PDBsum entry 2osq

RNA binding protein

PDB id: 2osq

Contents

Protein chain

74 a.a. *

* Residue conservation analysis

PDB id:

2osq

Name:

RNA binding protein

Title:

Nmr structure of rrm-1 of yeast npl3 protein

Structure:

Nucleolar protein 3. Chain: a. Fragment: rrm 1 domain (residues 121-194). Synonym: mitochondrial targeting suppressor 1 protein, nuclear polyadenylated RNA-binding protein 1. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: nop3, mts1, nab1, npl3. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

P.Deka,M.Bucheli,L.Skrisovska,F.H.Allain,C.Moore,S.Buratowski, G.Varani

Key ref:

P.Deka et al. (2008). Structure of the yeast SR protein Npl3 and Interaction with mRNA 3'-end processing signals. J Mol Biol, 375, 136-150. PubMed id: 18022637 DOI: 10.1016/j.jmb.2007.09.029

Date:

06-Feb-07 Release date: 18-Dec-07

Protein chain

Q01560  (NOP3_YEAST) -  Serine/arginine (SR)-type shuttling mRNA binding protein NPL3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 414 a.a.

Struc: 74 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.jmb.2007.09.029

J Mol Biol 375:136-150 (2008)

PubMed id: 18022637

Structure of the yeast SR protein Npl3 and Interaction with mRNA 3'-end processing signals.

P.Deka, M.E.Bucheli, C.Moore, S.Buratowski, G.Varani.

ABSTRACT

Yeast Npl3 is homologous to SR proteins in higher eukaryotes, a family of RNA-binding proteins that have multiple essential roles in RNA metabolism. This protein competes with 3'-end processing factors for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. The NMR structure of its RNA-binding domain shows two unusually compact RNA recognition motifs (RRMs), and identifies the RNA recognition surface in Npl3. Biochemical and NMR studies identify a class of G+U-rich RNA sequences with high specificity for this protein. The protein binds to RNA and forms a single globular structure, but the two RRMs of Npl3 are not equivalent, with the second domain forming much stronger interactions with G+U-rich RNA sequences that occur independently of the interaction of the first RRM. The specific binding to G+U-rich RNAs observed for the two RRMs of Npl3 is masked in the full-length protein by a much stronger but non-sequence-specific RNA-binding activity residing outside of its RRMs. The preference of Npl3 for G+U-rich sequences supports the model for its function in regulating recognition of 3'-end processing sites through competition with the Rna15 (yeast analog of human CstF-64 protein) subunit of the processing complex.

Selected figure(s)

Figure 1.
Figure 1. Structure of Npl3. (a) Ribbon diagrams of the two RRM domains of Npl3 as determined by NMR; the two domains are structurally independent and connected by an eight residue flexible linker. (b) and (c) Overlays of the 20 lowest energy structures on the left, and ribbon representations of the lowest energy structure on the right. Structures for RRM-1 and RRM-2 are shown in (b) and (c), respectively; the two domains are shown separately here for clarity of presentation. (d) Amino acid sequence for the full-length Npl3 protein. Residues 121–280 were the subject of NMR structure determination; residues belonging to RRM-1 and RRM-2 are colored blue and pink, respectively.

Figure 2.
Figure 2. Structural comparison of the two RRM domains of Npl3 to each other and to those of SxL protein (PDB 1B7F). (a) Superposition of the structure of RRM-1 (gray) on RRM-2 (orange) shows that the two domains are very similar, with an r.m.s.d. between them of only 1.3 Å, despite the differences in the loop between β2 and β3. (b) Superposition of the RRM-1 domain of Npl3 (gray) with the RRM-1 domain of SxL (blue) gives an r.m.s.d. of only 1.1 Å, while (c) superposition of the RRM-2 domain of Npl3 (orange) with the RRM-2 domain of SxL (green) gives an r.m.s.d. of 1.3 Å. The Figure was generated using PyMOL [http://pymol.sourceforge.net/].

The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2008, 375, 136-150) copyright 2008.

Figures were selected by an automated process.