Crystal structures of human and murine deoxyribonucleotidases: Insights into recognition of substrates and nucleotide analogues

Biochemistry

Volumn 46, Issue 48, 2007, Pages 13809-13818

  Walldén, Karin ^a,b   Rinaldo Matthis, Agnes ^a   Ruzzenente, Benedetta ^c   Rampazzo, Chiara ^c   Bianchi, Vera ^c   Nordlund, Pär ^b  

^a STOCKHOLM UNIVERSITY   (Sweden)

^b KAROLINSKA INSTITUTE   (Sweden)

^c UNIVERSITY OF PADOVA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYST ACTIVITY; CRYSTAL STRUCTURE; DNA; ENZYMES; MOLECULAR INTERACTIONS;

DEOXYRIBONUCLEOTIDASE (CDN); DEPHOSPHORYLATION; MITOCHONDRIA;

NUCLEOTIDES;

DEOXYRIBONUCLEOTIDE; DEOXYURIDINE; PURINE NUCLEOTIDE;

ARTICLE; BINDING AFFINITY; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; CYTOSOL; DEPHOSPHORYLATION; DNA REPLICATION; HUMAN; MITOCHONDRION; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL;

5'-NUCLEOTIDASE; AMINO ACID SEQUENCE; ANIMALS; CRYSTALLOGRAPHY, X-RAY; HUMANS; MICE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHOSPHORYLATION; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTRATE SPECIFICITY;

MURINAE;

EID: 36849030719     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi7014794     Document Type: Article

References (39)

1. Reichard, P. (1988) Interactions between Deoxyribonucleotide and DNA-Synthesis, Annu. Rev. Biochem. 57, 349-374.
2. Bianchi, V., and Spychala, J. (2003) Mammalian 5′-nucleotidases, J. Biol. Chem. 278, 46195-46198.
3. Hunsucker, S. A., Mitchell, B. S., and Spychala, J. (2005) The 5′-nucleotidases as regulators of nucleotide and drug metabolism, Pharmacol. Ther. 107, 1-30.
4. Rampazzo, C., Gallinaro, L., Milanesi, E., Frigimelica, E., Reichard, P., and Bianchi, V. (2000) A deoxyribonucleotidase in mitochondria: involvement in regulation of dNTP pools and possible link to genetic disease, Proc. Natl. Acad. Sci., U.S.A. 97, 8239-8244.
5. Mazzon, C., Rampazzo, C., Scaini, M. C., Gallinaro, L., Karlsson, A., Meier, C., Balzarini, J., Reichard, P., and Bianchi, V. (2003) Cytosolic and mitochondrial deoxyribonucleotidases: activity with Substrate analogs, inhibitors and implications for therapy, Biochem. Pharmacol. 66, 471-479.
6. Höglund, L., and Reichard, P. (1990) Cytoplasmic 5′(3′)-Nucleotidase from Human Placenta, J. Biol. Chem. 265, 6589-6595.
7. Rampazzo, C., Johansson, M., Gallinaro, L., Ferraro, P., Hellman, U., Karlsson, A., Reichard, P., and Bianchi, V. (2000) Mammalian 5′(3′)-deoxyribonucleotidase, cDNA cloning, and overexpression of the enzyme in Escherichia coli and mammalian cells, J. Biol. Chem. 275, 5409-5415.
8. Carson, D. A., Carrera, C. J., Wasson, D. B., and Iizasa, T. (1991) Deoxyadenosine-resistant human T lymphoblasts with elevated 5′- nucleotidase activity, Biochim. Biophys. Acta 1091, 22-28.
9. Hunsucker, S. A., Spychala, J., and Mitchell, B. S. (2001) Human cytosolic 5′-nucleotidase I - Characterization and role in nucleoside analog resistance, J. Biol. Chem. 276, 10498-10504.
10. Lotfi, K., Mansson, E., Chandra, J., Wang, Y. Y., Xu, D. W., Knaust, E., Spasokoukotskaja, T., Liliemark, E., Eriksson, S., and Albertioni, F. (2001) Pharmacological basis for cladribine resistance in a human acute T lymphoblastic leukaemia cell line selected for resistance to etoposide, Br. J. Haematol. 113, 339-346.
11. Schirmer, M., Stegmann, A. P. A., Geisen, F., and Konwalinka, G. (1998) Lack of cross-resistance with gemcitabine and cytarabine in cladribine-resistant HL60 cells with elevated 5′-nucleotidase activity, Exp. Hematol. 26, 1223-1228.
12. Galmarini, C. M., Thomas, X., Graham, K., El, Jafaari, A., Cros, E., Jordheim, L., Mackey, J. R., and Dumontet, C. (2003) Deoxycytidine kinase and cN-II nucleotidase expression in blast cells predict survival in acute myeloid leukaemia patients treated with cytarabine, Br. J. Haematol. 122, 53-60.
13. Kawasaki, H., Carrera, C. J., Piro, L. D., Saven, A., Kipps, T. J., and Carson, D. A. (1993) Relationship of Deoxycytidine Kinase and Cytoplasmic 5′-Nucleotidase to the Chemotherapeutic Efficacy of 2- Chlorodeoxyadenosine, Blood 81, 597-601.
14. Rinaldo-Matthis, A., Rampazzo, C., Reichard, P., Bianchi, V., and Nordlund, P. (2002) Crystal structure of a human mitochondrial deoxyribonucleotidase, Nat. Struct. Biol. 9, 779-787.
15. Walldén, K., Stenmark, P., Nyman, T., Flodin, S., Gräslund, S., Loppnau, P., Bianchi, V., and Nordlund, P. (2007) Crystal structure of human cytosolic 5′-nucleotidase II: Insights into allosteric regulation and substrate recognition, J. Biol. Chem. 282, 17828-17836.
16. Bitto, E., Bingman, C. A., Wesenberg, G. E., McCoy, J. G., and Phillips, G. N. (2006) Structure of pyrimidine 5′-nucleotidase type 1 - Insight into mechanism of action arid inhibition during lead poisoning, J. Biol. Chem. 281, 20521-20529.
17. Lahiri, S. D., Zhang, G. F., Dunaway-Mariano, D., and Allen, K. N. (2003) The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction, Science 299, 2067-2071.
18. Allegrini, S., Pesi, R., Tozzi, M. G., Fiol, C. J., Johnson, R. B., and Eriksson, S. (1997) Bovine cytosolic IMP/GMP-specific 5′-nucleotidase: cloning and expression of active enzyme in Escherichia coli, Biochem. J. 328, 483-487.
19. Collet, J. F., Stroobant, V., Pirard, M., Delpierre, G., and Van Shaftingen, E. (1998) A new class of phosphotransferases phosphorylated on an aspartate residue in an amino-terminal DXDX-(T/V) motif, J. Biol. Chem. 273, 14107-14112.
20. Wallden, K., Ruzzenente, B., Rinaldo-Matthis, A., Bianchi, V., and Nordlund, P. (2005) Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase, Structure 13, 1081-1088.
21. Furman, P. A., Fyfe, J. A., Stclair, M. H., Weinhold, K., Rideout, J. L., Freeman, G. A., Lehrman, S. N., Bolognesi, D. P., Broder, S., Mitsuya, H., and Barry, D. W. (1986) Phosphorylation of 3′-Azido-3′-deoxythymidine and Selective Interaction of the 5′-Triphosphate with Human- Immunodeficiency-Virus Reverse-Transcriptase, Proc. Natl. Acad. Sci. U.S.A. 83, 8333-8337.
22. Lewis, W., Day, B. J., and Copeland, W. C. (2003) Mitochondrial toxicity of NRTI antiviral drugs: An integrated cellular perspective, Nat. Rev. Drug Discovery 2, 812-822.
23. De, Clercq, E. (2005) (E)5-(2-bromovinyl)-2′ deoxyuridine (BVDU), Med. Res. Rev. 25, 1-20.
24. Bradford, M. M. (1976) Rapid and Sensitive Method for Quantitation of Microgram Quantities of Protein Utilizing Principle of Protein-Dye Binding, Anal. Biochem. 72, 248-254.
25. Kabsch, W. (1988) Automatic-Indexing of Rotation Diffraction Patterns, J. Appl. Crystallogr. 21, 67-71.
26. Leslie, A. G. W. (1992) Recent changes to the MOSFLM package for processing film and image plate data, Joint CCP4 + ESF-EAMCB Newsletter on Protein Crystallography 26.
27. Kabsch, W. (1988) Evaluation of Single-Crystal X-Ray-Diffraction Data from a Position-Sensitive Detector, J. Appl. Crystallogr. 21, 916-924.
28. Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination, Acta Crystallogr. D 54, 905-921.
29. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method, Acta Crystallogr. D 53, 240-255.
30. Harding, M. M. (2006) Small revisions to predicted distances around metal sites in proteins, Acta Crystallogr. D 62, 678-682.
31. Vagin, A., and Teplyakov, A. (1997) MOLREP: an automated program for molecular replacement, J. Appl. Crystallogr. 30, 1022-1025.
32. Emsley, P., and Cowtan, K. (2004) Coot: model-building tools for molecular graphics, Acta Crystallogr. D 60, 2126-2132.
33. DeLano, W. L. (2002) The PyMOL Molecular Graphics System, DeLano Scientific, Palo Alto, CA, U.S.A.
34. Wang, W. R., Cho, H. S., Kim, R., Jancarik, J., Yokota, H., Nguyen, H. H., Grigoriev, I. V., Wemmer, D. E., and Kim, S. H. (2002) Structural characterization of the reaction pathway in phosphoserine phosphatase: Crystallographic "snapshots" of intermediate states, J. Mol. Biol. 319, 421-431.
35. Kabsch, W. (1976) Solution for Best Rotation to Relate 2 Sets of Vectors, Acta Crystallogr. A 32, 922-923.
36. Bloomfield, V. A., Crothers, D. M., and Tinoco, I., Jr. (2000) Nucleic Acids: Structures, Properties and Functions, University Science Books, Sausalito, CA.
37. Rampazzo, C., Ferraro, P., Pontarin, G., Fabris, S., Reichard, P., arid Bianchi, V. (2004) Mitochondrial deoxyribonucleotides, pool sizes, synthesis, and regulation, J. Biol. Chem. 279, 17019-17026.
38. Laskowski, R. A., Macarthur, M. W., Moss, D. S., and Thornton, J. M. (1993) Procheck - a Program to Check the Stereochemical Quality of Protein Structures, J. Appl. Crystallogr. 26, 283-291.
39. Gouet, P., Courcelle, E., Stuart, D. I., and Metoz, F. (1999) ESPript: analysis of multiple sequence alignments in PostScript, Bioinformatics 15, 305-308.