The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase

Molecular Cell

Volumn 44, Issue 3, 2011, Pages 385-396

  Garces, Fernando ^a   Pearl, Laurence H ^a   Oliver, Antony W ^a  

^a UNIVERSITY OF SUSSEX   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CURVED DNA; DOUBLE STRANDED DNA; PHOSPHOTRANSFERASE; POLYNUCLEOTIDE KINASE 3' PHOSPHATASE; SINGLE STRANDED DNA; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; DNA STRUCTURE; DOUBLE STRANDED DNA BREAK; ENZYME ACTIVE SITE; ENZYME SUBSTRATE; ENZYME SUBSTRATE COMPLEX; PROTEIN DOMAIN; SINGLE STRANDED DNA BREAK;

ANIMALS; BINDING SITES; CRYSTALLOGRAPHY; DNA BREAKS, DOUBLE-STRANDED; DNA BREAKS, SINGLE-STRANDED; DNA REPAIR ENZYMES; DNA, SINGLE-STRANDED; MICE; MODELS, MOLECULAR; MUTATION; NUCLEIC ACID CONFORMATION; PHOSPHOTRANSFERASES (ALCOHOL GROUP ACCEPTOR); PROTEIN CONFORMATION; STRUCTURE-ACTIVITY RELATIONSHIP;

MAMMALIA; MURINAE;

EID: 80555144193     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2011.08.036     Document Type: Article

References (34)

1. Abramoff M.D., Magelhaes P.J., Ram S.J. Image Processing with ImageJ. Biophotonics International 2004, 11:36-42.
2. Adams P.D., Grosse-Kunstleve R.W., Hung L.W., Ioerger T.R., McCoy A.J., Moriarty N.W., Read R.J., Sacchettini J.C., Sauter N.K., Terwilliger T.C. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D Biol. Crystallogr. 2002, 58:1948-1954.
3. Ali A.A., Jukes R.M., Pearl L.H., Oliver A.W. Specific recognition of a multiply phosphorylated motif in the DNA repair scaffold XRCC1 by the FHA domain of human PNK. Nucleic Acids Res. 2009, 37:1701-1712.
4. Bernstein N.K., Williams R.S., Rakovszky M.L., Cui D., Green R., Karimi-Busheri F., Mani R.S., Galicia S., Koch C.A., Cass C.E., et al. The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase. Mol. Cell 2005, 17:657-670.
5. Bernstein N.K., Hammel M., Mani R.S., Weinfeld M., Pelikan M., Tainer J.A., Glover J.N. Mechanism of DNA substrate recognition by the mammalian DNA repair enzyme, Polynucleotide Kinase. Nucleic Acids Res. 2009, 37:6161-6173.
6. Caldecott K.W., Aoufouchi S., Johnson P., Shall S. XRCC1 polypeptide interacts with DNA polymerase beta and possibly poly (ADP-ribose) polymerase, and DNA ligase III is a novel molecular 'nick-sensor' in vitro. Nucleic Acids Res. 1996, 24:4387-4394.
7. Cappelli E., Taylor R., Cevasco M., Abbondandolo A., Caldecott K., Frosina G. Involvement of XRCC1 and DNA ligase III gene products in DNA base excision repair. J. Biol. Chem. 1997, 272:23970-23975.
8. Cho H., Wang W., Kim R., Yokota H., Damo S., Kim S.H., Wemmer D., Kustu S., Yan D. BeF(3)(-) acts as a phosphate analog in proteins phosphorylated on aspartate: structure of a BeF(3)(-) complex with phosphoserine phosphatase. Proc. Natl. Acad. Sci. USA 2001, 98:8525-8530.
9. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 1994, 50:760-763. CCP4 (Collaborative Computational Project, Number 4).
10. Deshpande R.A., Wilson T.E. Identification of DNA 3'-phosphatase active site residues and their differential role in DNA binding, Mg2+ coordination, and catalysis. Biochemistry 2004, 43:8579-8589.
11. Dobson C.J., Allinson S.L. The phosphatase activity of mammalian polynucleotide kinase takes precedence over its kinase activity in repair of single strand breaks. Nucleic Acids Res. 2006, 34:2230-2237.
12. Emsley P., Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 2004, 60:2126-2132.
13. Gravel S., Chapman J.R., Magill C., Jackson S.P. DNA helicases Sgs1 and BLM promote DNA double-strand break resection. Genes Dev. 2008, 22:2767-2772.
14. Habraken Y., Verly W.G. The DNA 3'-phosphatase and 5'-hydroxyl kinase of rat liver chromatin. FEBS Lett. 1983, 160:46-50.
15. Habraken Y., Verly W.G. Chromatin 3'-phosphatase/5'-OH kinase cannot transfer phosphate from 3' to 5' across a strand nick in DNA. Nucleic Acids Res. 1986, 14:8103-8110.
16. Jilani A., Ramotar D., Slack C., Ong C., Yang X.M., Scherer S.W., Lasko D.D. Molecular cloning of the human gene, PNKP, encoding a polynucleotide kinase 3'-phosphatase and evidence for its role in repair of DNA strand breaks caused by oxidative damage. J. Biol. Chem. 1999, 274:24176-24186.
17. Johnson L.N., Noble M.E., Owen D.J. Active and inactive protein kinases: structural basis for regulation. Cell 1996, 85:149-158.
18. Kocsis E., Trus B.L., Steer C.J., Bisher M.E., Steven A.C. Image averaging of flexible fibrous macromolecules: the clathrin triskelion has an elastic proximal segment. J. Struct. Biol. 1991, 107:6-14.
19. Kubota Y., Nash R.A., Klungland A., Schär P., Barnes D.E., Lindahl T. Reconstitution of DNA base excision-repair with purified human proteins: interaction between DNA polymerase beta and the XRCC1 protein. EMBO J. 1996, 15:6662-6670.
20. Leslie A.G.W. MOSFLM Users Guide 1995, MRC Laboratory of Molecular Biology, Cambridge, UK.
21. Loizou J.I., El-Khamisy S.F., Zlatanou A., Moore D.J., Chan D.W., Qin J., Sarno S., Meggio F., Pinna L.A., Caldecott K.W. The protein kinase CK2 facilitates repair of chromosomal DNA single-strand breaks. Cell 2004, 117:17-28.
22. Lu M., Mani R.S., Karimi-Busheri F., Fanta M., Wang H., Litchfeld D.W., Weinfeld M. Independent mechanisms of stimulation of polynucleotide kinase/phosphatase by phosphorylated and non-phosphorylated XRCC1. Nucleic Acids Res. 2010, 38:510-521.
23. Mani R.S., Karimi-Busheri F., Cass C.E., Weinfeld M. Physical properties of human polynucleotide kinase: hydrodynamic and spectroscopic studies. Biochemistry 2001, 40:12967-12973.
24. McCoy A.J. Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr. D Biol. Crystallogr. 2007, 63:32-41.
25. Mimitou E.P., Symington L.S. Sae2, Exo1 and Sgs1 collaborate in DNA double-strand break processing. Nature 2008, 455:770-774.
26. Nash R.A., Caldecott K.W., Barnes D.E., Lindahl T. XRCC1 protein interacts with one of two distinct forms of DNA ligase III. Biochemistry 1997, 36:5207-5211.
27. Nimonkar A.V., Genschel J., Kinoshita E., Polaczek P., Campbell J.L., Wyman C., Modrich P., Kowalczykowski S.C. BLM-DNA2-RPA-MRN and EXO1-BLM-RPA-MRN constitute two DNA end resection machineries for human DNA break repair. Genes Dev. 2011, 25:350-362.
28. Noble M.E., Endicott J.A., Johnson L.N. Protein kinase inhibitors: insights into drug design from structure. Science 2004, 303:1800-1805.
29. Potterton L., McNicholas S., Krissinel E., Gruber J., Cowtan K., Emsley P., Murshudov G.N., Cohen S., Perrakis A., Noble M. Developments in the CCP4 molecular-graphics project. Acta Crystallogr. D Biol. Crystallogr. 2004, 60:2288-2294.
30. Rass U., Ahel I., West S.C. Defective DNA repair and neurodegenerative disease. Cell 2007, 130:991-1004.
31. Sheldrick G.M. A short history of SHELX. Acta Crystallogr. A 2008, 64:112-122.
32. Weinfeld M., Mani R.S., Abdou I., Aceytuno R.D., Glover J.N. Tidying up loose ends: the role of polynucleotide kinase/phosphatase in DNA strand break repair. Trends Biochem Sci 2011, 36:262-271.
33. Whitehouse C.J., Taylor R.M., Thistlethwaite A., Zhang H., Karimi-Busheri F., Lasko D.D., Weinfeld M., Caldecott K.W. XRCC1 stimulates human polynucleotide kinase activity at damaged DNA termini and accelerates DNA single-strand break repair. Cell 2001, 104:107-117.
34. Zhu Z., Chung W.H., Shim E.Y., Lee S.E., Ira G. Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-strand break ends. Cell 2008, 134:981-994.