Recognition of essential purines by the U1A protein

BMC Biochemistry

Volumn 8, Issue , 2007, Pages

  Benitex, Yulia ^a   Baranger, Anne M ^a,b  

^a WESLEYAN UNIVERSITY   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN; PURINE; RNA; SMALL NUCLEAR RNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR U1A; UNCLASSIFIED DRUG; PURINE DERIVATIVE; RNA BINDING PROTEIN; SMALL NUCLEAR RIBONUCLEOPROTEIN; SPLICED LEADER RNA; U1A PROTEIN;

ARTICLE; HYDROGEN BOND; MELTING POINT; PROTEIN BINDING; PROTEIN MODIFICATION; PROTEIN MOTIF; RNA SEQUENCE; RNA STABILITY; WILD TYPE; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME SPECIFICITY; GENETICS; METABOLISM; TRANSITION TEMPERATURE;

MODELS, MOLECULAR; MOLECULAR STRUCTURE; PURINES; RIBONUCLEOPROTEIN, U1 SMALL NUCLEAR; RNA STABILITY; RNA, SPLICED LEADER; RNA-BINDING PROTEINS; SUBSTRATE SPECIFICITY; TRANSITION TEMPERATURE;

EID: 38349068648     PISSN: None     EISSN: 14712091     Source Type: Journal    
DOI: 10.1186/1471-2091-8-22     Document Type: Article

References (45)

1. Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. E Birney S Kumar AR Krainer, Nucleic Acids Res 1993 21 5803 5816 8290338 10.1093/nar/21.25.5803
2. Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant Arabidopsis thaliana. ZJ Lorkovic A Barta, Nucleic Acids Res 2002 30 623 635 11809873 10.1093/nar/30.3.623
3. Comparitive Genomics of the Eukaryotes. GM Rubin MD Yandell JR Wortman GLG Miklos CR Nelson IK Hariharan ME Fortini PW Li R Apweiler W Fleischmann JM Cherry S Henikoff MP Skupski S Misra M Ashburner E Birney MS Boguski T Brody P Brokstein SE Celniker SA Chervitz D Coates A Cravchik A Gabrielian RF Galle WM Gelbart RA George LSB Goldstein F Gong P.Guan NL Harris BA Hay RA Hoskins J Li Z Li RO Hynes SJM Jones PM Kuehl B Lemaitre JT Litleton DK Morrison C Mungall PH O'Farrell OK Pickeral C Shue LB Vosshall J Zhang Q Zhao XH Zheng F Zhong W.Zhong R Gibbs JC Venter MD Adams S Lewis, Science 2000 287 2204 2215 10.1126/science.287.5461.2204 10731134
4. hnRNP complexes: composition, structure and function. AM Krecic MS Swanson, Curr Opin Cell Biol 1999 11 363 371 10.1016/S0955-0674(99)80051-9 10395553
5. RNA recognition by RNP proteins during RNA processing. G Varani K Nagai, Annu Rev Biophys Biomol Struct 1998 27 407 445 10.1146/annurev.biophys.27.1.407 9646873
6. Conserved structures and diversity of functions of RNA-binding proteins. CG Burd G Dreyfuss, Science 1994 265 615 621 10.1126/science.8036511 8036511
7. Structural Basis for Polypyrimidine Tract Recognition by the Essential Pre-mRNA Splicing Factor U2AF65. EA Sickmier KE Frato H Shen SR Paranawithana MR Green CL Kielkopf, Mol Cell 2006 23 49 59 16818232 10.1016/j.molcel.2006.05.025
8. The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. C Maris C Dominguez FHT Allain, FEBS J 2005 272 2118 2131 10.1111/j.1742-4658.2005.04653.x 15853797
9. Interaction of RNA hairpins with the human U1A N-terminal RNA binding domain. KB Hall, Biochemistry 1994 33 10076 10088 10.1021/bi00199a035 7520277
10. Interaction of N-terminal domain of U1A protein with an RNA stem/loop. KB Hall WT Stump, Nucleic Acids Res 1992 20 4283 4290 1508720 10.1093/nar/20.16. 4283
11. Identification of molecular contacts between the U1A small nuclear ribonucleoprotein and U1 RNA. TH Jessen C Oubridge CH Teo C Pritchard K Nagai, EMBO J 1991 10 3447 3456 1833186
12. Complex role of the b2-b3 Loop in the Interaction of U1A with U1 Hairpin II RNA. PS Katsamba M Bayramyan IS Haworth DG Myszka IA Laird-Offringa, J Biol Chem 2002 277 33267 33274 10.1074/jbc.M200304200 12082087
13. RNA recognition by the human U1A protein is mediated by a network of local cooperative interactions that create the optimal binding surface. JK Kranz KB Hall, J Mol Biol 1999 285 215 231 10.1006/jmbi.1998.2296 9878401
14. Kinetic analysis of the role of the tyrosine 13, phenylalanine 56 and glutamine 54 network in the U1A/U1 hairpin II interaction. MJ Law EJ Chambers PS Katsamba IS Haworth IA Laird-Offinga, Nucleic Acids Res 2005 33 2917 2928 15914668 10.1093/nar/gki602
15. Recognition of an essential adenine at a protein-RNA interface: comparison of the contributions of hydrogen bonds and a stacking interaction. SJ Nolan JC Shiels JB Tuite KL Cecere AM Baranger, J Am Chem Soc 1999 121 8951 8952 10.1021/ja991617n
16. Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. C Oubridge N Ito PR Evans CH Teo K Nagai, Nature 1994 372 432 438 10.1038/372432a0 7984237
17. Target discrimination by RNA-binding proteins: Role of the ancillary protein U2A' and a critical leucine residue in differentiating the RNA-binding specificity of spliceosomal proteins U1A and U2B". ME Rimmele JG Belasco, RNA 1998 4 1386 1396 9814759 10.1017/S1355838298981171
18. Investigation of a conserved stacking interaction in target site recognition by the U1A protein. JC Shiels JB Tuite SJ Nolan AM Baranger, Nucleic Acids Res 2002 30 550 558 11788718 10.1093/nar/30.2.550
19. Substitution of an Essential Adenine in the U1A-RNA Complex with a Non-polar Isostere. JB Tuite JC Shiels AM Baranger, Nucleic Acids Res 2002 30 5269 5275 12466552 10.1093/nar/gkf636
20. The NMR structure of the 38 kDa U1A protein-PIE RNA complex reveals the basis of cooperativity in regulation of polyadenylation by human U1A protein. L Varani SI Gunderson IW Mattaj LE Kay D Neuhaus G Varani, Nature Struct Biol 2000 7 329 335 10.1038/74101 10742179
21. Design of an Adenosine Analog that Selectively Improves the Affinity of a Mutant U1A Protein for RNA. Y Zhao AM Baranger, J Am Chem Soc 2003 125 2480 2488 10.1021/ja021267w 12603136
22. Do Collective Atomic Fluctuations Account for Cooperative Effects? Molecular Dynamics Studies of the U1A-RNA Complex. BL Kormos AM Baranger DL Beveridge, J Am Chem Soc 2006 128 8992 8993 10.1021/ja0606071 16834346
23. The human U1 snRNP-specific U1A protein inhibits polyadenylation of its own pre-mRNA. WC Boelens EJR Jansen WJ van Venrooij R Stripecke IW Mattaj SI Gunderson, Cell 1993 72 881 892 10.1016/0092-8674(93)90577-D 8458082
24. Biochemical mechanisms of constitutive and regulated pre-mRNA splicing. MR Green, Annu Rev Cell Biol 1991 7 559 599 10.1146/annurev.cb.07.110191.003015 1839712
25. Arrangement of RNA and proteins in the spliceosomal U1 small nuclear ribonucleoprotein particle. H Stark P Dube R Lührmann B Kastner, Nature 2001 409 539 542 10.1038/35054102 11206553
26. U1-snRNP-A selects a ten nucleotide consensus sequence from a degenerate RNA pool presented in various structural contexts. DE Tsai DS Harper JD Keene, Nucl Acids Res 1991 19 4931 4936 1717938 10.1093/nar/19.18.4931
27. A Functional Role for Correlated Motion in the N-terminal RNA-binding Domain of Human U1A Protein. SA Showalter KB Hall, J Mol Biol 2002 322 533 542 10.1016/S0022-2836(02)00804-5 12225747
28. Altering the RNA-binding Mode of the U1A RBD1 Protein. SA Showalter KB Hall, J Mol Biol 2004 335 465 480 10.1016/j.jmb.2003.10.055 14672656
29. Correlated Motions in the U1 snRNA Stem/Loop 2: U1A RBD1 Complex. SA Showalter KB Hall, Biophys J 2005 89 2046 2058 15951381 10.1529/biophysj.104. 058032
30. A Study of Collective Atomic Fluctuations and Cooperativity in a U1A-RNA Complex Based on Molecular Dynamics Simulations. BL Kormos AM Baranger DL Beveridge, J Struct Biol 2007 157 500 513 10.1016/j.jsb.2006.10.022 17194603
31. RNA binding mediates the local cooperativity between the b-sheet and the C-terminal tail of the human U1A RBD1 protein. JK Kranz KB Hall, J Mol Biol 1998 275 465 481 10.1006/jmbi.1997.1441 9466924
32. Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein A. K Nagai C Oubridge TH Jessen J.Li PR Evans, Nature 1990 348 515 520 10.1038/348515a0 2147232
33. Analysis of in vitro binding of U1-A protein mutants to U1 snRNA. W Boelens D Scherly EJR Jansen K Kolen IW Mattaj WJ van Venrooij, Nucleic Acids Res 1991 19 4611 4618 1832492 10.1093/nar/19.17.4611
34. Two functionally distinct steps mediate high affinity binding of U1A protein to U1 hairpin II RNA. PS Katsamba DG Myszka IA Laird-Offringa, J Biol Chem 2001 276 21476 21481 10.1074/jbc.M101624200 11297556
35. Major determinants of the specificity of interaction between small nuclear ribonucleoprotein U1A and U2B" and their cognate RNAs. D Scherly W Boelens NA Dathan WJ van Venrooij IW Mattaj, Nature 1990 345 502 506 10.1038/345502a0 2140872
36. Human UP1 as a Model for Understanding Purine Recognition in the Family of Protein Containing the RNA Recognition Motif (RRM). JC Myers Y Shamoo, J Mol BIol 2004 342 743 756 10.1016/j.jmb.2004.07.029 15342234
37. Modifying the Specificity of an RNA Backbone Contact. D Dertinger T Dale OC Uhlenbeck, J Mol Biol 2001 314 649 654 10.1006/jmbi.2001.5132 11733985
38. Structural Basis of RNA Binding Discrimination between Bacteriophages QB and MS2. WT Horn K Tars E Grahn C Helgstrand AJ Baron H Lago CJ Adams DS Peabody SEV Phillips NJ Stonehouse L Liljas PG Stockley, Structure 2006 14 487 495 10.1016/j.str.2005.12.006 16531233
39. The role of modified purine 64 in initiator/elongator discrimination of tRNAiMet from yeast and wheat germ. S Kiesewetter G Ott M Sprinzl, Nucleic Acids Res 1990 18 4677 4682 2395634 10.1093/nar/18.16.4677
40. Relaxation of a transfer RNA specificity by removal of modified nucleotides. V Perret A Garcia H Grosjean JP Ebel C Flroentz R Giegé Nature 1990 344 783 789 10.1038/344787a0
41. Functional group recognition at the aminoacylation and editing sites of E. coli valyl-tRNA synthetase. KD Tardif J Horowitz, RNA 2004 10 493 503 14970394 10.1261/rna.5166704
42. The Energetic Basis of Specificity in the Eco RI Endonuclease-DNA Interaction. DR Lesser MR Kurpiewski L Jen-Jacobson, Science 1990 250 776 786 10.1126/science.2237428 2237428
43. On the specificity of DNA-protein interactions. PH von Hippel OG Berg, Proc Natl Acad Sci 1986 83 1608 1612 3456604 10.1073/pnas.83.6.1608
44. Thermodynamics of sequence-specific protein-DNA interactions. T Härd T Lundbäck, Biophys Chem 1996 62 121 139 10.1016/S0301-4622(96)02197-7 17029807
45. Protein-RNA interactions: exploring binding patterns with three-dimensional superposition analysis of high resolution structures. N Morozova J Allers J Myers Y Shamoo, Bioinformatics 2006 22 2746 2752 10.1093/bioinformatics/btl470 16966360