PDBsum entry 2k0a

Metal binding protein

PDB id: 2k0a

Contents

Protein chain

109 a.a. *

Metals

_ZN ×3

* Residue conservation analysis

PDB id:

2k0a

Name:

Metal binding protein

Title:

1h, 15n and 13c chemical shift assignments for rds3 protein

Structure:

Pre-mRNA-splicing factor rds3. Chain: a. Synonym: regulator of drug sensitivity 3. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Gene: rds3. Expressed in: escherichia coli. Other_details: protein was expressed as an n-terminal glutathione-s- transferase fusion protein

NMR struc:

20 models

Authors:

N.Loening,A.Van Roon,J.Yang,K.Nagai,D.Neuhaus

Key ref:

A.M.van Roon et al. (2008). Solution structure of the U2 snRNP protein Rds3p reveals a knotted zinc-finger motif. Proc Natl Acad Sci U S A, 105, 9621-9626. PubMed id: 18621724 DOI: 10.1073/pnas.0802494105

Date:

31-Jan-08 Release date: 22-Jul-08

Protein chain

Q06835  (RDS3_YEAST) -  Pre-mRNA-splicing factor RDS3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 107 a.a.

Struc: 109 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1073/pnas.0802494105

Proc Natl Acad Sci U S A 105:9621-9626 (2008)

PubMed id: 18621724

Solution structure of the U2 snRNP protein Rds3p reveals a knotted zinc-finger motif.

A.M.van Roon, N.M.Loening, E.Obayashi, J.C.Yang, A.J.Newman, H.Hernández, K.Nagai, D.Neuhaus.

ABSTRACT

Rds3p, a component of the U2 snRNP subcomplex SF3b, is essential for pre-mRNA splicing and is extremely well conserved in all eukaryotic species. We report here the solution structure of Rds3p, which reveals an unusual knotted fold unrelated to previously known knotted proteins. Rds3p has a triangular shape with a GATA-like zinc finger at each vertex. Pairs of cysteines contributing to each finger are arranged nonsequentially in a permuted arrangement reminiscent of domain-swapping but which here involves segments of subdomains within a single chain. We suggest that the structure arose through a process of segment swapping after gene duplication. The fingers are connected through beta-strands and loops, forming an overall topology strongly resembling a "triquetra knot." The conservation and surface properties of Rds3p suggest that it functions as a platform for protein assembly within the multiprotein SF3b complex of U2 snRNP. The recombinant protein used for structure determination is biologically active, as it restores splicing activity in a yeast splicing extract depleted of native Rds3p.

Selected figure(s)

Figure 4.
Hydrophobic core of Rds3p. (A) The strands connecting the three zinc fingers form a β-triangle and are highly stabilized by hydrogen bonds. (B) Conserved hydrophobic residues between the face of the zinc fingers and the β-triangle stabilize the core of Rds3p.

Figure 6.
Electrostatic surface of Rds3p. Regions of positive charge are shown in blue, and regions of negative charge are shown in red. (Left) The bottom view (same orientation as in Fig. 1) shows a basic patch formed by lysine and arginine residues on strand 2 at the base of the triangle. (Right) The top view (same orientation as in Fig. 2 B and C) shows a slightly acidic patch, but otherwise the surface is relatively featureless. The missing area in the top view results from truncation of the flexible tails.

Figures were selected by an automated process.