Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3

Xiaodong Zhang, Takashi Nakashima, Yoshimitsu Kakuta, Min Yao, Isao Tanaka, Makoto Kimura

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

The Ski complex composed of Ski2p, Ski3p, and Ski8p plays an essential role in the 3′ to 5′ cytoplasmic mRNA degradation pathway in yeast. Ski2p is a putative RNA helicase, belonging in the DExD/H-box protein families and conserved in eukarya as well as in archaea. The gene product (Ph1280p) from the hyperthermophilic archaeon Pyrococcus horikoshii OT3 shows sequence homology with Ski2p, sharing 22.6% identical amino acids with a central region of Ski2p. In order to gain structural information about the Ski2p-like RNA helicase, we overproduced Ph1280p in Escherichia coli cells, and purified it to apparent homogeneity. Ph1280p exhibits DNA/RNA-dependent ATPase activity with an optimal temperature at ∼90°C. The crystal structure of Ph1280p has been solved at a resolution of 3.5 Å using single-wavelength anomalous dispersion (SAD) and selenomethionyl (Se-Met)-substituted protein. Ph1280p comprises four subdomains; the two N-terminal subdomains (N1 and N2) fold into an RecA-like architecture with the conserved helicase motifs, while the two C-terminal subdomains (C1 and C2) fold into α-helical structures containing a winged helix (WH)-fold and helix-hairpin-helix (HhH)-fold, respectively. Although the structure of each of the Ph1280p subdomains can be individually superimposed on the corresponding domains in other helicases, such as the Escherichia coli DNA helicase RecQ, the relative orientation of the helicase and C-terminal subdomains in Ph1280p is significantly different from that of other helicases. This structural feature is implicated in substrate specificity for the Ski2-like helicase and would play a critical role in the 3′ to 5′ cytoplasmic mRNA degradation in the Ski complex. Published by Cold Spring Harbor Laboratory Press.

Original languageEnglish
Pages (from-to)136-145
Number of pages10
JournalProtein Science
Volume17
Issue number1
DOIs
Publication statusPublished - Jan 1 2008

Fingerprint

Pyrococcus horikoshii
RNA Helicases
Archaea
RNA Stability
Escherichia coli
Crystal structure
DNA Helicases
Degradation
Messenger RNA
Sequence Homology
Ports and harbors
Substrate Specificity
Eukaryota
Yeast
Adenosine Triphosphatases
Proteins
Genes
Yeasts
Amino Acids
Wavelength

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology

Cite this

Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3. / Zhang, Xiaodong; Nakashima, Takashi; Kakuta, Yoshimitsu; Yao, Min; Tanaka, Isao; Kimura, Makoto.

In: Protein Science, Vol. 17, No. 1, 01.01.2008, p. 136-145.

Research output: Contribution to journalArticle

Zhang, Xiaodong ; Nakashima, Takashi ; Kakuta, Yoshimitsu ; Yao, Min ; Tanaka, Isao ; Kimura, Makoto. / Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3. In: Protein Science. 2008 ; Vol. 17, No. 1. pp. 136-145.
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abstract = "The Ski complex composed of Ski2p, Ski3p, and Ski8p plays an essential role in the 3′ to 5′ cytoplasmic mRNA degradation pathway in yeast. Ski2p is a putative RNA helicase, belonging in the DExD/H-box protein families and conserved in eukarya as well as in archaea. The gene product (Ph1280p) from the hyperthermophilic archaeon Pyrococcus horikoshii OT3 shows sequence homology with Ski2p, sharing 22.6{\%} identical amino acids with a central region of Ski2p. In order to gain structural information about the Ski2p-like RNA helicase, we overproduced Ph1280p in Escherichia coli cells, and purified it to apparent homogeneity. Ph1280p exhibits DNA/RNA-dependent ATPase activity with an optimal temperature at ∼90°C. The crystal structure of Ph1280p has been solved at a resolution of 3.5 {\AA} using single-wavelength anomalous dispersion (SAD) and selenomethionyl (Se-Met)-substituted protein. Ph1280p comprises four subdomains; the two N-terminal subdomains (N1 and N2) fold into an RecA-like architecture with the conserved helicase motifs, while the two C-terminal subdomains (C1 and C2) fold into α-helical structures containing a winged helix (WH)-fold and helix-hairpin-helix (HhH)-fold, respectively. Although the structure of each of the Ph1280p subdomains can be individually superimposed on the corresponding domains in other helicases, such as the Escherichia coli DNA helicase RecQ, the relative orientation of the helicase and C-terminal subdomains in Ph1280p is significantly different from that of other helicases. This structural feature is implicated in substrate specificity for the Ski2-like helicase and would play a critical role in the 3′ to 5′ cytoplasmic mRNA degradation in the Ski complex. Published by Cold Spring Harbor Laboratory Press.",
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