The recognition of local DNA conformation by the human papillomavirus type 6 E2 protein

Nucleic Acids Research

Volumn 34, Issue 14, 2006, Pages 3897-3908

  Hooley, Elizabeth ^a   Fairweather, Victoria ^a   Clarke, Anthony R ^a   Gaston, Kevin ^a   Brady, R Leo ^a  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; DOUBLE STRANDED DNA; GLYCOPROTEIN E2; THYMINE; TRANSCRIPTION FACTOR; DNA; DNA BINDING PROTEIN; VIRUS PROTEIN;

ARTICLE; AT RICH SEQUENCE; BINDING KINETICS; CANCER RISK; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA CONFORMATION; DNA SEQUENCE; DNA STRUCTURE; HUMAN PAPILLOMAVIRUS TYPE 18; HUMAN PAPILLOMAVIRUS TYPE 6; INFECTION RISK; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; NONHUMAN; PAPILLOMA VIRUS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN STRUCTURE; RISK ASSESSMENT; STRUCTURE ANALYSIS; UTERINE CERVIX CANCER; VERRUCA VULGARIS; VIRUS REPLICATION; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; METABOLISM; PROTEIN BINDING; SPECTROFLUOROMETRY; X RAY CRYSTALLOGRAPHY;

BOVINE PAPILLOMAVIRUS; HUMAN PAPILLOMAVIRUS; HUMAN PAPILLOMAVIRUS TYPE 6; PAPILLOMAVIRIDAE;

BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DNA; DNA-BINDING PROTEINS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PAPILLOMAVIRIDAE; PROTEIN BINDING; PROTEIN CONFORMATION; SPECTROMETRY, FLUORESCENCE; TRANSCRIPTION FACTORS; VIRAL PROTEINS;

EID: 33748579930     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl466     Document Type: Article

References (37)

1. Dell,G. and Gaston,K. (2001) Human papillomaviruses and their role in cervical cancer. Cell. Mol. Life Sci., 58, 1923-1942.
2. Hegde,R. (2002) The papillomavirus E2 proteins: Strucuture, function and biology. Annu. Rev. Biophys. Biomol. Struct., 31, 343-360.
3. Abbate,E.A., Berger,J.M. and Botchan,M.R. (2004) The X-ray structure of the papillomavirus helicase in complex with its molecular matchmaker E2. Genes Dev., 18, 1981-1996.
4. You,J., Croyle,J.L., Nishimura,A., Ozato,K. and Howley,P.M. (2004) Interaction of the bovine papillomavirus E2 protein with Brd4 tethers the viral DNA to host mitotic chromosomes. Cell, 117, 349-360.
5. Harris,S.F. and Botchan,M.R. (1999) Crystal structure of the human papillomavirus type 18 E2 activation domain. Science, 284, 1673-1677.
6. Antson,A.A., Burns,J.E., Moroz,O.V., Scott,D.J., Sanders,C.M., Bronstein,I.B., Dodson,G.G., Wilson,K.S. and Maitland,N.J. (2000) Structure of the intact transactivation domain of the human papillomavirus E2 protein. Nature, 403, 805-809.
7. Dell,G., Wilkinson,K.W., Tranter,R., Parish,J., Leo Brady,R. and Gaston,K. (2003) Comparison of the structure and DNA-binding properties of the E2 proteins from an oncogenic and a non-oncogenic human papillomavirus. J. Mol. Biol., 334, 979-991.
8. Hegde,R.S. and Androphy,E.J. (1998) Crystal structure of the E2 DNA-binding domain from human papillomavirus type 16: Implications for its DNA binding-site selection mechanism. J. Mol. Biol., 284, 1479-1489.
9. Bussiere,D.E., Kong,X., Egan,D.A., Walter,K., Holzman,T.F., Lindh,F., Robins,T. and Giranda,V.L. (1998) Structure of the E2 DNA-binding domain from human papillomavirus serotype 31 at 2.4 A. Acta Crystallogr. D Biol. Crystallogr., 54, 1367-1376.
10. Kim,S.S., Tam,J.K., Wang,A.F. and Hegde,R.S. (2000) The structural basis of DNA target discrimination by papillomavirus E2 proteins. J. Biol. Chem., 275, 31245-31254.
11. Hegde,R.S., Wang,A.F., Kim,S.S. and Schapira,M. (1998) Subunit rearrangement accompanies sequence-specific DNA binding by the bovine papillomavirus-1 E2 protein. J. Mol. Biol., 276, 797-808.
12. Veeraraghavan,S., Mello,C.C., Androphy,E.J. and Baleja,J.D. (1999) Structural correlates for enhanced stability in the E2 DNA-binding domain from bovine papillomavirus. Biochemistry, 38, 16115-16124.
13. Liang,H., Petros,A.M., Meadows,R.P., Yoon,H.S., Egan,D.A., Walter,K., Holzman,T.F., Robins,T. and Fesik,S.W. (1996) Solution structure of the DNA-binding domain of a human papillomavirus E2 protein: Evidence for flexible DNA-binding regions. Biochemistry, 35, 2095-2103.
14. Nadra,A.D., Eliseo,T., Mok,Y.K., Almeida,C.L., Bycroft,M., Paci,M., de Prat-Gay,G. and Cicero,D.O. (2004) Solution structure of the HPV-16 E2 DNA binding domain, a transcriptional regulator with a dimeric beta-barrel fold. J. Biomol. NMR, 30, 211-214.
15. Cicero,D.O., Nadra,A.D., Eliseo,T., Dellarole,M., Paci,M, and de Prat-Gay,G. (2006) Structural and thermodynamic basis for the enhanced transcriptional control by the human papillomavirus strain-16 E2 protein. Biochemistry, 45, 6551-6560.
16. Hines,C.S., Meghoo,C., Shetty,S., Biburger,M., Brenowitz,M. and Hegde,R.S. (1998) DNA structure and flexibility in the sequence-specific binding of papillomavirus E2 proteins. J. Mol. Biol., 276, 809-818.
17. Hizver,J., Rozenberg,H., Frolow,F., Rabinovich,D. and Shakked,Z. (2001) DNA bending by an adenine-thymine tract and its role in gene regulation. Proc. Natl Acad. Sci. USA, 98, 8490-8495.
18. Blakaj,D.M., Kattamuri,C., Khrapunov,S., Hegde,R.S. and Brenowitz,M. (2006) Indirect readout of DNA sequence by papillomavirus E2 Droteins depends upon net cation uptake. J. Mol. Biol., 358, 224.
19. Sambrook,J., Fritsch,E.F. and Maniatis,T. (1987) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Press, Woodbury, New York, USA.
20. Otwinowski,Z.M.W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326.
21. Storoni,L.C., McCoy,A.J. and Read,R.J. (2004) Likelihood-enhanced fast rotation functions. Acta Crystallogr. D Biol. Crystallogr., 60, 432-438.
22. Emsley,P. and Cowtan,K. (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr., 60, 2126-2132.
23. Winn,M.D., Isupov,M.N. and Murshudov,G.N. (2001) Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D Biol. Crystallogr., 57, 122-133.
24. Ferreiro,D.U. and de Prat-Gay,G. (2003) A protein-DNA binding mechanism proceeds through multi-state or two-state parallel pathways. J. Mol. Biol., 331, 89-99.
25. McBride,A.A., Klausner,R.D. and Howley,P.M. (1992) Conserved cysteine residue in the DNA-binding domain of the bovine papillomavirus type 1 E2 protein confers redox regulation of the DNA-binding activity in vitro. Proc. Natl Acad. Sci. USA, 89, 7531-7535.
26. Ferreiro,D.U., Dellarole,M., Nadra,A.D. and de Prat-Gay,G. (2005) Free energy contributions to direct readout of a DNA sequence. J. Biol. Chem., 280, 32480-32484.
27. Thain,A., Webster,K., Emery,D., Clarke,A.R. and Gaston,K. (1997) DNA binding and bending by the human papillomavirus type 16 E2 protein. Recognition of an extended binding site. J. Biol. Chem., 272, 8236-8242.
28. Collaborative Computational Project, Number 4. (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr., 50, 760-763.
29. Crothers,D.M., Haran,T.E. and Nadeau,J.G. (1990) Intrinsically bent DNA. J. Biol. Chem., 265, 7093-7096.
30. Rozenberg,H., Rabinovich,D., Frolow,F., Hegde,R.S. and Shakked,Z. (1998) Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets. Proc. Natl Acad. Sci. USA, 95, 15194-15199.
31. Zimmerman,J.M. and Maher,L.J. III (2003) Solution measurement of DNA curvature in papillomavirus E2 binding sites. Nucleic Acids Res., 31, 5134-5139.
32. Shinoda,T., Arai,K., Shigematsu-Iida,M., Ishikura,Y., Tanaka,S., Yamada,T., Kimber,M.S., Pai,E.F., Fushinobu,S. and Taguchi,H. (2005) Distinct conformation-mediated functions of an active site loop in the catalytic reactions of NAD-dependent D-Lactate dehydrogenase and formate dehydrogenase. J. Biol. Chem., 280, 17068-17075.
33. Strahs,D. and Schlick,T. (2000) A-Tract bending: Insights into experimental structures by computational models. J. Mol. Biol., 301, 643-663.
34. Dickerson,R.E. (1998) DNA bending: The prevalence of kinkiness and the virtues of normality. Nucleic Acids Res., 26, 1906-1926.
35. Kovelman,R., Bilter,G.K., Glezer,E., Tsou,A.Y. and Barbosa,M.S. (1996) Enhanced transcriptional activation by E2 proteins from the oncogenic human papillomaviruses. J. Virol., 70, 7549-7560.
36. Hou,S.Y., Wu,S.Y. and Chiang,C.M. (2002) Transcriptional activity among high and low risk human papillomavirus E2 proteins correlates with E2 DNA binding. J. Biol. Chem., 277, 45619-45629.
37. DeLano,W.L. (2002) The PyMOL Molecular Graphics System.