PDBsum entry 1sq9

Antiviral protein, recombination

PDB id: 1sq9

Contents

Protein chain

378 a.a. *

Ligands

SO4 ×2

Waters ×230

* Residue conservation analysis

PDB id:

1sq9

Name:

Antiviral protein, recombination

Title:

Structure of ski8p, a wd repeat protein involved in mRNA degradation and meiotic recombination

Structure:

Antiviral protein ski8. Chain: a. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ski8, rec103, ygl213c. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.191 R-free: 0.246

Authors:

A.Y.Madrona,D.K.Wilson

Key ref:

A.Y.Madrona and D.K.Wilson (2004). The structure of Ski8p, a protein regulating mRNA degradation: Implications for WD protein structure. Protein Sci, 13, 1557-1565. PubMed id: 15152089 DOI: 10.1110/ps.04704704

Date:

18-Mar-04 Release date: 25-May-04

Protein chain

Q02793  (SKI8_YEAST) -  Antiviral protein SKI8 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 397 a.a.

Struc: 378 a.a.

DOI no: 10.1110/ps.04704704

Protein Sci 13:1557-1565 (2004)

PubMed id: 15152089

The structure of Ski8p, a protein regulating mRNA degradation: Implications for WD protein structure.

A.Y.Madrona, D.K.Wilson.

ABSTRACT

Ski8p is a 44-kD protein that primarily functions in the regulation of exosome-mediated, 3'--> 5' degradation of damaged mRNA. It does so by forming a complex with two partner proteins, Ski2p and Ski3p, which complete a complex that is capable of recruiting and activating the exosome/Ski7p complex that functions in RNA degradation. Ski8p also functions in meiotic recombination in complex with Spo11 in yeast. It is one of the many hundreds of primarily eukaryotic proteins containing tandem copies of WD repeats (also known as WD40 or beta-transducin repeats), which are short ~40 amino acid motifs, often terminating in a Trp-Asp dipeptide. Genomic analyses have demonstrated that WD repeats are found in 1%-2% of proteins in a typical eukaryote, but are extremely rare in prokaryotes. Almost all structurally characterized WD-repeat proteins are composed of seven such repeats and fold into seven-bladed beta propellers. Ski8p was thought to contain five WD repeats on the basis of primary sequence analysis implying a five-bladed propeller. The 1.9 A crystal structure unexpectedly exhibits a seven-bladed propeller fold with seven structurally authentic WD repeats. Structure-based sequence alignments show additional sequence diversity in the two undetected repeats. This demonstrates that many WD repeats have not yet been identified in sequences and also raises the possibility that the seven-bladed propeller may be the predominant fold for this family of proteins.

Selected figure(s)

Figure 3.
Figure 3. A superimposition of Ski8p (blue), G (green), and Tup1p (red) in an orientation similar to that shown in Figure 1A Go-indicate that the core fold is preserved. Structural divergence is concentrated in the loops, particularly those on the top of the propeller (directed out of the page).

Figure 5.
Figure 5. Divergence and disappearance of the structural tetrad in representative Ski8p blades. (A) Blade 1 contains a nearly conventional tetrad involving hydrogen bonding between the side chains of Trp 41, Ser 31, and His 15. The aspartate completes the tetrad in the canonical structure. (B) Blade 3 has Trp 153 and Asp 145 at the expected positions, but other residues are divergent. The core of this blade is stabilized via a mixture of hydrogen bonding and hydrophobic interactions. (C) Blade 7 contains residues that are homologous in sequence to a conventional tetrad. The positions are structurally divergent, however.

The above figures are reprinted by permission from the Protein Society: Protein Sci (2004, 13, 1557-1565) copyright 2004.

Figures were selected by the author.