PDBsum entry 1u2f

RNA binding protein

PDB id: 1u2f

Contents

Protein chain

90 a.a. *

* Residue conservation analysis

PDB id:

1u2f

Name:

RNA binding protein

Title:

Solution structure of the first RNA-binding domain of hu2af65

Structure:

Protein (splicing factor u2af 65 kd subunit). Chain: a. Fragment: first RNA-binding domain. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: bl21 (de3).

NMR struc:

1 models

Authors:

T.Ito,Y.Muto,M.R.Green,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

T.Ito et al. (1999). Solution structures of the first and second RNA-binding domains of human U2 small nuclear ribonucleoprotein particle auxiliary factor (U2AF(65)). EMBO J, 18, 4523-4534. PubMed id: 10449418 DOI: 10.1093/emboj/18.16.4523

Date:

26-May-99 Release date: 20-Aug-99

Protein chain

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

Seq: 475 a.a.

Struc: 90 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1093/emboj/18.16.4523

EMBO J 18:4523-4534 (1999)

PubMed id: 10449418

Solution structures of the first and second RNA-binding domains of human U2 small nuclear ribonucleoprotein particle auxiliary factor (U2AF(65)).

T.Ito, Y.Muto, M.R.Green, S.Yokoyama.

ABSTRACT

The large subunit of the human U2 small nuclear ribonucleoprotein particle auxiliary factor (hU2AF(65)) is an essential RNA-splicing factor required for the recognition of the polypyrimidine tract immediately upstream of the 3' splice site. In the present study, we determined the solution structures of two hU2AF(65) fragments, corresponding to the first and second RNA-binding domains (RBD1 and RBD2, respectively), by nuclear magnetic resonance spectroscopy. The tertiary structure of RBD2 is similar to that of typical RNA-binding domains with the beta1-alpha1-beta2-beta3-alpha2-beta4 topology. In contrast, the hU2AF(65) RBD1 structure has unique features: (i) the alpha1 helix is elongated by one turn toward the C-terminus; (ii) the loop between alpha1 and beta2 (the alpha1/beta2 loop) is much longer and has a defined conformation; (iii) the beta2 strand is (188)AVQIN(192), which was not predicted by sequence alignments; and (iv) the beta2/beta3 loop is much shorter. Chemical shift perturbation experiments showed that the U2AF-binding RNA fragments interact with the four beta-strands of RBD2 whereas, in contrast, they interact with beta1, beta3 and beta4, but not with beta2 or the alpha1/beta2 loop, of RBD1. The characteristic alpha1-beta2 structure of the hU2AF(65) RBD1 may interact with other proteins, such as UAP56.

Selected figure(s)

Figure 1.
Figure 1 A schematic diagram of the domain structure of hU2AF^65. The RS domain refers to the arginine/serine-rich domain, and RBD stands for an RNA-binding domain. The arrows indicate the N- and C-terminal positions of the polypeptides used in this study.

Figure 8.
Figure 8 Possible base-binding positions of the hU2AF^65 RBD1 and RBD2. The amino acid residues that might stack with bases in the first, second and third canonical base-binding sites are shown, colored in magenta, green and cyan, respectively. On each binding site, a schematic pyrimidine base and a N1–C1' bond are presented.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 4523-4534) copyright 1999.

Figures were selected by an automated process.