Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase

Nucleic Acids Research

Volumn 32, Issue 2, 2004, Pages 653-660

  Eastberg, Jennifer H ^b   Pelletier, John ^a   Stoddard, Barry L ^b  

^a NEW ENGLAND BIOLABS   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; PHOSPHATASE; PHOSPHODIESTERASE; POLYNUCLEOTIDE 5' HYDROXYL KINASE; SINGLE STRANDED DNA; VIRUS DNA;

ARTICLE; BACTERIOPHAGE T4; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA CONFORMATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME PHOSPHORYLATION; ENZYME SUBSTRATE; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; X RAY DIFFRACTION;

BACTERIOPHAGE T4; BASE SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DNA, SINGLE-STRANDED; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PHOSPHORYLATION; POLYNUCLEOTIDE 5'-HYDROXYL-KINASE; PROTEIN CONFORMATION; SUBSTRATE SPECIFICITY;

T4 BACTERIOPHAGE; T4 PHAGE;

EID: 1342327713     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh212     Document Type: Article

References (50)

1. Richardson,C.C. (1965) Phosphorylation of nucleic acid by an enzyme from T4 bacteriophage-infected Escherichia coli. Proc. Natl Acad. Sci. USA, 54, 158-165.
2. Novogrodsky,A. and Hurwitz,J. (1966) The enzymatic phosphorylation of ribonucleic acid and deoxyribonucleic acid. I. Phosphorylation at 5′-hydroxyl termini. J. Biol. Chem., 241, 2923-2932.
3. Novogrodsky,A., Tal,M., Traub,A. and Hurwitz,J. (1966) The enzymatic phosphorylation of ribonucleic acid and deoxyribonucleic acid. II. Further properties of the 5′-hydroxyl polynucleotide kinase. J. Biol. Chem., 241, 2933-2943.
4. Berkner,K.L. and Folk,W.R. (1980) Polynucleotide kinase exchange as an assay for class II restriction endonucleases. Methods Enzymol., 65, 28-36.
5. Chaconas,G. and van de Sande,J.H. (1980) 5′-32P labeling of RNA and DNA restriction fragments. Methods Enzymol., 65, 75-85.
6. Sambrook,J., Fritsch,E.F. and Maniatis,T. (1989) Enzymes used in molecular cloning. Molecular Cloning: A Laboratory Manual, Vol. 1, 2nd Edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
7. Richardson,C.C. (1981) Bacteriophage T4 Polynucleotide Kinase. In Boyer,P.D. (ed.), The Enzymes. Academic Press, San Diego, CA, Vol. 14, pp. 299-314.
8. Sirotkin,K., Cooley,W., Runnels,J. and Snyder,L.R. (1978) A role in true-late gene expression for the T4 bacteriophage 5′ polynucleotide kinase 3′ phosphatase. J. Mol. Biol., 123, 221-233.
9. Cameron,V. and Uhlenbeck,O.C. (1977) 3′-Phosphatase activity in T4 polynucleotide kinase. Biochemistry, 16, 5120-5126.
10. Amitsur,M., Levitz,R. and Kaufmann,G. (1987) Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase reprocess the host lysine tRNA. EMBO J., 6, 2499-2503.
11. Lillehaug,J.R., Kleppe,R.K. and Kleppe,K. (1976) Phosphorylation of dsDNAs by T4 polynucleotide kinase. Biochemistry, 15, 1858-1865.
12. Lillehaug,J.R. and Kleppe,K. (1975) Kinetics and specificity of T4 polynucleotide kinase. Biochemistry, 14, 1221-1225.
13. vanHouten,V., Denkers,F., van Dijk,M., van den Brekel,M. and Brakenhoff,R. (1998) Labeling efficiency of oligonucleotides by T4 polynucleotide kinase depends on 5′-nucleotide. Anal. Biochem., 265, 386-389.
14. van de Sande,J.H. and Bilsker,M. (1973) Phosphorylation of N-protected deoxyoligonucleotides by T4 polynucleotide kinase. Biochemistry, 12, 5056-5062.
15. Fontanel,M.L., Bazin,H. and Teoule,R. (1994) Sterical recognition by T4 polynucleotide kinase of non-nucleosidic moieties 5′-attached to oligonucleotides. Nucleic Acids Res., 22, 2022-2027.
16. Jarvest,R.L. and Lowe,G. (1981) The stereochemical course of phosphoryl transfer catalysed by polynucleotide kinase (bacteriophage-T4-infected Escherichia coli B). Biochem. J., 199, 273-276.
17. Lillehaug,J.R. (1978) Inhibition of T4 polynucleotide kinase by the ATP analog, beta, gamma-imidoadenylyl 5′-triphosphate. Biochim. Biophys. Acta, 525, 357-363.
18. Wang,L.K. and Shuman,S. (2001) Domain structure and mutational analysis of T4 polynucleotide kinase. J. Biol. Chem., 276, 26868-26874.
19. Wang,L.K. and Shuman,S. (2002) Mutational analysis defines the 5′-kinase and 3′-phosphatase active sites of T4 polynucleotide kinase. Nucleic Acids Res., 30, 1073-1080.
20. Panet,A., van de Sande,J.H., Loewen,P.C., Khorana,H.G., Raae,A.J., Lillehaug,J.R. and Kleppe,K. (1973) Physical characterization and simultaneous purification of bacteriophage T4 induced polynucleotide kinase, polynucleotide ligase and deoxyribonucleic acid polymerase. Biochemistry, 12, 5045-5050.
21. Lillehaug,J.R. (1977) Physicochemical properties of T4 polynucleotide kinase. Eur. J. Biochem., 73, 499-506.
22. Soltis,D.A. and Uhlenbeck,O.C. (1982) Independent locations of kinase and 3′-phosphatase activities on T4 polynucleotide kinase. J. Biol. Chem., 257, 11340-11345.
23. Wang,L.K., Lima,C.D. and Shuman,S. (2002) Structure and mechanism of T4 polynucleotide kinase: an RNA repair enzyme. EMBO J., 21, 3873-3880.
24. Galburt,E.A., Pelletier,J., Wilson,G. and Stoddard,B.L. (2002) Structure of a tRNA repair enzyme and molecular biology workhorse: T4 polynucleotide kinase. Structure (Camb), 10, 1249-1260.
25. Hasemann,C.A., Istvan,E.S., Uyeda,K. and Deisenhofer,J. (1996) The crystal structure of the bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase reveals distinct domain homologies. Structure, 4, 1017-1029.
26. Berry,M.B., Meador,B., Bilderback,T., Liang,P., Glaser,M. and Phillips,G.N.,Jr (1994) The closed conformation of a highly flexible protein: the structure of E.coli adenylate kinase with bound AMP and AMPPNP. Proteins, 19, 183-198.
27. Otwinowski,Z. and Minor,W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326.
28. Kissinger,C.R., Gehlhaar,D.K. and Fogel,D.B. (1999) Rapid automated molecular replacement by evolutionary search. Acta Crystallogr. D Biol. Crystallogr., 55 (Pt 2), 484-491.
29. 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. et al. (1998) Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr., 54 (Pt 5), 905-921.
30. Kleywegt,G.J. and Brunger,A.T. (1996) Checking your imagination: applications of the free R value. Structure, 4, 897-904.
31. McRee,D.E. (1999) XtalView/Xfit-A versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol., 125, 156-165.
32. Laskowski,R.J., 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.
33. Guex,N. and Peitsch,M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.
34. DeLano,W.L. (2002) DeLano Scientific, San Carlos, CA.
35. Horvath,M.P., Schweider,V.L., Bevilacqua,J.M., Ruggles,J.A. and Schultz,S.C. (1998) Crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand DNA. Cell, 95, 939-950.
36. Lei,M., Podell,E.R., Baumann,P. and Cech,T.R. (2003) DNA self-recognition in the structure of Pot1 bound to telomeric single-stranded DNA. Nature, 426, 198-203.
37. Raghunathan,S., Kozlov,A.G., Lohman,T.M. and Waksman,G. (2000) Structure of the DNA binding domain of E. coli SSB bound to ssDNA. Nat. Struct. Biol., 7, 648-652.
38. Bochkarev,A., Pfuetzner,R.A., Edwards,A.M. and Frappier,L. (1997) Structure of the single-stranded DNA binding domain of replication protein A bound to DNA. Nature, 385, 176-181.
39. Yang,H., Jeffrey,P.D., Miller,J., Kinnucan,E., Sun,Y., Thoma,N.H., Zheng,N., Chen,P.L., Lee,W.H. and Pavletich,N.P. (2002) BRCA2 function in DN binding and recombination from a BRCA2-DSS1-ssDNA structure. Science, 297, 1837-1848.
40. Shamoo,Y., Friedman,A.M., Parsons,M.R., Konigsberg,W.H. and Steitz,T.A. (1995) Crystals structure of a replication fork single-stranded DNA binding protein (T4 gp32) complexed to DNA. Nature, 376, 362-366.
41. Agback,P., Baumann,H., Knapp,S., Ladenstein,R. and Hard,T. (1998) Architecture of nonspecific protein-DNA interactions in the Sso7d-DNA complex. Nat. Struct. Biol., 5, 579-584.
42. Robinson,H., Gao,Y.G., McCrary,B.S., Edmondson,S.P., Shriver,J.W. and Wang,A.H. (1998) The hyperthermophile chromosomal protein Sac7d sharply kinks DNA. Nature, 392, 202-205.
43. Luger,K., Mader,A.W., Richmond,R.K., Sargent,D.F. and Richmond,T.J. (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature, 389, 251-260.
44. Masse,J.E., Wong,B., Yen,Y.M., Allain,F.H., Johnson,R.C. and Feigon,J. (2002) The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding. J. Mol. Biol., 323, 263-284.
45. Murphy,F.V.T., Sweet,R.M. and Churchill,M.E. (1999) The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition. EMBO J., 18, 6610-6618.
46. Li,C.L., Hor,L.I., Chang,Z.F., Tsai,L.C., Yang,W.Z. and Yuan,H.S. (2003) DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site. EMBO J., 22, 4014-4025.
47. Suck,D., Lahm,A. and Oefner,C. (1988) Structure refined to 2Å of a nicked DNA octanucleotide complex with DNase I. Nature, 332, 464-468.
48. Eom,S.H., Wang,J. and Steitz,T.A. (1996) Structure of Taq ploymerase with DNA at the polymerase active site. Nature, 382, 278-281.
49. Luscombe,N.M. and Thornton,J.M. (2002) Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. J. Mol. Biol., 320, 991-1009.
50. Saenger,W. (1984) Forces stabilizing associations between bases: hydrogen bonding and base stacking. Principles of Nucleic Acid Structure. Springer-Verlag, New York, NY, pp. 116-158.