The crystal structure and mutational analysis of human NUDT9

Journal of Molecular Biology

Volumn 332, Issue 2, 2003, Pages 385-398

  Shen, Betty W ^a   Perraud, Anne Laure ^b,c   Scharenberg, Andrew ^b   Stoddard, Barry L ^a  

^a USA   (United States)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^c NATIONAL JEWISH MEDICAL AND RESEARCH CENTER   (United States)

Author keywords

ADP ribose pyrophosphatase; Hydrolase; Nudix; TRPM2 ion channel

Indexed keywords

ADENOSINE DIPHOSPHATE RIBOSE PYROPHOSPHATASE NUDT9; APYRASE; HYDROLASE; ION CHANNEL; MONOMER; RIBOSE 5 PHOSPHATE; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CONFORMATION; CRYSTAL STRUCTURE; ESCHERICHIA COLI; GENE MUTATION; HUMAN; MUTATIONAL ANALYSIS; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN INTERACTION; WILD TYPE;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0041507097     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00954-9     Document Type: Article

References (31)

1. Perraud A.L., Fleig A., Dunn C.A., Bagley L.A., Launay P., Schmitz C., et al. ADP-ribose gating of the calcium-permeable LTRPC2 channel revealed by Nudix motif homology. Nature. 411:2001;595-599.
2. Bessman M.J., Frick D.N., O'Handley S.F. The MutT proteins or "Nudix" hydrolases, a family of versatile, widely distributed, "housecleaning" enzymes. J. Biol. Chem. 271:1996;25059-25062.
3. Zocchi E., Guida L., Franco L., Silvestro L., Guerrini M., Benatti U., De Flora A. Free ADP-ribose in human erythrocytes: pathways of intra-erythrocytic conversion and non-enzymic binding to membrane proteins. Biochem. J. 295:1993;121-130.
4. + channels in rat ventricular myocytes. Am. J. Physiol. 271:1996;C464-C468.
5. Dunn C.A., O'Handley S.F., Frick D.N., Bessman M.J. Studies on the ADP-ribose pyrophosphatase subfamily of the nudix hydrolases and tentative identification of trgB, a gene associated with tellurite resistance. J. Biol. Chem. 274:1999;32318-32324.
6. Sheikh S., O'Handley S.F., Dunn C.A., Bessman M.J. Identification and characterization of the Nudix hydrolase from the Archaeon, Methanococcus jannaschii, as a highly specific ADP-ribose pyrophosphatase. J. Biol. Chem. 273:1998;20924-20928.
7. Bessman M.J., Walsh J.D., Dunn C.A., Swaminathan J., Weldon J.E., Shen J. The gene ygdP, associated with the invasiveness of Escherichia coli K1, designates a Nudix hydrolase, Orf176, active on adenosine (5′)-pentaphospho-(5′)-adenosine (Ap5A). J. Biol. Chem. 276:2001;37834-37838.
8. Abeygunawardana C., Weber D.J., Gittis A.G., Frick D.N., Lin J., Miller A.F., et al. Solution structure of the MutT enzyme, a nucleoside triphosphate pyrophosphohydrolase. Biochemistry. 34:1995;14997-15005.
9. Gabelli S.B., Bianchet M.A., Bessman M.J., Amzel L.M. The structure of ADP-ribose pyrophosphatase reveals the structural basis for the versatility of the Nudix family. Nature Struct. Biol. 8:2001;467-472.
10. Gabelli S.B., Bianchet M.A., Ohnishi Y., Ichikawa Y., Bessman M.J., Amzel L.M. Mechanism of the Escherichia coli ADP-ribose pyrophosphatase, a Nudix hydrolase. Biochemistry. 41:2002;9279-9285.
11. Swarbrick J.D., Bashtannyk T., Maksel D., Zhang X.R., Blackburn G.M., Gayler K.R., Gooley P.R. The three-dimensional structure of the Nudix enzyme diadenosine tetraphosphate hydrolase from Lupinus angustifolius L. J. Mol. Biol. 302:2000;1165-1177.
12. Bailey S., Sedelnikova S.E., Blackburn G.M., Abdelghany H.M., Baker P.J., McLennan A.G., Rafferty J.B. The crystal structure of diadenosine tetraphosphate hydrolase from Caenorhabditis elegans in free and binary complex forms. Structure (Camb). 10:2002;589-600.
13. Lin J., Abeygunawardana C., Frick D.N., Bessman M.J., Mildvan A.S. The role of Glu 57 in the mechanism of the Escherichia coli MutT enzyme by mutagenesis and heteronuclear NMR. Biochemistry. 35:1996;6715-6726.
14. Abdelghany H.M., Bailey S., Blackburn G.M., Rafferty J.B., McLennan A.G. Analysis of the catalytic and binding residues of the diadenosine tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans by site-directed mutagenesis. J. Biol. Chem. 278:2003;4435-4439.
15. Bernet D., Pinto R.M., Costas M.J., Canales J., Cameselle J.C. Rat liver mitochondrial ADP-ribose pyrophosphatase in the matrix space with low Km for free ADP-ribose. Biochem. J. 299:1994;679-682.
16. Canales J., Pinto R.M., Costas M.J., Hernandez M.T., Miro A., Bernet D., et al. Rat liver nucleoside diphosphosugar or diphosphoalcohol pyrophosphatases different from nucleotide pyrophosphatase or phosphodiesterase I: substrate specificities of Mg(2+)- and/or Mn(2+)-dependent hydrolases acting on ADP-ribose. Biochim. Biophys. Acta. 1246:1995;167-177.
17. Ribeiro J.M., Carloto A., Costas M.J., Cameselle J.C. Human placenta hydrolases active on free ADP-ribose: an ADP-sugar pyrophosphatase and a specific ADP-ribose pyrophosphatase. Biochim. Biophys. Acta. 1526:2001;86-94.
18. Lin S., Gasmi L., Xie Y., Ying K., Gu S., Wang Z., et al. Cloning, expression and characterisation of a human Nudix hydrolase specific for adenosine 5′-diphosphoribose (ADP-ribose). Biochim. Biophys. Acta. 1594:2002;127-135.
19. Perraud A.L., Shen B., Dunn C.A., Rippe K., Smith M.K., Bessman M.J., et al. NUDT9, a member of the nudix hydrolase family, is an evolutionarily conserved mitochondrial ADP-ribose pyrophosphatase. J. Biol. Chem. 278:2002;1794-1801.
20. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1993;123-128.
21. Rafty L.A., Schmidt M.T., Perraud A.L., Scharenberg A.M., Denu J.M. Analysis of O-acetyl-ADP-ribose as a target for Nudix ADP-ribose hydrolases. J. Biol. Chem. 277:2002;47114-47122.
22. 2+ permeable cation channels:from gene to biological function. Cell Calcium. 382:2003;1-13.
23. 2+ influx system mediated by LTRPC2. Science. 293:2001;1327-1330.
24. ++-permeable channel activated by changes in redox status confers susceptibility to cell death. Mol. Cell. 9:2002;163-173.
25. Doublie S. Preparation of selenomethyl proteins for phase determination. Methods Enzymol. 276:1997;523-530.
26. Otwinowski Z., Schevitz R.W., Zhang R.G., Lawson C.L., Joachimiak A., Marmorstein R.Q., et al. Crystal structure of trp repressor/operator complex at atomic resolution. Nature. 335:1988;321-329.
27. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
28. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallog. sect. D. 54:1998;905-921.
29. Jones T.A., Zou J.-Y., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A. 47:1991;110-119.
30. Klegwegt G.J.J. xdlMAPMAN and xdlDATAMAN - programs for reformating, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets. Acta Crystallog. sect. D. 52:1996;826-828.
31. Klegwegt G.J., Zou J.Y., Kjeldgaard M., Jones A. Rossmann M.G., Arnold E. International Tables for Crystallography. International Tables for Crystallography. 2001;Kluwer Academic, Dordrecht.