Nucleic Acids Research, 1995, Vol. 23, No. 5 725-728
© 1995
SURVEY AND SUMMARY |
Multiple RNA binding domains (RBDs) just don't add up
Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine 333, Cedar Street, New Haven, CT 06510-8024, USA 1Howard Hughes Medical Institute, Yale University School of Medicine 333, Cedar Street, New Haven, CT 06510-8024, USA
*To whom correspondence should be addressed
Received September 30, 1994. Revised January 5, 1995. Accepted January 5, 1995.
One of the most common motifs for binding RNA In eukaryotes is the RNA binding domain (RBD) or RNA Recognition Motif (RRM). One of the more intriguing aspects of these proteins Is their modular nature. Proteins have been found containing from one to four RRMs. In most instances, these domains have some basal level of non-sequence specific RNA binding affinity. In addition, many also have a higher affinity for a specific structure or sequence of RNA. In the cases of heterogenous nuclear ribonucleoprotein A1 (hnRNP A1), yeast poly-A binding protein and splicing factor U2AF65, the Individual free energy of binding of the RBDs for RNA are not strictly additive. By invoking a model in which the amino acids connecting adjoining RBDs are considered to be flexible linkers with an interresidue spacing of about 3.5 Å, it Is possible to predict the apparent association constants for at least some multl-RBD proteins to single-stranded RNA. We have surveyed the literature and found that individual RBDs are separated by ‘linker’ sequences of highly variable length. These linkers provide a critical determinant of binding affinity and may modulate cis versus trans binding. A clearer understanding of multi-RBD binding is essential to critically evaluating the role of these proteins In RNA splicing, packaging and transport.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  P. Lundkvist, S. Jupiter, A. Segerstolpe, Y. N. Osheim, A. L. Beyer, and L. Wieslander Mrd1p Is Required for Release of Base-Paired U3 snoRNA within the Preribosomal Complex Mol. Cell. Biol., November 1, 2009; 29(21): 5763 - 5774. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Khazina and O. Weichenrieder Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame PNAS, January 20, 2009; 106(3): 731 - 736. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. Keren, L. Klipcan, A. Bezawork-Geleta, M. Kolton, F. Shaya, and O. Ostersetzer-Biran Characterization of the Molecular Basis of Group II Intron RNA Recognition by CRS1-CRM Domains J. Biol. Chem., August 22, 2008; 283(34): 23333 - 23342. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Soller and K. White ELAV Multimerizes on Conserved AU4-6 Motifs Important for ewg Splicing Regulation Mol. Cell. Biol., September 1, 2005; 25(17): 7580 - 7591. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Anyanful, K. Ono, R. C. Johnsen, H. Ly, V. Jensen, D. L. Baillie, and S. Ono The RNA-binding protein SUP-12 controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans J. Cell Biol., November 22, 2004; 167(4): 639 - 647. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. BANERJEE, A. RAHN, B. GAWANDE, S. GUTH, J. VALCARCEL, and R. SINGH The conserved RNA recognition motif 3 of U2 snRNA auxiliary factor (U2AF65) is essential in vivo but dispensable for activity in vitro RNA, February 1, 2004; 10(2): 240 - 253. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Rappsilber, U. Ryder, A. I. Lamond, and M. Mann Large-Scale Proteomic Analysis of the Human Spliceosome Genome Res., August 1, 2002; 12(8): 1231 - 1245. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Vitali, J. Ding, J. Jiang, Y. Zhang, A. R. Krainer, and R.-M. Xu Correlated alternative side chain conformations in the RNA-recognition motif of heterogeneous nuclear ribonucleoprotein A1 Nucleic Acids Res., April 1, 2002; 30(7): 1531 - 1538. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. Rossoll, A.-K. Kroning, U.-M. Ohndorf, C. Steegborn, S. Jablonka, and M. Sendtner Specific interaction of Smn, the spinal muscular atrophy determining gene product, with hnRNP-R and gry-rbp/hnRNP-Q: a role for Smn in RNA processing in motor axons? Hum. Mol. Genet., January 1, 2002; 11(1): 93 - 105. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. J. Maraia and R. V. A. Intine Recognition of Nascent RNA by the Human La Antigen: Conserved and Divergent Features of Structure and Function Mol. Cell. Biol., January 15, 2001; 21(2): 367 - 379. [Full Text]
|
|
|
|
 |
|
 L.M. PARKER, I. FIERRO-MONTI, T.W. REICHMAN, S. GUNNERY, and M.B. MATHEWS Double-stranded RNA-binding Proteins and the Control of Protein Synthesis and Cell Growth Cold Spring Harb Symp Quant Biol, January 1, 2001; 66(0): 485 - 498. [Abstract] [PDF]
|
|
|
|
|
|
E. Lalli, K. Ohe, C. Hindelang, and P. Sassone-Corsi Orphan Receptor DAX-1 Is a Shuttling RNA Binding Protein Associated with Polyribosomes via mRNA Mol. Cell. Biol., July 1, 2000; 20(13): 4910 - 4921. [Abstract] [Full Text]
|
|
|
|
 |
|
 J. Ding, M. K. Hayashi, Y. Zhang, L. Manche, A. R. Krainer, and R.-M. Xu Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA Genes & Dev., May 1, 1999; 13(9): 1102 - 1115. [Abstract] [Full Text]
|
|
|
|
|
|
S. M. Crowder, R. Kanaar, D. C. Rio, and T. Alber Absence of interdomain contacts in the crystal structure of the RNA recognition motifs of Sex-lethal PNAS, April 27, 1999; 96(9): 4892 - 4897. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Sun and J. L. Woolford Jr. The Yeast Nucleolar Protein Nop4p Contains Four RNA Recognition Motifs Necessary for Ribosome Biogenesis J. Biol. Chem., October 3, 1997; 272(40): 25345 - 25352. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Serin, G. Joseph, L. Ghisolfi, M. Bauzan, M. Erard, F. Amalric, and P. Bouvet Two RNA-binding Domains Determine the RNA-binding Specificity of Nucleolin J. Biol. Chem., May 16, 1997; 272(20): 13109 - 13116. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. J. Good, Q. Chen, S. J. Warner, and D. C. Herring A Family of Human RNA-binding Proteins Related to the Drosophila Bruno Translational Regulator J. Biol. Chem., September 8, 2000; 275(37): 28583 - 28592. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Shan, K. Moran-Jones, T. P. Munro, G. J. Kidd, D. J. Winzor, K. S. Hoek, and R. Smith Binding of an RNA Trafficking Response Element to Heterogeneous Nuclear Ribonucleoproteins A1 and A2 J. Biol. Chem., December 1, 2000; 275(49): 38286 - 38295. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D.-J. Jung, S.-Y. Na, D. S. Na, and J. W. Lee Molecular Cloning and Characterization of CAPER, a Novel Coactivator of Activating Protein-1 and Estrogen Receptors J. Biol. Chem., January 4, 2002; 277(2): 1229 - 1234. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Huttelmaier, S. Illenberger, I. Grosheva, M. Rudiger, R. H. Singer, and B. M. Jockusch Raver1, a dual compartment protein, is a ligand for PTB/hnRNPI and microfilament attachment proteins J. Cell Biol., November 26, 2001; 155(5): 775 - 786. [Abstract] [Full Text] [PDF]
|
|