PDBsum entry 2hzc

RNA binding protein

PDB id: 2hzc

Contents

Protein chain

87 a.a. *

Ligands

P6G

Metals

_ZN ×2

Waters ×193

* Residue conservation analysis

PDB id:

2hzc

Name:

RNA binding protein

Title:

Crystal structure of the n-terminal rrm of the u2af large subunit

Structure:

Splicing factor u2af 65 kda subunit. Chain: a. Fragment: rrm 1. Synonym: u2 auxiliary factor 65 kda subunit, u2 snrnp auxiliary factor large subunit, hu2af65. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: u2af2, u2af65. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

1.47Å R-factor: 0.137 R-free: 0.226

Authors:

K.R.Thickman,E.A.Sickmier,C.L.Kielkopf

Key ref:

K.R.Thickman et al. (2007). Alternative conformations at the RNA-binding surface of the N-terminal U2AF(65) RNA recognition motif. J Mol Biol, 366, 703-710. PubMed id: 17188295 DOI: 10.1016/j.jmb.2006.11.077

Date:

08-Aug-06 Release date: 29-Aug-06

Supersedes:

2fzr

Protein chain

P26368  (U2AF2_HUMAN) -  Splicing factor U2AF 65 kDa subunit from Homo sapiens

Seq: 475 a.a.

Struc: 87 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.jmb.2006.11.077

J Mol Biol 366:703-710 (2007)

PubMed id: 17188295

Alternative conformations at the RNA-binding surface of the N-terminal U2AF(65) RNA recognition motif.

K.R.Thickman, E.A.Sickmier, C.L.Kielkopf.

ABSTRACT

The essential pre-mRNA splicing factor, U2 auxiliary factor 65KD (U2AF(65)) recognizes the polypyrimidine tract (Py-tract) consensus sequence of the pre-mRNA using two RNA recognition motifs (RRMs), the most prevalent class of eukaryotic RNA-binding domain. The Py-tracts of higher eukaryotic pre-mRNAs are often interrupted with purines, yet U2AF(65) must identify these degenerate Py-tracts for accurate pre-mRNA splicing. Previously, the structure of a U2AF(65) variant in complex with poly(U) RNA suggested that rearrangement of flexible side-chains or bound water molecules may contribute to degenerate Py-tract recognition by U2AF(65). Here, the X-ray structure of the N-terminal RRM domain of U2AF(65) (RRM1) is described at 1.47 A resolution in the absence of RNA. Notably, RNA-binding by U2AF(65) selectively stabilizes pre-existing alternative conformations of three side-chains located at the RNA interface (Arg150, Lys225, and Arg227). Additionally, a flexible loop connecting the beta2/beta3 strands undergoes a conformational change to interact with the RNA. These pre-existing alternative conformations may contribute to the ability of U2AF(65) to recognize a variety of Py-tract sequences. This rare, high-resolution view of an important member of the RRM class of RNA-binding domains highlights the role of alternative side-chain conformations in RNA recognition.

Selected figure(s)

Figure 1.
Figure 1. Overall structure of U2AF^65-RRM1. Alternative conformations are shown as ball-and-stick representations with the major conformation in yellow and the minor conformation in red. (a) Ribbon diagram of U2AF^65-RRM1 with α-helices in blue and β-strands in green. Bound PEG MME550 and zinc ions from the crystallization solution are shown in magenta. (b) View as in (a), rotated 180° about the y-axis. (c) Backbone trace representations of U2AF^65-RRM1 (blue) compared with X-ray structures of other RRMs determined in the absence of RNA, including the N-terminal RRM of U1A^24 (purple), N and C-terminal RRMs of Sex-lethal^16 (red and green, respectively), and N and C-terminal RRMs of hnRNP A1^17 (yellow and cyan, respectively). The unique α1/β2 loop and β2/β3 loop of U2AF^65-RRM1 are labeled. Images were created using MolScript,^25 Bobscript,^26 and Raster3D.^27

Figure 2.
Figure 2. Comparison of apo- and RNA-bound U2AF^65-RRM1. U2AF^65-RRM1 in the presence (green) or in the absence (blue) of RNA ligand. When alternative conformations are present, major conformations of the apo-RRM1 side-chains are colored yellow, minor conformations are colored orange. (a) Superimposed ribbon diagrams. (b) View of the α1/β2 loop. (c) Comparison of aromatic residues (Phe197, Phe199, and Tyr152) in the RNP motifs. The σA-weighted, |F[o]|–|F[c]| omit electron density for side-chain atoms was calculated using Shelxpro^28 and is shown at the 5σ contour level. (d) View of Arg150. (e) View of Lys225 and Arg227.

The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2007, 366, 703-710) copyright 2007.

Figures were selected by an automated process.