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PDBsum entry 2f5g
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Gene regulation
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PDB id
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2f5g
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References listed in PDB file
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Key reference
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Title
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Crystal structure of a metal ion-Bound is200 transposase.
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Authors
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H.H.Lee,
J.Y.Yoon,
H.S.Kim,
J.Y.Kang,
K.H.Kim,
D.J.Kim,
J.Y.Ha,
B.Mikami,
H.J.Yoon,
S.W.Suh.
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Ref.
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J Biol Chem, 2006,
281,
4261-4266.
[DOI no: ]
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PubMed id
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Abstract
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IS200 transposases, present in many bacteria and Archaea, appear to be distinct
from other groups of transposases. To provide a structural basis for
understanding the action of IS200 transposases, we have determined the crystal
structure of the SSO1474 protein from Sulfolobus solfataricus, a member of the
IS200 family, in both Mn(2+)-bound and Mn(2+)-free forms. Its monomer fold is
distinct from other classes of structurally characterized transposases. Two
monomers form a tight dimer by exchanging the C-terminal alpha-helix and by
merging the two central beta-sheets into a large beta-sheet. Glu(55), His(62),
and four water molecules provide the direct coordination sphere of the
catalytically essential metal ion in the Mn(2+)-bound structure. His(16),
Asp(59), and His(60) also play important roles in maintaining the metal binding
site. The catalytic site is formed at the interface between monomers. The
candidate nucleophile in the transposition mechanism, strictly conserved
Tyr(121) coming from the other monomer, is turned away from the active site,
suggesting that a conformational change is likely to occur during the catalytic
cycle.
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Figure 3.
A close-up view of a metal ion binding by the HUH motif. A,
2F[o] - F[c] electron density map around the Mn^2+ binding site.
Residues near the HUH motif (His^60 and His^62) are shown in
sticks. Octahedral coordination of Mn^2+ is represented by black
dotted lines, whereas blue dotted lines denote hydrogen bonds.
Red balls represent water molecules. B, superposition of the
Mn^2+-bound (orange sticks) and Mn^2+-free (cyan sticks) S.
solfataricus transposase structures. Black dotted lines indicate
Mn^2+ coordination, whereas green dotted lines denote hydrogen
bonds. C, superposition of the Mn^2+-bound S. solfataricus
transposase (orange sticks) and Mn^2+-free structure of the H.
pylori IS608 transposase (green sticks). Black dotted lines
denote Mn^2+ coordination and blue dotted lines, hydrogen bonds.
D, binding of a divalent metal ion by the HUH motif in other
proteins. Black dotted lines denote Mn^2+ coordination and
hydrogen bonds.
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Figure 4.
A surface view of a dimer and DNA binding model of S.
solfataricus transposase. A, the electrostatic potential at the
molecular surface of a dimer of S. solfataricus transposase is
shown (blue, positive; red, negative). B, stem-loop DNA binding
to S. solfataricus transposase modeled by superposition of S.
solfataricus transposase (Mn^2+-free, blue) and the H. pylori
IS608 transposase (PDB code 2A6O, orange).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2006,
281,
4261-4266)
copyright 2006.
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