PDBsum entry 2err

RNA binding protein

PDB id: 2err

Contents

Protein chain

88 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

2err

Name:

RNA binding protein

Title:

Nmr structure of the RNA binding domain of human fox-1 in complex with ugcaugu

Structure:

Ugcaugu. Chain: b. Engineered: yes. Ataxin-2-binding protein 1. Chain: a. Fragment: RNA binding domain. Engineered: yes

Source:

Synthetic: yes. Other_details: this sequence occurs naturally in humans.. Homo sapiens. Human. Organism_taxid: 9606. Gene: a2bp1, a2bp. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

30 models

Authors:

F.H.Allain,S.D.Auweter

Key ref:

S.D.Auweter et al. (2006). Molecular basis of RNA recognition by the human alternative splicing factor Fox-1. EMBO J, 25, 163-173. PubMed id: 16362037 DOI: 10.1038/sj.emboj.7600918

Date:

25-Oct-05 Release date: 10-Jan-06

Protein chain

Q9NWB1  (RFOX1_HUMAN) -  RNA binding protein fox-1 homolog 1 from Homo sapiens

Seq: 397 a.a.

Struc: 88 a.a.

DNA/RNA chain

U-G-C-A-U-G-U 7 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1038/sj.emboj.7600918

EMBO J 25:163-173 (2006)

PubMed id: 16362037

Molecular basis of RNA recognition by the human alternative splicing factor Fox-1.

S.D.Auweter, R.Fasan, L.Reymond, J.G.Underwood, D.L.Black, S.Pitsch, F.H.Allain.

ABSTRACT

The Fox-1 protein regulates alternative splicing of tissue-specific exons by binding to GCAUG elements. Here, we report the solution structure of the Fox-1 RNA binding domain (RBD) in complex with UGCAUGU. The last three nucleotides, UGU, are recognized in a canonical way by the four-stranded beta-sheet of the RBD. In contrast, the first four nucleotides, UGCA, are bound by two loops of the protein in an unprecedented manner. Nucleotides U1, G2, and C3 are wrapped around a single phenylalanine, while G2 and A4 form a base-pair. This novel RNA binding site is independent from the beta-sheet binding interface. Surface plasmon resonance analyses were used to quantify the energetic contributions of electrostatic and hydrogen bond interactions to complex formation and support our structural findings. These results demonstrate the unusual molecular mechanism of sequence-specific RNA recognition by Fox-1, which is exceptional in its high affinity for a defined but short sequence element.

Selected figure(s)

Figure 2.
Figure 2 Overview of the solution structure of the RBD of Fox-1 in complex with UGCAUGU. (A) Overlay of the final 30 structures superposed on the heavy atoms of the structured parts of the protein and of the RNA. The protein backbone is gray, the RNA backbone is orange, the phosphate groups are red, and the RNA bases are yellow. Only the ordered region of the protein (residues 116-194) is shown. (B) Surface (heavy atoms of residues 116-194) and stick (heavy atoms of the RNA) representation of the lowest energy structure. The protein surface is painted according to surface potential with red indicating negative charges and blue indicating positive charges. The RNA is colored as in panel (A). (C) The lowest energy structure in ribbon (protein backbone) and stick (RNA) representation. The color scheme is the same as in (A), important protein side chains involved in hydrophobic interactions with the RNA are represented as green sticks. (D) Same as (C) but rotated by 90° around the indicated axis. Figures were generated with MOLMOL (Koradi et al, 1996).

Figure 3.
Figure 3 Molecular recognition of UGCAUGU by the RBD of Fox-1. Close-up views of the RNA binding interface of the overlay of the final 30 structures superposed on the heavy atoms of the structured parts of the protein and of the RNA (left), single structures showing the intermolecular and intra-RNA interactions that are most commonly observed in the 30 structures (middle; see Supplementary Table SI) and schematic representations of the hydrogen bonding interactions that are most commonly observed in the 30 structures (right). The ribbon representation of the protein backbone is shown in grey, side chains of the protein are in green and the RNA is in yellow. Recognition of U[1] and C[3] (A), of G[2] and A[4] (B), of U[5] (C), and of G[6] and U[7] (D). Figures were generated with MOLMOL (Koradi et al, 1996).

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 163-173) copyright 2006.

Figures were selected by an automated process.