Structure of the La Motif: a Winged Helix Domain Mediates RNA Binding Via a Conserved Aromatic Patch

Overview

Journal EMBO J

Specialties Biotechnology
Molecular Biology

Date 2004 Feb 21

PMID 14976553

Citations 56

Authors

Gang Dong

Ghadiyaram Chakshusmathi

Sandra L Wolin

Karin M Reinisch

Affiliations

Soon will be listed here.

Abstract

The La protein is a ubiquitous nuclear phosphoprotein that recognizes the 3' uridylates found in all newly synthesized RNA polymerase III transcripts. La binding stabilizes these transcripts from exonucleases and may also assist their folding. Here we present the first structural insights into how the La protein specifically interacts with its RNA substrates. The most conserved region of the La protein is the La motif, a domain also found in several other RNA-binding proteins. We have determined the structure of the La motif from the Trypanosoma brucei La protein to 1.6 A resolution (PDB code 1S29). The La motif adopts a winged helix-turn-helix architecture that has a highly conserved patch of mainly aromatic surface residues. Mutagenesis experiments support a critical role for this patch in RNA binding and show that it partly determines binding specificity for RNAs ending in 3' hydroxyl, a defining characteristic of the La protein. These findings reveal that the La motif is essential for high-affinity binding and also contributes to specificity.

Citing Articles

A guide to the biogenesis and functions of endogenous small non-coding RNAs in animals.

Jouravleva K, Zamore P Nat Rev Mol Cell Biol. 2025; .

PMID: 39856370 DOI: 10.1038/s41580-024-00818-9.

Phage anti-CRISPR control by an RNA- and DNA-binding helix-turn-helix protein.

Birkholz N, Kamata K, Feussner M, Wilkinson M, Cuba Samaniego C, Migur A Nature. 2024; 631(8021):670-677.

PMID: 38987591 DOI: 10.1038/s41586-024-07644-1.

In silico identification, characterization, and expression analysis of RNA recognition motif (RRM) containing RNA-binding proteins in Aedes aegypti.

Sumitha M, Kalimuthu M, Aarthy M, Paramasivan R, Kumar A, Gupta B Parasitol Res. 2023; 122(12):2847-2857.

PMID: 37735272 DOI: 10.1007/s00436-023-07969-2.

Structure of LARP7 Protein p65-telomerase RNA Complex in Telomerase Revealed by Cryo-EM and NMR.

Wang Y, He Y, Wang Y, Yang Y, Singh M, Eichhorn C J Mol Biol. 2023; 435(11):168044.

PMID: 37330293 PMC: 10988774. DOI: 10.1016/j.jmb.2023.168044.

Altered tRNA processing is linked to a distinct and unusual La protein in Tetrahymena thermophila.

Kerkhofs K, Garg J, Fafard-Couture E, Elela S, Scott M, Pearlman R Nat Commun. 2022; 13(1):7332.

PMID: 36443289 PMC: 9705548. DOI: 10.1038/s41467-022-34796-3.

References

Selmer M, Su X . Crystal structure of an mRNA-binding fragment of Moorella thermoacetica elongation factor SelB. EMBO J. 2002; 21(15):4145-53. PMC: 126154. DOI: 10.1093/emboj/cdf408. View

Fan H, Sakulich A, Goodier J, Zhang X, Qin J, Maraia R . Phosphorylation of the human La antigen on serine 366 can regulate recycling of RNA polymerase III transcription complexes. Cell. 1997; 88(5):707-15. DOI: 10.1016/s0092-8674(00)81913-3. View

Otwinowski Z, Minor W . Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997; 276:307-26. DOI: 10.1016/S0076-6879(97)76066-X. View

Yisraeli J, Melton D . Synthesis of long, capped transcripts in vitro by SP6 and T7 RNA polymerases. Methods Enzymol. 1989; 180:42-50. DOI: 10.1016/0076-6879(89)80090-4. View

Chong S, Hu P, Hernandez N . Reconstitution of transcription from the human U6 small nuclear RNA promoter with eight recombinant polypeptides and a partially purified RNA polymerase III complex. J Biol Chem. 2001; 276(23):20727-34. DOI: 10.1074/jbc.M100088200. View

Varani G, Nagai K . RNA recognition by RNP proteins during RNA processing. Annu Rev Biophys Biomol Struct. 1998; 27:407-45. DOI: 10.1146/annurev.biophys.27.1.407. View

Goodier J, Fan H, Maraia R . A carboxy-terminal basic region controls RNA polymerase III transcription factor activity of human La protein. Mol Cell Biol. 1997; 17(10):5823-32. PMC: 232430. DOI: 10.1128/MCB.17.10.5823. View

Ohndorf U, Steegborn C, Knijff R, Sondermann P . Contributions of the individual domains in human La protein to its RNA 3'-end binding activity. J Biol Chem. 2001; 276(29):27188-96. DOI: 10.1074/jbc.M102891200. View

Clarkson S . Efficient synthesis, termination and release of RNA polymerase III transcripts in Xenopus extracts depleted of La protein. EMBO J. 1998; 17(7):2033-41. PMC: 1170548. DOI: 10.1093/emboj/17.7.2033. View

10.

Maraia R, Intine R . Recognition of nascent RNA by the human La antigen: conserved and divergent features of structure and function. Mol Cell Biol. 2001; 21(2):367-79. PMC: 86573. DOI: 10.1128/MCB.21.2.367-379.2001. View

11.

Rodgers D . [13] Practical cryocrystallography. Methods Enzymol. 1997; 276:183-203. DOI: 10.1016/S0076-6879(97)76059-2. View

12.

Yoo C, Wolin S . La proteins from Drosophila melanogaster and Saccharomyces cerevisiae: a yeast homolog of the La autoantigen is dispensable for growth. Mol Cell Biol. 1994; 14(8):5412-24. PMC: 359060. DOI: 10.1128/mcb.14.8.5412-5424.1994. View

13.

Van Horn D, Yoo C, Xue D, Shi H, Wolin S . The La protein in Schizosaccharomyces pombe: a conserved yet dispensable phosphoprotein that functions in tRNA maturation. RNA. 1997; 3(12):1434-43. PMC: 1369584. View

14.

MER G, Bochkarev A, Gupta R, Bochkareva E, Frappier L, Ingles C . Structural basis for the recognition of DNA repair proteins UNG2, XPA, and RAD52 by replication factor RPA. Cell. 2000; 103(3):449-56. DOI: 10.1016/s0092-8674(00)00136-7. View

15.

Allers J, Shamoo Y . Structure-based analysis of protein-RNA interactions using the program ENTANGLE. J Mol Biol. 2001; 311(1):75-86. DOI: 10.1006/jmbi.2001.4857. View

16.

Marchetti M, Tschudi C, Kwon H, Wolin S, Ullu E . Import of proteins into the trypanosome nucleus and their distribution at karyokinesis. J Cell Sci. 2000; 113 ( Pt 5):899-906. DOI: 10.1242/jcs.113.5.899. View

17.

Brunger A, Adams P, Clore G, DeLano W, Gros P, Grosse-Kunstleve R . Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr. 1998; 54(Pt 5):905-21. DOI: 10.1107/s0907444998003254. View

18.

Sobel S, Wolin S . Two yeast La motif-containing proteins are RNA-binding proteins that associate with polyribosomes. Mol Biol Cell. 1999; 10(11):3849-62. PMC: 25684. DOI: 10.1091/mbc.10.11.3849. View

19.

Nicholls A, Sharp K, Honig B . Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins. 1991; 11(4):281-96. DOI: 10.1002/prot.340110407. View

20.

Pannone B, Xue D, Wolin S . A role for the yeast La protein in U6 snRNP assembly: evidence that the La protein is a molecular chaperone for RNA polymerase III transcripts. EMBO J. 1998; 17(24):7442-53. PMC: 1171088. DOI: 10.1093/emboj/17.24.7442. View