PDBsum entry: 1k1g

Gene regulation/RNA

PDB id: 1k1g

Contents

Protein chain

122 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

1k1g

Name:

Gene regulation/RNA

Title:

Structural basis for recognition of the intron branch site RNA by splicing factor 1

Structure:

Sf1-bo isoform. Chain: a. Fragment: residues 133-260, kh-qua2 region. Synonym: splicing factor 1. Engineered: yes. 5'-r( Up Ap Up Ap Cp Up Ap Ap Cp Ap A)-3'. Chain: b. Engineered: yes. Other_details: yeast and mammalian consensus bps sequence

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes

NMR struc:

10 models

Authors:

Z.Liu,I.Luyten,M.J.Bottomley,A.C.Messias,S.Houngninou- Molango,R.Sprangers,K.Zanier,A.Kramer,M.Sattler

Key ref:

Z.Liu et al. (2001). Structural basis for recognition of the intron branch site RNA by splicing factor 1. Science, 294, 1098-1102. PubMed id: 11691992 DOI: 10.1126/science.1064719

Date:

25-Sep-01 Release date: 07-Nov-01

Protein chain

Q15637  (SF01_HUMAN) -  Splicing factor 1

Seq: 639 a.a.

Struc: 122 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: RNA binding (1 term)

DOI no: 10.1126/science.1064719

Science 294:1098-1102 (2001)

PubMed id: 11691992

Structural basis for recognition of the intron branch site RNA by splicing factor 1.

Z.Liu, I.Luyten, M.J.Bottomley, A.C.Messias, S.Houngninou-Molango, R.Sprangers, K.Zanier, A.Krämer, M.Sattler.

ABSTRACT

During spliceosome assembly, splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hn RNP K) fold which is necessary and sufficient for BPS binding. The 3' part of the BPS (UAAC), including the conserved branch point adenosine (underlined), is specifically recognized in a hydrophobic cleft formed by the Gly-Pro-Arg-Gly motif and the variable loop of the KH domain. The QUA2 region recognizes the 5' nucleotides of the BPS (ACU). The branch point adenosine acting as the nucleophile in the first biochemical step of splicing is deeply buried. BPS RNA recognition suggests how SF1 may facilitate subsequent formation of the prespliceosomal complex A.

Selected figure(s)

Figure 2.
Fig. 2. Structure of the SF1/branch site RNA complex. (A) Stereoview of the NMR ensemble of the SF1 KH-QUA2/BPS RNA complex. RNA heavy atoms are shown in red; the N, C , C' trace of the protein is shown in gray and colored blue for secondary structure elements. (B) Ribbon representation of the SF1 KH-QUA2 domain bound to the BPS. Side chains of conserved hydrophobic core residues are shown in yellow; residues in the KH/QUA2 interface and the QUA2 helix 4 are colored magenta. The Gly-Pro-Arg-Gly motif and the variable loop of the KH domain are colored green and red, respectively. (C) Ribbon and (D) surface representation of the KH-QUA2/BPS complex. Secondary structure elements of the KH-QUA2 protein are labeled; RNA nucleotides are colored by atom type and annotated in magenta. The surface of the KH-QUA2 region is colored white, blue, and red for neutral, positive, and negative electrostatic potential, respectively.

Figure 3.
Fig. 3. RNA recognition. (A) Schematic overview of protein/RNA interactions. RNA nucleotides [single-letter code (42)] and protein side chains (three-letter code) are indicated. Hydrophobic interactions (red dotted lines), hydrogen bonds and electrostatic interactions (dashed blue lines) stabilizing the protein/RNA complex are shown. (B) Recognition of the branch point adenosine (Ade 8) and C9-A10-A11. Hydrogen bonds are indicated by black dashed lines. (C) Recognition of Ade7 by the KH domain. (D) Recognition of Ura6 and Cyt5 by the 158GPRG161 loop near the KH/QUA2 interface, and by the QUA2 helix ( 4).

The above figures are reprinted by permission from the AAAs: Science (2001, 294, 1098-1102) copyright 2001.

Figures were selected by an automated process.