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

A. Yarrow Madrona, David K. Wilson

Research output: Contribution to journalArticle

39 Citations (Scopus)

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 β-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 β propellers. Ski8p was thought to contain five WD repeats on the basis of primary sequence analysis implying a five-bladed propeller. The 1.9 Å 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.

Original languageEnglish (US)
Pages (from-to)1557-1565
Number of pages9
JournalProtein Science
Volume13
Issue number6
DOIs
StatePublished - Jun 2004

Fingerprint

RNA Stability
Propellers
Degradation
Messenger RNA
Exosomes
Proteins
Transducin
Amino Acid Motifs
Dipeptides
Sequence Alignment
Eukaryota
Yeast
Genetic Recombination
Sequence Analysis
WD40 Repeats
Yeasts
Crystal structure
RNA
Amino Acids

Keywords

  • Rec103
  • Ski8
  • YDR267c

ASJC Scopus subject areas

  • Biochemistry

Cite this

The structure of Ski8p, a protein regulating mRNA degradation : Implications for WD protein structure. / Madrona, A. Yarrow; Wilson, David K.

In: Protein Science, Vol. 13, No. 6, 06.2004, p. 1557-1565.

Research output: Contribution to journalArticle

Madrona, A. Yarrow ; Wilson, David K. / The structure of Ski8p, a protein regulating mRNA degradation : Implications for WD protein structure. In: Protein Science. 2004 ; Vol. 13, No. 6. pp. 1557-1565.
@article{a2210d07380845bcb2491945e33e1fb9,
title = "The structure of Ski8p, a protein regulating mRNA degradation: Implications for WD protein structure",
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 β-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 β propellers. Ski8p was thought to contain five WD repeats on the basis of primary sequence analysis implying a five-bladed propeller. The 1.9 {\AA} 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.",
keywords = "Rec103, Ski8, YDR267c",
author = "Madrona, {A. Yarrow} and Wilson, {David K.}",
year = "2004",
month = "6",
doi = "10.1110/ps.04704704",
language = "English (US)",
volume = "13",
pages = "1557--1565",
journal = "Protein Science",
issn = "0961-8368",
publisher = "Cold Spring Harbor Laboratory Press",
number = "6",

}

TY - JOUR

T1 - The structure of Ski8p, a protein regulating mRNA degradation

T2 - Implications for WD protein structure

AU - Madrona, A. Yarrow

AU - Wilson, David K.

PY - 2004/6

Y1 - 2004/6

N2 - 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 β-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 β propellers. Ski8p was thought to contain five WD repeats on the basis of primary sequence analysis implying a five-bladed propeller. The 1.9 Å 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.

AB - 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 β-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 β propellers. Ski8p was thought to contain five WD repeats on the basis of primary sequence analysis implying a five-bladed propeller. The 1.9 Å 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.

KW - Rec103

KW - Ski8

KW - YDR267c

UR - http://www.scopus.com/inward/record.url?scp=2442701467&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=2442701467&partnerID=8YFLogxK

U2 - 10.1110/ps.04704704

DO - 10.1110/ps.04704704

M3 - Article

C2 - 15152089

AN - SCOPUS:2442701467

VL - 13

SP - 1557

EP - 1565

JO - Protein Science

JF - Protein Science

SN - 0961-8368

IS - 6

ER -