Early Interrogation and Recognition of DNA Sequence by Indirect Readout

Structure

Volumn 16, Issue 12, 2008, Pages 1828-1837

  Little, Elizabeth J ^a   Babic, Andrea C ^a   Horton, Nancy C ^a  

^a UNIVERSITY OF ARIZONA   (United States)

Author keywords

DNA

Indexed keywords

DNA BASE; ENDONUCLEASE; HINCII ENZYME; PLASMID DNA; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; DNA BINDING; DNA CLEAVAGE; DNA SEQUENCE; DNA STRUCTURE; ENZYME ACTIVITY; GENE TARGETING; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN LOCALIZATION; PROTEIN METABOLISM; SITE DIRECTED MUTAGENESIS;

ALANINE; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; BASE PAIRING; BASE SEQUENCE; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DNA; DNA RESTRICTION ENZYMES; DNA, BACTERIAL; HAEMOPHILUS INFLUENZAE; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; X-RAY DIFFRACTION;

EID: 57049101786     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2008.09.009     Document Type: Article

References (49)

1. 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., and Terwilliger T.C. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D Biol. Crystallogr. 58 (2002) 1948-1954
2. Aggarwal A.K. Crystallization of DNA binding proteins with oligodeoxynucleotides. Methods 1 (1990) 83-90
3. Allingham J.S., and Haniford D.B. Mechanisms of metal ion action in Tn10 transposition. J. Mol. Biol. 319 (2002) 53-65
4. Babic A.C., Little E.J., Manohar V.M., Bitinaite J., and Horton N.C. DNA Distortion and Specificity in a Sequence Specific Endonuclease. J. Mol. Biol. (2008) in press
5. Baldwin G.S., Sessions R.B., Erskine S.G., and Halford S.E. DNA cleavage by the EcoRV restriction endonuclease: roles of divalent metal ions in specificity and catalysis. J. Mol. Biol. 288 (1999) 87-103
6. Blainey P.C., van Oijen A.M., Banerjee A., Verdine G.L., and Xie X.S. A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proc. Natl. Acad. Sci. USA 103 (2006) 5752-5757
7. Brünger 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. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54 (1998) 905-921
8. Cirino N.M., Cameron C.E., Smith J.S., Rausch J.W., Roth M.J., Benkovic S.J., and Le Grice S.F. Divalent cation modulation of the ribonuclease functions of human immunodeficiency virus reverse transcriptase. Biochemistry 34 (1995) 9936-9943
9. DeLano W.L. The PyMOL User's Manual (2002), DeLano Scientific, Palo Alto, CA
10. Elf J., Li G.W., and Xie X.S. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316 (2007) 1191-1194
11. Erie D.A., Yang G., Schultz H.C., and Bustamante C. DNA bending by Cro protein in specific and nonspecific complexes: implications for protein site recognition and specificity. Science 266 (1994) 1562-1566
12. Fasman G.D. CRC Handbook of Biochemistry and Molecular Biology. Third Edition (1975), CRC, Cleveland, OH
13. Garvie C.W., and Wolberger C. Recognition of specific DNA sequences. Mol. Cell 8 (2001) 937-946
14. Heinemann U., Lauble H., Frank R., and Blocker H. Crystal structure analysis of an A-DNA fragment at 1.8 A resolution: d(GCCCGGGC). Nucleic Acids Res. 15 (1987) 9531-9550
15. Horton N.C., and Perona J.J. Crystallographic snapshots along a protein-induced DNA-bending pathway. Proc. Natl. Acad. Sci. USA 97 (2000) 5729-5734
16. Horton N.C., Dorner L.F., and Perona J.J. Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation. Nat. Struct. Biol. 9 (2002) 42-47
17. Hsu M., and Berg P. Altering the specificity of restriction endonuclease: effect of replacing Mg2+ with Mn2+. Biochemistry 17 (1978) 131-138
18. Jeltsch A., Alves J., Oelgeschlager T., Wolfes H., Maass G., and Pingoud A. Mutational analysis of the function of Gln115 in the EcoRI restriction endonuclease, a critical amino acid for recognition of the inner thymidine residue in the sequence -GAATTC- and for coupling specific DNA binding to catalysis. J. Mol. Biol. 229 (1993) 221-234
19. Jeltsch A., Wenz C., Stahl F., and Pingoud A. Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme. EMBO J. 15 (1996) 5104-5111
20. Joshi H.K., Etzkorn C., Chatwell L., Bitinaite J., and Horton N.C. Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism. J. Biol. Chem. 281 (2006) 23852-23869
21. Kalodimos C.G., Biris N., Bonvin A.M., Levandoski M.M., Guennuegues M., Boelens R., and Kaptein R. Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science 305 (2004) 386-389
22. Kelly Jr. T.J., and Smith H.O. A restriction enzyme from Hemophilus influenzae. II. J. Mol. Biol. 51 (1970) 393-409
23. Kunkel T.A., and Loeb L.A. On the fidelity of DNA replication: effect of divalent metal ion activators and deoxyrionucleoside triphosphate pools on in vitro mutagenesis. J. Biol. Chem. 254 (1979) 5718-5725
24. Martin A.M., Sam M.D., Reich N.O., and Perona J.J. Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease. Nat. Struct. Biol. 6 (1999) 269-277
25. McRee D.E. XtalView/Xfit-A versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125 (1999) 156-165
26. Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53 (1997) 240-255
27. Niv M.Y., Ripoll D.R., Vila J.A., Liwo A., Vanamee E.S., Aggarwal A.K., Weinstein H., and Scheraga H.A. Topology of Type II REases revisited; structural classes and the common conserved core. Nucleic Acids Res. 35 (2007) 2227-2237
28. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. In: Carter Jr. C.W., and Sweet R.M. (Eds). Methods in Enzymology (1997), Academic Press, New York 307-326
29. Otwinowski Z., Schevitz R.W., Zhang R.G., Lawson C.L., Joachimiak A., Marmorstein R.Q., Luisi B.F., and Sigler P.B. Crystal structure of trp repressor/operator complex at atomic resolution. Nature 335 (1988) 321-329
30. Parry D., Moon S.A., Liu H.H., Heslop P., and Connolly B.A. DNA recognition by the EcoRV restriction endonuclease probed using base analogues. J. Mol. Biol. 331 (2003) 1005-1016
31. Pingoud A., and Jeltsch A. Structure and function of type II restriction endonucleases. Nucleic Acids Res. 29 (2001) 3705-3727
32. Richter P.H., and Eigen M. Diffusion controlled reaction rates in spheroidal geometry. Application to repressor-operator association and membrane bound enzymes. Biophys. Chem. 2 (1974) 255-263
33. Riggs A.D., Bourgeois S., and Cohn M. The lac repressor-operator interaction. 3. Kinetic studies. J. Mol. Biol. 53 (1970) 401-417
34. Sam M.D., and Perona J.J. Mn2+-dependent catalysis by restriction enzymes: pre-steady-state analysis of EcoRV endonuclease reveals burst kinetics and the origins of reduced activity. J. Am. Chem. Soc. 121 (1999) 1444-1447
35. Selent U., Ruter T., Kohler E., Liedtke M., Thielking V., Alves J., Oelgeschlager T., Wolfes H., Peters F., and Pingoud A. A site-directed mutagenesis study to identify amino acid residues involved in the catalytic function of the restriction endonuclease EcoRV. Biochemistry 31 (1992) 4808-4815
36. Tabor S., and Richardson C.C. Effect of manganese ions on the incorporation of dideoxynucleotides by bacteriophage T7 DNA polymerase and Escherichia coli DNA polymerase I. Proc. Natl. Acad. Sci. USA 86 (1989) 4076-4080
37. Taylor J.D., and Halford S.E. Discrimination between DNA sequences by the EcoRV restriction endonuclease. Biochemistry 28 (1989) 6198-6207
38. Townson S.A., Samuelson J.C., Xu S.Y., and Aggarwal A.K. Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence. Structure 13 (2005) 791-801
39. Townson S.A., Samuelson J.C., Bao Y., Xu S.Y., and Aggarwal A.K. BstYI bound to noncognate DNA reveals a "hemispecific" complex: implications for DNA scanning. Structure 15 (2007) 449-459
40. Vaisman A., Ling H., Woodgate R., and Yang W. Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis. EMBO J. 24 (2005) 2957-2967
41. Vermote C.L., Vipond I.B., and Halford S.E. EcoRV restriction endonuclease: communication between DNA recognition and catalysis. Biochemistry 31 (1992) 6089-6097
42. Viadiu H., and Aggarwal A.K. Structure of BamHI bound to nonspecific DNA: a model for DNA sliding. Mol. Cell 5 (2000) 889-895
43. Vipond I.B., Moon B.J., and Halford S.E. An isoleucine to leucine mutation that switches the cofactor requirement of the EcoRV restriction endonuclease from magnesium to manganese. Biochemistry 35 (1996) 1712-1721
44. von Hippel P.H. From "simple" DNA-protein interactions to the macromolecular machines of gene expression. Annu. Rev. Biophys. Biomol. Struct. 36 (2007) 79-105
45. von Hippel P.H., and Berg O.G. On the specificity of DNA-protein interactions. Proc. Natl. Acad. Sci. USA 83 (1986) 1608-1612
46. von Hippel P.H., and Berg O.G. Facilitated target location in biological systems. J. Biol. Chem. 264 (1989) 675-678
47. Winkler F.K., Banner D.W., Oefner C., Tsernoglou D., Brown R.S., Heathman S.P., Bryan R.K., Martin P.D., Petratos K., and Wilson K.S. The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 12 (1993) 1781-1795
48. Wolfe S.A., Grant R.A., Elrod-Erickson M., and Pabo C.O. Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes. Structure 9 (2001) 717-723
49. Xu S.Y., and Schildkraut I. Cofactor requirements of BamHI mutant endonuclease E77K and its suppressor mutants. J. Bacteriol. 173 (1991) 5030-5035