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PDBsum entry 1sq9
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Antiviral protein, recombination
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PDB id
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1sq9
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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The structure of ski8p, A protein regulating mRNA degradation: implications for wd protein structure.
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Authors
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A.Y.Madrona,
D.K.Wilson.
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Ref.
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Protein Sci, 2004,
13,
1557-1565.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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).
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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.
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The above figures are
reprinted
by permission from the Protein Society:
Protein Sci
(2004,
13,
1557-1565)
copyright 2004.
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