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Human 3’ (2’), 5’-bisphosphate nucleotidase 1 (BPNT1) in complex with AMP, Mg and PO4

PDB Code 2WEF Target Class Nucleotide metabolism Target BPNT1 Alias BPNT1, PIP Disease Area/Function neurobiology Date Deposited Mar 30 2009 Authors M.Moche, P.Schutz, C.H.Arrowsmith, H.Berglund, C.Bountra, R.Collins, L.G.Dahlgren, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, A.Johansson, I.Johansson, T.Karlberg, T.Kotenyova, M.E.Nilsson, T.Nyman, C.Persson, J.Sagemark, H.Schueler, M.I.Siponen, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, J.Weigelt, M.Welin, M.Wisniewska, P.Nordlund, Structural Genomics Consortium (SGC)

About this structure

3'(2'), 5'-bisphosphate nucleotidase 1 (BPNT1) is a dual specificity enzyme that hydrolyses the 3’-phosphate group of 3’-phosphoadenosine 5’-phosphate (PAP) into adenosine 5'-phosphate (AMP) [1]. BPNT1 also hydrolyses the 3’-phosphate group of 3’-phosphoadenosine 5’-phosphosulfate (PAPS), the activated form of sulfur used by sulfotransferases, and in addition the BPNT1 substrate PAP is a competitive sulfotransferase inhibitor, giving BPNT1 a role in sulfur metabolism. Human BPNT1 is uncompetetively inhibited by lithium[2] and PAP, the BPNT1 substrate, is accumulated in the brain of Li+-treated bipolar patients [3] mediating lithium toxicity[4].
BPNT1 can hydrolyze the 1’-phosphate from inositol-1,4-bisphosphate into inositol-4-phosphate that has been shown both for the human[4] and the rat[5] enzymes. The rat BPNT1 crystal structure is known (1JP4) [6]. The uncompetitive inhibition by lithium is hard to study using X-ray crystallography since the lithium ions contain only two electrons.
We have solved the crystal structure of human BPNT1 in complex with AMP, three magnesium ions and phosphate to 1.8 Å resolution (2WEF). To determine the structure we used the 1JP4 rat structure[6] for molecular replacement. The sequence identity between the rat and human structure is 91% and the root mean square deviation is 0.52 for 299 aligned alpha carbons. The active site contains three octahedrally coordinated Magnesium ions (Mg1, Mg2 and Mg3) where the high affinity Mg1 site involves a main chain carbonyl ligand of Leu119 (Val in 1JP4) and the two lower affinity sites involve side chain carboxylates, water and oxygen from sugar or phosphate products. The two products, AMP and a phosphate ion, originate from the PAP substrate used in crystallization.

References

  1. S.G. Ramaswamy, W.B. Jakoby, (2')3',5'-Bisphosphate nucleotidase, J Biol Chem 262 (1987) 10044-10047.
  2. B.D. Spiegelberg, J.P. Xiong, J.J. Smith, R.F. Gu, J.D. York, Cloning and characterization of a mammalian lithium-sensitive bisphosphate 3'-nucleotidase inhibited by inositol 1,4-bisphosphate, J Biol Chem 274 (1999) 13619-13628.
  3. A. Shaldubina, G. Agam, R.H. Belmaker, The mechanism of lithium action: state of the art, ten years later, Prog Neuropsychopharmacol Biol Psychiatry 25 (2001) 855-866.
  4. L. Yenush, J.M. Belles, J.M. Lopez-Coronado, R. Gil-Mascarell, R. Serrano, P.L. Rodriguez, A novel target of lithium therapy, FEBS Lett 467 (2000) 321-325.
  5. J.M. Lopez-Coronado, J.M. Belles, F. Lesage, R. Serrano, P.L. Rodriguez, A novel mammalian lithium-sensitive enzyme with a dual enzymatic activity, 3'-phosphoadenosine 5'-phosphate phosphatase and inositol-polyphosphate 1-phosphatase, J Biol Chem 274 (1999) 16034-16039.
  6. S. Patel, L. Yenush, P.L. Rodriguez, R. Serrano, T.L. Blundell, Crystal structure of an enzyme displaying both inositol-polyphosphate-1-phosphatase and 3'-phosphoadenosine-5'-phosphate phosphatase activities: a novel target of lithium therapy, J Mol Biol 315 (2002) 677-685.