7auk

From Proteopedia

Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in complex with 5-InsP7

Structural highlights

7auk is a 1 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DDP1_YEAST May eliminate potentially toxic dinucleoside polyphosphates during sporulation. Most active against diadenosine 5',5-P1,P6-hexaphosphate (Ap6A). Can also hydrolyze diadenosine 5',5-P1,P5-pentaphosphate (Ap5A), adenosine 5'-pentaphosphate, and adenosine 5'-tetraphosphate are also substrates, but not diadenosine 5',5-P1,P4-tetraphosphate (Ap4A) or other dinucleotides, mononucleotides, nucleotide sugars, or nucleotide alcohols. Also cleaves a beta-phosphate from the diphosphate groups in PP-InsP5 (diphosphoinositol pentakisphosphate) and [PP]2-InsP4 (bisdiphosphoinositol tetrakisphosphate).

Publication Abstract from PubMed

The yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase DDP1 is a Nudix enzyme with pyrophosphatase activity on diphosphoinositides, dinucleotides, and polyphosphates. These substrates bind to diverse protein targets and participate in signaling and metabolism, being essential for energy and phosphate homeostasis, ATPase pump regulation, or protein phosphorylation. An exhaustive structural study of DDP1 in complex with multiple ligands related to its three diverse substrate classes is reported. This allowed full characterization of the DDP1 active site depicting the molecular basis for endowing multisubstrate abilities to a Nudix enzyme, driven by phosphate anchoring following a defined path. This study, combined with multiple enzyme variants, reveals the different substrate binding modes, preferences, and selection. Our findings expand current knowledge on this important structural superfamily with implications extending beyond inositide research. This work represents a valuable tool for inhibitor/substrate design for ScDDP1 and orthologs as potential targets to address fungal infections and other health concerns.

Multiple substrate recognition by yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase through phosphate clamping.,Marquez-Monino MA, Ortega-Garcia R, Shipton ML, Franco-Echevarria E, Riley AM, Sanz-Aparicio J, Potter BVL, Gonzalez B Sci Adv. 2021 Apr 23;7(17). pii: 7/17/eabf6744. doi: 10.1126/sciadv.abf6744., Print 2021 Apr. PMID:33893105^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Marquez-Monino MA, Ortega-Garcia R, Shipton ML, Franco-Echevarria E, Riley AM, Sanz-Aparicio J, Potter BVL, Gonzalez B. Multiple substrate recognition by yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase through phosphate clamping. Sci Adv. 2021 Apr 23;7(17). pii: 7/17/eabf6744. doi: 10.1126/sciadv.abf6744., Print 2021 Apr. PMID:33893105 doi:http://dx.doi.org/10.1126/sciadv.abf6744