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PDBsum entry 1nyn
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Structural genomics, unknown function
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PDB id
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1nyn
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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 shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism.
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Authors
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A.Savchenko,
N.Krogan,
J.R.Cort,
E.Evdokimova,
J.M.Lew,
A.A.Yee,
L.Sánchez-Pulido,
M.A.Andrade,
A.Bochkarev,
J.D.Watson,
M.A.Kennedy,
J.Greenblatt,
T.Hughes,
C.H.Arrowsmith,
J.M.Rommens,
A.M.Edwards.
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Ref.
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J Biol Chem, 2005,
280,
19213-19220.
[DOI no: ]
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PubMed id
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Abstract
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A combination of structural, biochemical, and genetic studies in model organisms
was used to infer a cellular role for the human protein (SBDS) responsible for
Shwachman-Bodian-Diamond syndrome. The crystal structure of the SBDS homologue
in Archaeoglobus fulgidus, AF0491, revealed a three domain protein. The
N-terminal domain, which harbors the majority of disease-linked mutations, has a
novel three-dimensional fold. The central domain has the common winged
helix-turn-helix motif, and the C-terminal domain shares structural homology
with known RNA-binding domains. Proteomic analysis of the SBDS sequence
homologue in Saccharomyces cerevisiae, YLR022C, revealed an association with
over 20 proteins involved in ribosome biosynthesis. NMR structural genomics
revealed another yeast protein, YHR087W, to be a structural homologue of the
AF0491 N-terminal domain. Sequence analysis confirmed them as distant sequence
homologues, therefore related by divergent evolution. Synthetic genetic array
analysis of YHR087W revealed genetic interactions with proteins involved in RNA
and rRNA processing including Mdm20/Nat3, Nsr1, and Npl3. Our observations,
taken together with previous reports, support the conclusion that SBDS and its
homologues play a role in RNA metabolism.
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Figure 2.
FIG. 2. Structural comparison of YHR087W and AF0491. A,
stereo image of 20 superimposed NMR structures of S. cerevisiae
YHR087W. B, secondary structure of the AF0491 N-terminal domain.
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Figure 4.
FIG. 4. Electrostatic surface potential for YHR087W and
AF0491 N-terminal domain. A, electrostatic surface potential for
YHR087W. B, electrostatic surface potential for AF0491
N-terminal domain. Red and blue indicate potentials <-8 and >+8
k[B]T respectively, where k[B] is the Boltzmann constant and T
is temperature (K). Aligned ribbon structures for YHR087W and
AF0491 N-terminal domain are shown next to the corresponding
electrostatic surfaces for the same and opposite sides of each
structure as indicated. Calculations were made with GRASP (68).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2005,
280,
19213-19220)
copyright 2005.
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