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PDBsum entry 2com
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Oxidoreductase
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PDB id
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2com
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References listed in PDB file
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Key reference
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Title
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Solution structure of the swirm domain of human histone demethylase lsd1.
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Authors
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N.Tochio,
T.Umehara,
S.Koshiba,
M.Inoue,
T.Yabuki,
M.Aoki,
E.Seki,
S.Watanabe,
Y.Tomo,
M.Hanada,
M.Ikari,
M.Sato,
T.Terada,
T.Nagase,
O.Ohara,
M.Shirouzu,
A.Tanaka,
T.Kigawa,
S.Yokoyama.
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Ref.
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Structure, 2006,
14,
457-468.
[DOI no: ]
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PubMed id
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Abstract
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SWIRM is an evolutionarily conserved domain involved in several
chromatin-modifying complexes. Recently, the LSD1 protein, which bears a SWIRM
domain, was found to be a demethylase for Lys4-methylated histone H3. Here, we
report a solution structure of the SWIRM domain of human LSD1. It forms a
compact fold composed of 6 alpha helices, in which a 20 amino acid long helix
(alpha4) is surrounded by 5 other short helices. The SWIRM domain structure
could be divided into the N-terminal part (alpha1-alpha3) and the C-terminal
part (alpha4-alpha6), which are connected to each other by a salt bridge. While
the N-terminal part forms a SWIRM-specific structure, the C-terminal part adopts
a helix-turn-helix (HTH)-related fold. We discuss a model in which the SWIRM
domain acts as an anchor site for a histone tail.
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Figure 4.
Figure 4. Structural Fold of the N-Terminal SWIRM Part
(A) Conserved residues among the LSD1-type subfamily members.
The residues with a ConSurf score greater than 8 are shown in
red. The orientation is the same as in Figure 3A. The view on
the right is rotated 180° around the z axis from that on the
left.
(B) Electrostatic surface. The molecular surface is
represented, and it is contoured from negative (red) to positive
(blue) potentials. The orientation is the same as the left view
in (A).
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Figure 7.
Figure 7. Interaction between LSD1-SWIRM and the Peptides of
the Histone Sequences
(A–F) Biotinylated peptides were
immobilized onto the streptavidin chips, and 64 μM (blue), 32
μM (green), 16 μM (cyan), or 8 μM (magenta) LSD1-SWIRM
protein solution was passed over the chip at a 20 μl/min flow
rate for 2 min. Biotinylated peptides used are (A) H3(1–20),
(B) H3(1–20)-K4diMe, (C) H3(1–20)-K9diMe, (D)
H3(1–20)-R8E/T11K, (E) H3(122–135), and (F) H4(1–15). The
x axis indicates the time course. Each injection starts at 0 s
and ends at 120 s. The y axis indicates the difference in the
resonance units between the peptide bound and peptide unbound
flow cells.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(2006,
14,
457-468)
copyright 2006.
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