5ysp | pdb_00005ysp

Pyrophosphate-dependent kinase in the ribokinase family complexed with a pyrophosphate analog and myo-inositol

spinqualitylabelsall models 5ysp, resolution 1.70Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5ysp is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: INS, MDN, MG, SO4 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Almost all kinases utilize ATP as their phosphate donor, while a few kinases utilize pyrophosphate (PPi) instead. PPi-dependent kinases are often homologous to their ATP-dependent counterparts, but determinants of their different donor specificities remain unclear. We identify a PPi-dependent member of the ribokinase family, which differs from known PPi-dependent kinases, and elucidate its PPi-binding mode based on the crystal structures. Structural comparison and sequence alignment reveal five important residues: three basic residues specifically recognizing PPi and two large hydrophobic residues occluding a part of the ATP-binding pocket. Two of the three basic residues adapt a conserved motif of the ribokinase family for the PPi binding. Using these five key residues as a signature pattern, we discover additional PPi-specific members of the ribokinase family, and thus conclude that these residues are the determinants of PPi-specific binding. Introduction of these residues may enable transformation of ATP-dependent ribokinase family members into PPi-dependent enzymes. Identification of a pyrophosphate-dependent kinase and its donor selectivity determinants.,Nagata R, Fujihashi M, Sato T, Atomi H, Miki K Nat Commun. 2018 May 2;9(1):1765. doi: 10.1038/s41467-018-04201-z. PMID:29720581 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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