9GRH
Crystal structure of the C-terminal phosphatase domain from Saccharomyces cerevisiae Vip1 (apo)
Summary for 9GRH
| Entry DOI | 10.2210/pdb9grh/pdb |
| Descriptor | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase, ZINC ION (2 entities in total) |
| Functional Keywords | inositol pyrophosphate, inositol pyrophosphate phosphatase, histidine acid phosphatase, phytase, enzyme mechanism, gaf domain, phosphate homeostasis, biosynthetic protein |
| Biological source | Saccharomyces cerevisiae (brewer's yeast) |
| Total number of polymer chains | 4 |
| Total formula weight | 263416.14 |
| Authors | |
| Primary citation | Raia, P.,Lee, K.,Bartsch, S.M.,Rico-Resendiz, F.,Portugal-Calisto, D.,Vadas, O.,Panse, V.G.,Fiedler, D.,Hothorn, M. A small signaling domain controls PPIP5K phosphatase activity in phosphate homeostasis. Nat Commun, 16:1753-1753, 2025 Cited by PubMed Abstract: Inositol pyrophosphates (PP-InsPs) are eukaryotic nutrient messengers. The N-terminal kinase domain of diphosphoinositol pentakisphosphate kinase (PPIP5K) generates the messenger 1,5-InsP, the C-terminal phosphatase domain catalyzes PP-InsP breakdown. The balance between kinase and phosphatase activities regulates 1,5-InsP levels. Here, we present crystal structures of the apo and substrate-bound PPIP5K phosphatase domain from S. cerevisiae (ScVip1). ScVip1 is a phytase-like inositol 1-pyrophosphate histidine phosphatase with two conserved catalytic motifs. The enzyme has a strong preference for 1,5-InsP and is inhibited by inorganic phosphate. It contains an α-helical insertion domain stabilized by a structural Zn binding site, and a unique GAF domain that channels the substrate to the active site. Mutations that alter the active site, restrict the movement of the GAF domain, or change the substrate channel's charge inhibit the enzyme activity in vitro, and Arabidopsis VIH2 in planta. Our work reveals the structure, enzymatic mechanism and regulation of eukaryotic PPIP5K phosphatases. PubMed: 39966396DOI: 10.1038/s41467-025-56937-0 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3.2 Å) |
Structure validation
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