3T9B
Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP at pH 5.2
Summary for 3T9B
| Entry DOI | 10.2210/pdb3t9b/pdb |
| Related | 3T54 3T7A 3T99 3T9A 3T9C 3T9D 3T9E 3T9F |
| Descriptor | Inositol Pyrophosphate Kinase, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, MAGNESIUM ION, ... (4 entities in total) |
| Functional Keywords | atp-grasp fold, inositol pyrophosphate kinase, phosphoryl transferase, transferase |
| Biological source | Homo sapiens (human) |
| Cellular location | Cytoplasm, cytosol: O43314 |
| Total number of polymer chains | 1 |
| Total formula weight | 38148.00 |
| Authors | Wang, H.,Falck, J.,Hall, T.M.T.,Shears, S.B. (deposition date: 2011-08-02, release date: 2011-12-07, Last modification date: 2024-02-28) |
| Primary citation | Wang, H.,Falck, J.R.,Hall, T.M.,Shears, S.B. Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding. Nat.Chem.Biol., 8:111-116, 2011 Cited by PubMed Abstract: Inositol pyrophosphates (such as IP7 and IP8) are multifunctional signaling molecules that regulate diverse cellular activities. Inositol pyrophosphates have 'high-energy' phosphoanhydride bonds, so their enzymatic synthesis requires that a substantial energy barrier to the transition state be overcome. Additionally, inositol pyrophosphate kinases can show stringent ligand specificity, despite the need to accommodate the steric bulk and intense electronegativity of nature's most concentrated three-dimensional array of phosphate groups. Here we examine how these catalytic challenges are met by describing the structure and reaction cycle of an inositol pyrophosphate kinase at the atomic level. We obtained crystal structures of the kinase domain of human PPIP5K2 complexed with nucleotide cofactors and either substrates, product or a MgF(3)(-) transition-state mimic. We describe the enzyme's conformational dynamics, its unprecedented topological presentation of nucleotide and inositol phosphate, and the charge balance that facilitates partly associative in-line phosphoryl transfer. PubMed: 22119861DOI: 10.1038/nchembio.733 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.85 Å) |
Structure validation
Download full validation report
