Crystal Structure of the HEAT Domain from the Pre-mRNA Processing Factor Symplekin

Journal of Molecular Biology

Volumn 392, Issue 1, 2009, Pages 115-128

  Kennedy, Sarah A ^a   Frazier, Monica L ^b   Steiniger, Mindy ^c   Mast, Ann M ^a   Marzluff, William F ^b,c   Redinbo, Matthew R ^a,b  

^a University of North Carolina at Chapel Hill   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

crystal structure; HEAT repeat; molecular dynamics; mRNA processing; protein scaffold

Indexed keywords

NUCLEAR PROTEIN; SYMPLEKIN; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; DROSOPHILA MELANOGASTER; MOLECULAR DYNAMICS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; RNA PROCESSING; STRUCTURE ACTIVITY RELATION;

DROSOPHILA MELANOGASTER; EUKARYOTA; METAZOA;

EID: 68949196300     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.06.062     Document Type: Article

References (66)

1. Preiss T., and Hentze M.W. Dual function of the messenger RNA cap structure in poly(A)-tail-promoted translation in yeast. Nature 392 (1998) 516-520
2. Sachs A.B., Sarnow P., and Hentze M.W. Starting at the beginning, middle, and end: translation initiation in eukaryotes. Cell 89 (1997) 831-838
3. Mandel C.R., Bai Y., and Tong L. Protein factors in pre-mRNA 3′-end processing. Cell Mol. Life Sci. 65 (2008) 1099-1122
4. Wilusz C.J., Wormington M., and Peltz S.W. The cap-to-tail guide to mRNA turnover. Nat. Rev. Mol. Cell Biol. 2 (2001) 237-246
5. Dominski Z., and Marzluff W.F. Formation of the 3′ end of histone mRNA: getting closer to the end. Gene 396 (2007) 373-390
6. Takagaki Y., and Manley J.L. Complex protein interactions within the human polyadenylation machinery identify a novel component. Mol. Cell Biol. 20 (2000) 1515-1525
7. Shi Y., Di Giammartino D.C., Taylor D., Sarkeshik A., Rice W.J., Yates III J.R., et al. Molecular architecture of the human pre-mRNA 3′ processing complex. Mol. Cell 33 (2009) 365-376
8. Sullivan K.D., Steiniger M., and Marzluff W.F. A core complex of CPSF73, CPSF100, and Symplekin may form two different cleavage factors for processing of poly(A) and histone mRNAs. Mol. Cell 34 (2009) 322-332
9. Kolev N.G., and Steitz J.A. Symplekin and multiple other polyadenylation factors participate in 3′-end maturation of histone mRNAs. Genes Dev. 19 (2005) 2583-2592
10. Wagner E.J., Burch B.D., Godfrey A.C., Salzler H.R., Duronio R.J., and Marzluff W.F. A genome-wide RNA interference screen reveals that variant histones are necessary for replication-dependent histone pre-mRNA processing. Mol. Cell 28 (2007) 692-699
11. Ghazy M., He X., Singh B.N., Hampsey M., and Moore C. The essential N-terminus of the Pta1 scaffold protein is required for snoRNA transcription termination and Ssu72 function but is dispensable for pre-mRNA 3′-end processing. Mol. Cell Biol. 8 (2009) 2296-2307
12. Xing H., Mayhew C.N., Cullen K.E., Park-Sarge O.K., and Sarge K.D. HSF1 modulation of Hsp70 mRNA polyadenylation via interaction with symplekin. J. Biol. Chem. 279 (2004) 10551-10555
13. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
14. Bennett-Lovsey R.M., Herbert A.D., Sternberg M.J., and Kelley L.A. Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. Proteins 70 (2008) 611-625
15. Cuff J.A., Clamp M.E., Siddiqui A.S., Finlay M., and Barton G.J. JPred: a consensus secondary structure prediction server. Bioinformatics 14 (1998) 892-893
16. Finn R.D., Mistry J., Schuster-Bockler B., Griffiths-Jones S., Hollich V., Lassmann T., et al. Pfam: clans, web tools and services. Nucleic Acids Res. 34 (2006) D247-251
17. Kelley L.A., MacCallum R.M., and Sternberg M.J. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299 (2000) 499-520
18. Rost B., Yachdav G., and Liu J. The PredictProtein server. Nucleic Acids Res. 32 (2004) W321-W326
19. Zdobnov E.M., and Apweiler R. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17 (2001) 847-848
20. Andrade M.A., Petosa C., O'Donoghue S.I., Muller C.W., and Bork P. Comparison of ARM and HEAT protein repeats. J. Mol. Biol. 309 (2001) 1-18
21. Cho U.S., and Xu W. Crystal structure of a protein phosphatase 2A heterotrimeric holoenzyme. Nature 445 (2007) 53-57
22. Goldenberg S.J., Cascio T.C., Shumway S.D., Garbutt K.C., Liu J., Xiong Y., and Zheng N. Structure of the Cand1-Cul1-Roc1 complex reveals regulatory mechanisms for the assembly of the multisubunit cullin-dependent ubiquitin ligases. Cell 119 (2004) 517-528
23. Groves M.R., Hanlon N., Turowski P., Hemmings B.A., and Barford D. The structure of the protein phosphatase 2A PR65/A subunit reveals the conformation of its 15 tandemly repeated HEAT motifs. Cell 96 (1999) 99-110
24. Lee S.J., Matsuura Y., Liu S.M., and Stewart M. Structural basis for nuclear import complex dissociation by RanGTP. Nature 435 (2005) 693-696
25. Matsuura Y., and Stewart M. Nup50/Npap60 function in nuclear protein import complex disassembly and importin recycling. EMBO J. 24 (2005) 3681-3689
26. Paffenholz R., Kuhn C., Grund C., Stehr S., and Franke W.W. The arm-repeat protein NPRAP (neurojungin) is a constituent of the plaques of the outer limiting zone in the retina, defining a novel type of adhering junction. Exp. Cell Res. 250 (1999) 452-464
27. Sampietro J., Dahlberg C.L., Cho U.S., Hinds T.R., Kimelman D., and Xu W. Crystal structure of a beta-catenin/BCL9/Tcf4 complex. Mol. Cell 24 (2006) 293-300
28. Hunter S., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., et al. InterPro: the integrative protein signature database. Nucleic Acids Res. 37 (2008) D211-D215
29. Andrade M.A., Ponting C.P., Gibson T.J., and Bork P. Homology-based method for identification of protein repeats using statistical significance estimates. J. Mol. Biol. 298 (2000) 521-537
30. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
31. Kelley L.A., and Sternberg M.J. Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc. 4 (2009) 363-371
32. Holm L., and Sander C. Mapping the protein universe. Science 273 (1996) 595-603
33. Xu Y., Xing Y., Chen Y., Chao Y., Lin Z., Fan E., et al. Structure of the protein phosphatase 2A holoenzyme. Cell 127 (2006) 1239-1251
34. Wang X., McLachlan J., Zamore P.D., and Hall T.M. Modular recognition of RNA by a human pumilio-homology domain. Cell 110 (2002) 501-512
35. Neuwald A.F., and Hirano T. HEAT repeats associated with condensins, cohesins, and other complexes involved in chromosome-related functions. Genome Res. 10 (2000) 1445-1452
36. Conti E., and Kuriyan J. Crystallographic analysis of the specific yet versatile recognition of distinct nuclear localization signals by karyopherin alpha. Structure 8 (2000) 329-338
37. Fang X., Chen T., Tran K., and Parker C.S. Developmental regulation of the heat shock response by nuclear transport factor karyopherin-alpha3. Development 128 (2001) 3349-3358
38. Parmeggiani F., Pellarin R., Larsen A.P., Varadamsetty G., Stumpp M.T., Zerbe O., et al. Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core. J. Mol. Biol. 376 (2008) 1282-1304
39. Zachariae U., and Grubmuller H. A highly strained nuclear conformation of the exportin Cse1p revealed by molecular dynamics simulations. Structure 14 (2006) 1469-1478
40. Zachariae U., and Grubmuller H. Importin-beta: structural and dynamic determinants of a molecular spring. Structure 16 (2008) 906-915
41. Coseno M., Martin G., Berger C., Gilmartin G., Keller W., and Doublie S. Crystal structure of the 25 kDa subunit of human cleavage factor Im. Nucleic Acids Res. 36 (2008) 3474-3483
42. Qu X., Perez-Canadillas J.M., Agrawal S., De Baecke J., Cheng H., Varani G., and Moore C. The C-terminal domains of vertebrate CstF-64 and its yeast orthologue RNA15 form a new structure critical for mRNA 3′-end processing. J. Biol. Chem. 282 (2007) 2101-2115
43. Balbo P.B., Meinke G., and Bohm A. Kinetic studies of yeast polyA polymerase indicate an induced fit mechanism for nucleotide specificity. Biochemistry 44 (2005) 7777-7786
44. Deo R.C., Bonanno J.B., Sonenberg N., and Burley S.K. Recognition of polyadenylate RNA by the poly(A)-binding protein. Cell 98 (1999) 835-845
45. Perez-Canadillas J.M. Grabbing the message: structural basis of mRNA 3′UTR recognition by Hrp1. EMBO J. 25 (2006) 3167-3178
46. Mandel C.R., Kaneko S., Zhang H., Gebauer D., Vethantham V., Manley J.L., and Tong L. Polyadenylation factor CPSF-73 is the pre-mRNA 3′-end-processing endonuclease. Nature 444 (2006) 953-956
47. Bai Y., Auperin T.C., Chou C.Y., Chang G.G., Manley J.L., and Tong L. Crystal structure of murine CstF-77: dimeric association and implications for polyadenylation of mRNA precursors. Mol. Cell 25 (2007) 863-875
48. Meinhart A., and Cramer P. Recognition of RNA polymerase II carboxy-terminal domain by 3′-RNA-processing factors. Nature 430 (2004) 223-226
49. Noble C.G., Beuth B., and Taylor I.A. Structure of a nucleotide-bound Clp1-Pcf11 polyadenylation factor. Nucleic Acids Res. 35 (2007) 87-99
50. Isgro T.A., and Schulten K. Binding dynamics of isolated nucleoporin repeat regions to importin-beta. Structure 13 (2005) 1869-1879
51. He X., and Moore C. Regulation of yeast mRNA 3′ end processing by phosphorylation. Mol. Cell 19 (2005) 619-629
52. Rizzuti B., Sportelli L., and Guzzi R. Evidence of reduced flexibility in disulfide bridge-depleted azurin: a molecular dynamics simulation study. Biophys. Chem. 94 (2001) 107-120
53. Obenauer J.C., Cantley L.C., and Yaffe M.B. Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res. 31 (2003) 3635-3641
54. Yang Z.R., Thomson R., McNeil P., and Esnouf R.M. RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics 21 (2005) 3369-3376
55. Lupas A., Van Dyke M., and Stock J. Predicting coiled coils from protein sequences. Science 252 (1991) 1162-1164
56. Donnelly M.I., Zhou M., Millard C.S., Clancy S., Stols L., Eschenfeldt W.H., et al. An expression vector tailored for large-scale, high-throughput purification of recombinant proteins. Protein Expr. Purif. 47 (2006) 446-454
57. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. In: Carter Jr. C., and Sweet R. (Eds). Methods in Enzymology, Macromolecular Crystallography, Part A (1997), Academic Press, New York 276
58. Fu Z.Q., Rose J., and Wang B.C. SGXPro: a parallel workflow engine enabling optimization of program performance and automation of structure determination. Acta Crystallogr., Sect. D: Biol. Crystallogr. 61 (2005) 951-959
59. Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr., Sect. D: Biol. Crystallogr. 60 (2004) 2126-2132
60. Collaborative Computational Project. The CCP4 Suite: programs for protein crystallography. Acta Crystallogr., Sect. D: Biol. Crystallogr. D50 (1994) 760-763
61. Lovell S.C., Davis I.W., Arendall III W.B., de Bakker P.I., Word J.M., Prisant M.G., et al. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins 50 (2003) 437-450
62. Delano W.L. The PyMOL Molecular Graphics System (2002), DeLano Scientific, Palo Alto, CA
63. Case D.A., Cheatham III T.E., Darden T., Gohlke H., Luo R., Merz Jr. K.M., et al. The Amber biomolecular simulation programs. J. Comput. Chem. 26 (2005) 1668-1688
64. Jorgensen W., Chandrasekhar J., Madura J.D., Impey R.W., and Klein ML. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79 (1983) 926-935
65. Essman U.P.L., Berkowitz M.L., Darden T., Lee H., and Pedersen L. A smooth particle mesh Ewald method. J. Chem. Phys. 103 (1995) 8577-8593
66. Teotico D.G., Frazier M.L., Ding F., Dokholyan N.V., Temple B.R., and Redinbo M.R. Active nuclear receptors exhibit highly correlated AF-2 domain motions. PLoS Comput. Biol. 4 (2008) e1000111