{"entity": "publication", "iuid": "719471fc91f846649267b804f6b4a2b0", "timestamp": "2026-08-10T22:41:23.014Z", "links": {"self": {"href": "https://publications.scilifelab.se/publication/719471fc91f846649267b804f6b4a2b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/719471fc91f846649267b804f6b4a2b0"}}, "title": "Crystal Structures of Type-II Inositol Polyphosphate 5-Phosphatase INPP5B with Synthetic Inositol Polyphosphate Surrogates Reveal New Mechanistic Insights for the Inositol 5-Phosphatase Family.", "authors": [{"family": "Mills", "given": "Stephen J", "initials": "SJ"}, {"family": "Silvander", "given": "Camilla", "initials": "C"}, {"family": "Cozier", "given": "Gyles", "initials": "G"}, {"family": "Tr\u00e9saugues", "given": "Lionel", "initials": "L"}, {"family": "Nordlund", "given": "P\u00e4r", "initials": "P"}, {"family": "Potter", "given": "Barry V L", "initials": "BV"}], "type": "journal article", "published": "2016-03-08", "journal": {"volume": "55", "issn": "1520-4995", "issue": "9", "pages": "1384-1397", "title": "Biochemistry", "issn-l": "0006-2960"}, "abstract": "The inositol polyphosphate 5-phosphatase INPP5B hydrolyzes the 5-phosphate group from water- and lipid-soluble signaling messengers. Two synthetic benzene and biphenyl polyphosphates (BzP/BiPhPs), simplified surrogates of inositol phosphates and phospholipid headgroups, were identified by thermodynamic studies as potent INPP5B ligands. The X-ray structure of the complex between INPP5B and biphenyl 3,3',4,4',5,5'-hexakisphosphate [BiPh(3,3',4,4',5,5')P6, IC50 5.5 \u03bcM] was determined at 2.89 \u00c5 resolution. One inhibitor pole locates in the phospholipid headgroup binding site and the second solvent-exposed ring binds to the His-Tag of another INPP5B molecule, while a molecule of inorganic phosphate is also present in the active site. Benzene 1,2,3-trisphosphate [Bz(1,2,3)P3] [one ring of BiPh(3,3',4,4',5,5')P6] inhibits INPP5B ca. 6-fold less potently. Co-crystallization with benzene 1,2,4,5-tetrakisphosphate [Bz(1,2,4,5)P4, IC50 = 6.3 \u03bcM] yielded a structure refined at 2.9 \u00c5 resolution. Conserved residues among the 5-phosphatase family mediate interactions with Bz(1,2,4,5)P4 and BiPh(3,3',4,4',5,5')P6 similar to those with the polar groups present in positions 1, 4, 5, and 6 on the inositol ring of the substrate. 5-Phosphatase specificity most likely resides in the variable zone located close to the 2- and 3-positions of the inositol ring, offering insights to inhibitor design. We propose that the inorganic phosphate present in the INPP5B-BiPh(3,3',4,4',5,5')P6 complex mimics the postcleavage substrate 5-phosphate released by INPP5B in the catalytic site, allowing elucidation of two new key features in the catalytic mechanism proposed for the family of phosphoinositide 5-phosphatases: first, the involvement of the conserved Arg-451 in the interaction with the 5-phosphate and second, identification of the water molecule that initiates 5-phosphate hydrolysis. Our model also has implications for the proposed \"moving metal\" mechanism.", "doi": "10.1021/acs.biochem.5b00838", "pmid": "26854536", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC4785718"}, {"db": "mid", "key": "EMS67168"}], "notes": [], "created": "2017-05-03T13:02:40.993Z", "modified": "2017-09-06T11:42:09.145Z"}