entities in total) |
| Functional Keywords | purine metabolism, deaminase, n6-methyladensosine, tim-barrel, inosine, epigenetics, hydrolase |
| Biological source | Arabidopsis thaliana (Mouse-ear cress) |
| Total number of polymer chains | 1 |
| Total formula weight | 42558.85 |
| Authors | |
| Primary citation | Jia, Q.,Xie, W. Alternative conformation induced by substrate binding for Arabidopsis thalianaN6-methyl-AMP deaminase. Nucleic Acids Res., 47:3233-3243, 2019 Cited by PubMed Abstract: Adenosine deaminase is involved in adenosine degradation and salvage pathway, and plays important physiological roles in purine metabolism. Recently, a novel type of adenosine deaminase-like protein has been identified, which displays deamination activity toward N6-methyl-adenosine monophosphate but not adenosine or AMP, and was consequently named N6-methyl-AMP deaminase (MAPDA). The underlying structural basis of MAPDA recognition and catalysis is poorly understood. Here, we present the crystal structures of MAPDA from Arabidopsis thaliana in the free and in the ligand-bound forms. The protein contains a conserved (β/α)8 Tim-barrel domain and a typical zinc-binding site, but it also exhibits idiosyncratic local differences for two flexible helices important for substrate binding. The extensive interactions between the N6-methyl-AMP substrate or the inosine monophosphate product and the enzyme were identified, and subsequently evaluated by the deamination activity assays. Importantly, each structure reported here represents a different stage of the catalytic pathway and their structural differences suggested that the enzyme can exist in two distinct conformational states. The open state switches to the closed one upon the binding of ligands, brought about by the two critical helices. Our structural studies provide the first look of this important metabolic enzyme and shed lights on its catalytic pathway, which holds promise for the structure-based drug design for MAPDA-related diseases. PubMed: 30721978DOI: 10.1093/nar/gkz070 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.016 Å) |
Structure validation
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