The autoantigen La regulates the maturation of RNA polymerase III transcripts by binding to their poly(U) termination signal. The modular protein harbors a Nterminal RNA recognition motif (RRM), RRM1, and in the C-terminal domain, a second, atypical RRM2, in addition to a phosphorylation site, and a putative nucleotide binding site. This study presents a detailed investigation into the RNA 3-end binding properties of La by using binding titration and competition assays with subsequent gel mobility shift analysis. Two truncation mutants containing one (La-RRM1) or both (La-RRM1-RRM2) RNA-binding domains were constructed, overexpressed, and purified. A K d value of 25 ؎ 10 nM for La binding to a nonameric RNA ligand with the oligouridylate recognition sequence was obtained, discriminating with a specificity ratio of ϳ100 for this probe over a RNA ligand with a 3-poly(A) stretch. The N-terminal La-RRM1 region was identified as the major contributor of these properties to La, manifested in a 5-fold lower K d of 5 ؎ 3 nM and a slightly increased specificity ratio of 120 for the RNA ligand. The atypical RRM2 in the C-terminal domain of La has an unprecedented negative effect on 3-end RNA recognition, as indicated by a higher K d value of 90 ؎ 10 nM for the La-RRM1-RRM2 mutant but comparable specificity. Thus the C-terminal regions beyond RRM2 positively modulate the RNA binding affinity of La. Negative regulation, however, occurs through Ser 366 phosphorylation decreasing the binding affinity by 2-fold. ATP had no influence on RNA complex formation. The functional implications of these findings for the mechanism of action of La are discussed.Human La protein (lupus antigen or La/SS-B) was originally identified as a major target of the autoimmune response in patients suffering from the autoimmune diseases Sjögren's syndrome and systemic lupus erythematosus (1). It is a conserved RNA-binding protein that recognizes specifically 3Ј-oligouridylate stretches (2). Associated with all RNA polymerase III transcripts where the 3Ј-UUU-OH sequence is added as the transcription termination signal, La is thought to play a central role in the metabolism of these RNAs by acting as a molecular chaperone that stabilizes and/or structures them for further processing (3). In HeLa cell extracts, the 5Ј-and 3Ј-end processing of tRNA precursors is influenced by La (4), and in vitro, La activity has been suggested in RNA polymerase termination, recycling, and initiation reactions (5-8). Furthermore, a Walker A nucleotide-binding motif in La was postulated to confer ATP-dependent RNA/DNA and RNA/RNA helicase activity (9, 10), but recently, the binding of La to double-stranded nucleic acids was shown to be independent of this site, and La does not appear to unwind double-stranded RNA (11). The Walker A motif has instead been implicated in binding to the 5Ј-triphosphate ends of nascent tRNAs, with the affinity negatively modulated by phosphorylation of Ser 366 (4, 7). Cytoplasmic functions for La have also been described, including facilitatio...