Structure and RNA binding of the third KH domain of poly(C)-binding protein 1

Nucleic Acids Research

Volumn 33, Issue 4, 2005, Pages 1213-1221

  Sidiqi, M ^a   Wilce, J A ^a   Vivian, J P ^a,b   Porter, C J ^a   Barker, A ^a,b   Leedman, P J ^c   Wilce, M C J ^a,b,c  

^a UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^b UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^c UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ANDROGEN RECEPTOR; MESSENGER RNA; OLIGONUCLEOTIDE; POLY C BINDING PROTEIN 1; RNA BINDING PROTEIN; UNCLASSIFIED DRUG; POLYCYTIDYLIC ACID;

3' UNTRANSLATED REGION; ARTICLE; BETA SHEET; BINDING AFFINITY; CONTROLLED STUDY; CRYSTALLOGRAPHY; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN RNA BINDING; PROTEIN STRUCTURE; RNA SEQUENCE; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; SURFACE PLASMON RESONANCE; AMINO ACID SEQUENCE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT;

3' UNTRANSLATED REGIONS; AMINO ACID SEQUENCE; BINDING SITES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDES; POLY C; PROTEIN STRUCTURE, TERTIARY; RNA-BINDING PROTEINS; SEQUENCE ALIGNMENT; SURFACE PLASMON RESONANCE;

EID: 14844341912     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki265     Document Type: Article

References (46)

1. Ostareck-Lederer,A., Ostareck,D.H. and Hentze,M.W. (1998) Cytoplasmic regulatory functions of the KH-domain proteins hnRNPs K and E1/E2. Trends Biochem. Sci., 23, 409-411.
2. Makeyev,A.V. and Liebhaber,S.A. (2002) The poly(C)-binding proteins: A multiplicity of functions and a search for mechanisms. RNA, 8 265-278.
3. Wang,X., Kiledjian,M., Weiss,I.M. and Liebhaber,S.A. (1995) Detection and characterization of a 3′-untranslated region ribonucleoprotein complex associated with human α-globin mRNA stability. Mol. Cell. Biol., 15, 1769-1777.
4. Chkheidze,A.N., Lyakhov,D.L., Makeyev,A.V., Morales,J., Kong,J. and Liebhaber,S.A. (1999) Assembly of the α-globin mRNA stability complex reflects binary interaction between the pyrimidine-rich 3-untranslated region determinant and poly(C) binding protein αCP. Mol. Cell. Biol. 19, 4572-4581.
5. Wang,Z., Day,N., Trifillus,P. and Kiledjian,M. (1999) An mRNA stabiliy complex functions with poly(A)-binding protein to stabilize mRNA in vitro. Mol. Cell. Biol., 19, 4552-4560.
6. Wang,Z. and Kiledjian,M. (2000) The poly(A)-binding protein and an mRNA stability protein jointly regulate an endoribonuclease activity. Mol. Cell. Biol., 20, 6334-6341.
7. Kiledjian,M., Wang,X. and Liebhaber,S.A. (1995) Identification of two KH domain proteins in the α-globin stability complex. EMBO J., 14 4357-4364.
8. Paulding,W.R. and Czyzyk-Krzeska,M.F. (1999) Regulation of tyrosine hydroxylase mRNA stability by the protein-binding, pyrimidine-rich sequence in the 3′-untranslated region. J. Biol. Chem., 274 2532-2538.
9. Czyzyk-Krzeska,M.F. and Bendixen,A.C. (1999) Identification of the poly(C) binding protein in the complex associated with the 3′ untranslated region of erythropoietin messenger RNA. Blood, 93 2111-2120.
10. Yu,J. and Russell,J.E. (2001) Structural and functional analysis of an mrnp complex that mediates the high stability of human beta-globin mRNA. Mol. Cell. Biol., 21, 5879-5888.
11. Stefanovic,B., Hellerbrand,C., Holcik,M., Briendl,M., Liebhaber,S.A. and Brenner,D.A. (1997) Posttranscriptional regulation of collagen alpha1 (I) mRNA in hepatic stellate cells. Mol. Cell. Biol., 17, 5201-5209.
12. Yeap,B.B., Voon,D.C., Vivian,J.P., McCulloch,R.K., Thomson,A.M., Giles,K.M., Czyzyk-Krzeska,M.F., Furneaux,H., Wilce,M.C., Wilce,J.A. and Leedman,P.J. (2002) Novel binding of HuR and poly(C)-binding protein to a conserved UC-rich motif within the 3′-untranslated region of the androgen receptor messenger RNA. J. Biol. Chem., 277, 27183-27192.
13. Ostareck,D.H., Ostareck-Lederer,A., Wilm,M., Theile,B.J., Mann,M. and Hentze,M.W. (1997) mRNA silencing in erythroid differentiation: HnRNP K and hnRNP E1 regulate 15-lipoxygenase translation from the 3′ end. Cell, 89, 597-606.
14. Ostareck,D.H., Ostareck-Lederer,A., Shatsky,I.N. and Hentze,M.W. (2001) Lipoxygenase mRNA silencing in erythroid differentiation. The 3′-UTR regulatory complex controls 60S ribosomal subunit joining. Cell, 104, 281-290.
15. Collier,B., Goobar-Larsson,L., Sokolowski,M. and Schwartz,S. (1998) Translational inhibition in vitro of human papillomavirus type 16 L2 mRNA mediated through interaction with heterogeneous ribonucleoprotein K and poly(rC)-binding proteins 1 and 2. J. Biol. Chem., 273, 22648-22656.
16. Blyn,L.B., Swiderek,K.M., Richards,O., Stahl,D.C., Semier,B.L. and Ehrenfeld,E. (1996) Poly(rC) binding protein 2 binds to stem-loop IV of the poliovirus RNA 5′ noncoding region: Identification by automated liquid chromatography-tandem mass spectrometry. Proc. Natl Acad. Sci. USA, 93, 11115-11120.
17. Blyn,L.B., Towner,J.S., Semier,B.L. and Ehrenfeld,E. (1997) Requirement of poly(rC) binding protein 2 for translation of poliovirus RNA. J. Virol., 71, 6243-6246.
18. Graff,J., Cha,J., Blyn,L.B. and Ehrenfeld,E (1998) Interaction of poly(rC) binding protein 2 with the 5′ noncoding region of hepatitis A virus RNA and its effects on translation. J. Virol., 72, 9668-9675.
19. Spangberg,K. and Schwartz,S. (1999) Poly(C)-binding protein interacts with the hepatitis C virus 5′ untranslated region. J. Gen. Virol. 80, 1371-1376.
20. Siomi,H., Matunis,M.J., Michael,M.W. and Dreyfuss,G. (1993) The pre-mRNA binding K protein contains a novel evolutionary conserved motif. Nucleic Acids Res., 21, 1193-1198.
21. Musco,G., Stier,G., Joseph,C., Castiglione Morelli,M.A., Nilges,M., Gibson,T.J. and Pastore,A. (1996) Three-dimensional structure and stability of the KH domain: Molecular insights into the fragile X syndrome. Cell, 85, 237-245.
22. Musco,G., Kharrat,A., Stier,G., Fraternali,F., Gibson,T.J., Nilges,M. and Pastore,A. (1997) The solution structure of the first KH domain of FMR1, the protein responsible for the fragile X syndrome [Erratum (1997) Nature Struct. Biol., 4, 840.]. Nature Struct. Biol., 4, 712-716.
23. Lewis,H.A., Chen,H., Edo,C., Buckanovich,R.J., Yang,Y.Y., Musunuru,K., Zhong,R., Darnell,R.B. and Burley,S.K. (1999) Crystal structures of Nova-1 and Nova-2 K-homology RNA-binding domains. Structure Fold. Des., 15, 191-203.
24. Baber,J.L., Libutti,D., Levens,D. and Tjandra,N. (1999) High precision solution structure of the C-terminal KH domain of heterogeneous nuclear ribonucleoprotein K, a c-myc transcription factor. J. Mol. Biol., 289, 949-262.
25. Lewis,H.A., Musunuru,K., Jensen,K.B., Edo,C., Chen,H., Darnell,R.B. and Burley,S.K. (2000) Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome. Cell, 100, 323-332.
26. Braddock,D.T., Baber,J.L., Levens,D. and Clore,G.M. (2002) Molecular basis of sequence-specific single-stranded DNA recognition by KH domains: Solution structure of a complex between hnRNP K KH3 and single-stranded DNA. EMBO J., 21, 3476-3485.
27. Braddock,D.T., Louis,J.M., Baber,J.L., Levens,D. and Clore,G.M. (2002) Structure and dynamics of KH domains from FBP bound to single-stranded DNA. Nature, 415, 1051-1056.
28. Grishin,N.V. (2001) KH domain: One motif, two folds. Nucleic Acids Res., 29, 638-643.
29. Siomi,H., Choi,M., Siomi,M.C., Nussbaum,R.L. and Dreyfuss,G. (1994) Essential role for KH domains in RNA binding: Impaired RNA binding by a mutation in the KH domain in FMR1 that causes fragile X syndrome. Cell, 77, 33-39.
30. Dejgaard,K. and Leffers,H. (1996) Characterisation of the nucleic-acid-binding activity of KH domains. Different properties of different domains. Eur. J. Biochem., 241, 425-431.
31. Weiss,I.M. and Liebhaber,S.A. (1995) Erythroid cell-specific mRNA stability elements in the alpha 2-globin 3′ non-translated region. Mol. Cell. Biol., 15, 2456-2465.
32. Thisted,T., Lyakhov,D.L. and Liebhaber,S.A. (2001) Optimized RNA targets of two closely related triple KH domain proteins, heterogeneous nuclear ribonucleoprotein K and αCP-2KL, suggest distinct modes of RNA recognition. J. Biol. Chem., 276, 17484-17496.
33. Otwinowski,Z. and Minor,W. (1997) Processing pf X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326.
34. Collaborative Computational Project Number 4. (1994), The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr., 50, 760-763.
35. Matthews,B.W. (1977) X ray Structure of Proteins. In Neurath,H. and Hill,R.L. (eds), vol 3, Academic Press, NY, pp. 468-477.
36. Kleywegt,G.J. (1996) Use of non-crystallographic symmetry in protein structure refinement. Acta Crystallogr. D Biol. Crystallogr., 52, 842-857.
37. Kalé,L., Skeel,R., Bhandarkar,M., Brunner,R., Gursoy,A., Krawetz,N., Phillips,J., Shinozaki,A., Varadarajan,K. and Schulten,K. (1999) NAMD2: greater scalability for parallel molecular dynamics. J. Comput. Phys. 151, 283-312.
38. Brooks,B.R., Bruccoleri,R.E., Olafson,B.D., States,D.J., Swaminathan,S. and Karplus,M. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem., 4 187-217.
39. Baker,N.A., Sept,D., Joseph,S., Holst,M.J. and McCammon,J.A. (2001) Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc. Natl Acad. Sci. USA, 98, 10037-10041.
40. Holst,M. and Saied,F. (1993) Multigrid solution of the Poisson-Boltzmann equation. J. Comput. Chem., 14, 105-113.
41. Holst,M. and Saied,F. (1995) Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods. J. Comput. Chem., 16, 337-364.
42. Holst,M. (2001) Adaptive numerical treatment of elliptic systems on manifolds. Adv. Comput. Math., 15, 139-191.
43. Bank,R. and Holst,M. (2003) A new paradigm for parallel adaptive meshing algorithms. SIAM Rev., 45, 291-323.
44. Davis,M.E. and McCammon,J.A. (1990) Electrostatics in biomolecular structure and dynamics. Chem. Rev., 94, 7684-7692.
45. Honig,B. and Nicholls,A. (1995) Classical electrostatics in biology and chemistry. Science, 268, 1144-1149.
46. Sidiqi,M., Wilce,J.A., Porter,C.J., Barker,A., Leedman,P.J. and Wilce,M.C.J. (2005) Formation of CP1-KH3 complexed with UC-rich RNA. Eur. Biophys. J., in press.