Solution structure of the U2 snRNP protein Rds3p reveals a knotted zinc-finger motif

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 28, 2008, Pages 9621-9626

  Van Roon, Anne Marie M ^a   Loening, Nikolaus M ^a,b   Obayashi, Eiji ^a,d   Yang, Ji Chun ^a   Newman, Andrew J ^a   Hernández, Helena ^c   Nagai, Kiyoshi ^a   Neuhaus, David ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^b LEWIS AND CLARK COLLEGE   (United States)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d YOKOHAMA CITY UNIVERSITY   (Japan)

Author keywords

Knot; NMR; Splicing

Indexed keywords

CYSTEINE; MULTIPROTEIN COMPLEX; RDS3P PROTEIN; RECOMBINANT PROTEIN; SMALL NUCLEAR RIBONUCLEOPROTEIN; SMALL NUCLEAR RIBONUCLEOPROTEIN U2; TRANSCRIPTION FACTOR GATA; ZINC FINGER PROTEIN;

ARTICLE; GENE DUPLICATION; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PROCESSING; PROTEIN STRUCTURE;

CARRIER PROTEINS; CYSTEINE; PROTEIN CONFORMATION; RIBONUCLEOPROTEIN, U2 SMALL NUCLEAR; SACCHAROMYCES CEREVISIAE PROTEINS; SOLUTIONS; ZINC FINGERS;

EUKARYOTA;

EID: 47749095590     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0802494105     Document Type: Article

References (35)

1. Jurica MS, Moore MJ (2003) Pre-mRNA splicing: Awash in a sea of proteins. Mol Cell 12:5-14.
2. Will CL, Lührmann R (2006) Spliceosome structure and function. The RNA World, ed Gesteland RF (Cold Spring Harbor Laboratory, New York), pp 369-400.
3. Brosi R, Hauri HP, Krämer A (1993) Separation of splicing factor SF3 into two components and purification of SF3a activity. J Biol Chem 268:17640-17646.
4. Krämer A (1996) The structure and function of proteins involved in mammalian pre-mRNA splicing. Annu Rev Biochem 65:367-409.
5. Dziembowski A, et al. (2004) Proteomic analysis identifies a new complex required for nuclear pre-mRNA retention and splicing. EMBO J 23:4847-4856.
6. Wang Q, He J, Lynn B, Rymond BC (2005) Interactions of the yeast SF3b splicing factor. Mol Cell Biol 25:10745-10754.
7. Wang Q, Rymond BC (2003) Rds3p is required for stable U2 snRNP recruitment to the splicing apparatus. Mol Cell Biol 23:7339-7349.
8. Dybkov O, et al. (2006) U2 snRNA-protein contacts in purified human 17S U2 snRNPs and in spliceosomal A and B complexes. Mol Cell Biol 26:2803-2816.
9. Staknis D, Reed R (1994) Direct interactions between pre-mRNA and six U2 small nuclear ribonucleoproteins during spliceosome assembly. Mol Cell Biol 14:2994-3005.
10. Yan D, Ares M, Jr (1996) Invariant U2 RNA sequences bordering the branchpoint recognition region are essential for interaction with yeast SF3a and SF3b subunits. Mol Cell Biol 16:818-828.
11. Golas MM, Sander B, Will CL, Lührmann R, Stark H (2003) Molecular architecture of the multiprotein splicing factor SF3b. Science 300:980-984.
12. Golas MM, Sander B, Will CL, Lührmann R, Stark H (2005) Major conformational change in the complex SF3b upon integration into the spliceosomal U11/U12 di-snRNP as revealed by electron cryomicroscopy. Mol Cell 17:869-883.
13. Schellenberg MJ, et al. (2006) Crystal structure of a core spliceosomal protein interface. Proc Natl Acad Sci USA 103:1266-1271.
14. Spadaccini R, et al. (2006) Biochemical and NMR analyses of an SF3b155-p14-U2AF-RNA interaction network involved in branch point definition during pre-mRNA splicing. RNA 12:410-425.
15. Deane JE, et al. (2004) Tandem LIM domains provide synergistic binding in the LMO4:Ldb1 complex. EMBO J 23:3589-3598.
16. Grishin NV (2001) Treble clef finger-a functionally diverse zinc-binding structural motif. Nucleic Acids Res 29:1703-1714.
17. Liu Y, Eisenberg D (2002) 3D domain swapping: As domains continue to swap. Protein Sci 11:1285-1299.
18. Andreeva A, Murzin AG (2006) Evolution of protein fold in the presence of functional constraints. Curr Opin Struct Biol 16:399-408.
19. Takusagawa F, Kamitori S, Misaki S, Markham GD (1996) Crystal structure of Sadenosylmethionine synthetase. J Biol Chem 271:136-147.
20. Houben K, et al. (2005) Dynamics and metal exchange properties of C4C4 RING domains from CNOT4 and the p44 subunit of TFIIH. J Mol Biol 349:621-637.
21. Linge JP, O'Donoghue SI, Nilges M (2001) Automated assignment of ambiguous nuclear overhauser effects with ARIA. Methods Enzymol 339:71-90.
22. Herrmann T, Güntert P, Wüthrich K (2002) Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. J Biomol NMR 24:171-189.
23. Herrmann T, Güntert P, Wüthrich K (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319:209-227.
24. Taylor WR (2007) Protein knots and fold complexity: Some new twists. Comput Biol Chem 31:151-162.
25. Virnau P, Mirny LA, Kardar M (2006) Intricate knots in proteins: Function and evolution. PLoS Comput Biol 2:e122.
26. Yeates TO, Norcross TS, King NP (2007) Knotted and topologically complex proteins as models for studying folding and stability. Curr Opin Chem Biol 11:595-603.
27. Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536-540.
28. Vincent K, Wang Q, Jay S, Hobbs K, Rymond BC (2003) Genetic interactions with CLF1 identify additional pre-mRNA splicing factors and a link between activators of yeast vesicular transport and splicing. Genetics 164:895-907.
29. Oltra E, Pfeifer I, Werner R (2003) Ini, a small nuclear protein that enhances the response of the connexin43 gene to estrogen. Endocrinology 144:3148-3158.
30. Oltra E, Verde F, Werner R, D'Urso G (2004) A novel RING-finger-like protein Ini1 is essential for cell cycle progression in fission yeast. J Cell Sci 117:967-974.
31. Trappe R, et al. (2002) Identification and characterization of a novel murine multigene family containing a PHD-finger-like motif. Biochem Biophys Res Commun 293:816-826.
32. Brünger AT, et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54:905-921.
33. Hernández H, Robinson CV (2007) Determining the stoichiometry and interactions of macromolecular assemblies from mass spectrometry. Nat Protoc 2:715-726.
34. Santoro MM, Bolen DW (1988) Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants. Biochemistry 27:8063-8068.
35. Lin RJ, Newman AJ, Cheng SC, Abelson J (1985) Yeast mRNA splicing in vitro. J Biol Chem 260:14780-14792.