PDBsum entry 1s4u

Antiviral protein

PDB id: 1s4u

Contents

Protein chain

356 a.a. *

Waters ×158

* Residue conservation analysis

PDB id:

1s4u

Name:

Antiviral protein

Title:

Crystal structure analysis of the beta-propeller protein ski8p

Structure:

Antiviral protein ski8. Chain: x. Synonym: ski8. Engineered: yes

Source:

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

Resolution:

2.10Å R-factor: 0.253 R-free: 0.283

Authors:

Z.Cheng,H.Song

Key ref:

Z.Cheng et al. (2004). Crystal structure of Ski8p, a WD-repeat protein with dual roles in mRNA metabolism and meiotic recombination. Protein Sci, 13, 2673-2684. PubMed id: 15340168 DOI: 10.1110/ps.04856504

Date:

18-Jan-04 Release date: 28-Dec-04

Protein chain

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

Seq: 397 a.a.

Struc: 356 a.a.

DOI no: 10.1110/ps.04856504

Protein Sci 13:2673-2684 (2004)

PubMed id: 15340168

Crystal structure of Ski8p, a WD-repeat protein with dual roles in mRNA metabolism and meiotic recombination.

Z.Cheng, Y.Liu, C.Wang, R.Parker, H.Song.

ABSTRACT

Ski8p is a WD-repeat protein with an essential role for the Ski complex assembly in an exosome-dependent 3'-to-5' mRNA decay. In addition, Ski8p is involved in meiotic recombination by interacting with Spo11p protein. We have determined the crystal structure of Ski8p from Saccharomyces cerevisiae at 2.2 A resolution. The structure reveals that Ski8p folds into a seven-bladed beta propeller. Mapping sequence conservation and hydrophobicities of amino acids on the molecular surface of Ski8p reveals a prominent site on the top surface of the beta propeller, which is most likely involved in mediating interactions of Ski8p with Ski3p and Spo11p. Mutagenesis combined with yeast two-hybrid and GST pull-down assays identified the top surface of the beta propeller as being required for Ski8p binding to Ski3p and Spo11p. The functional implications for Ski8p function in both mRNA decay and meiotic recombination are discussed.

Selected figure(s)

Figure 2.
Figure 2. Sequence alignment of S. cerevisiae Ski8, S. macrospora Ski8, Schizosaccharmyces pombe Rec14, Homo sapiens Rec14, and Mus musculus Rec14. The secondary structures of S. cerevisiae Ski8 are shown. Invariant residues are white letters, similar residues are red, and others are black. Residues speculated for interactions with Ski3 and Spo11 are indicated by *.

Figure 4.
Figure 4. Molecular surface views of Ski8p. (A) Surface representation of Ski8p showing the regions of high-to-low sequence conservation shared by the eukaryotic Ski8 proteins, corresponding to a color ramp from red to blue, respectively. Invariant residues are labeled. The view is as in Figure 1A Go-. (B) Molecular surface of Ski8p colored according to residue property, with hydrophobic residues green and other residues gray. The hydrophobic residues are labeled. The view is as in A. (C) The worm model showing the C backbones of Ski8p. Residues located either in hydrophobic patch or in conserved patch are shown in stick models. The view is as in A. A and B were produced using GRASP (Nicholls et al. 1991).

The above figures are reprinted by permission from the Protein Society: Protein Sci (2004, 13, 2673-2684) copyright 2004.

Figures were selected by an automated process.