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PDBsum entry 1rep
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Replication/DNA
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PDB id
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1rep
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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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Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 a resolution.
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Authors
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H.Komori,
F.Matsunaga,
Y.Higuchi,
M.Ishiai,
C.Wada,
K.Miki.
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Ref.
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EMBO J, 1999,
18,
4597-4607.
[DOI no: ]
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PubMed id
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Abstract
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The initiator protein (RepE) of F factor, a plasmid involved in sexual
conjugation in Escherichia coli, has dual functions during the initiation of DNA
replication which are determined by whether it exists as a dimer or as a
monomer. A RepE monomer functions as a replication initiator, but a RepE dimer
functions as an autogenous repressor. We have solved the crystal structure of
the RepE monomer bound to an iteron DNA sequence of the replication origin of
plasmid F. The RepE monomer consists of topologically similar N- and C-terminal
domains related to each other by internal pseudo 2-fold symmetry, despite the
lack of amino acid similarities between the domains. Both domains bind to the
two major grooves of the iteron (19 bp) with different binding affinities. The
C-terminal domain plays the leading role in this binding, while the N-terminal
domain has an additional role in RepE dimerization. The structure also suggests
that superhelical DNA induced at the origin of plasmid F by four RepEs and one
HU dimer has an essential role in the initiation of DNA replication.
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Figure 1.
Figure 1 A schematic drawing of the functions of the RepE
initiator protein in mini-F plasmid replication. The RepE
monomers bind to the four iterons (direct repeats) of ori2 to
initiate replication, whereas the RepE dimers bind to the
inverted repeat of the repE promoter -operator to repress repE
transcription. Parts of the repeated sequences (iterons) are
shown at the top of the Figure where portions shared by the
direct and inverted repeats are underlined (common 8 bp). The
box indicates the RepE54 -iteron DNA complex determined in this
study.
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Figure 6.
Figure 6 (A) Positions of the conserved hydrophobic residues
that form the hydrophobic core (in stereo). They are related by
2-fold symmetry, and the position of the 2-fold axis is
indicated in black. (B) Polar interactions between the N- and
C-terminal domains (in stereo). Arg37 in the  2
helix of the N-terminal domain interacts with the carbonyl
oxygen of Lys155 in the 1'
helix of the C-terminal domain. Arg167 in the 2'
helix of the C-terminal domain interacts with the carbonyl
oxygen of Ala27 in the 1'
helix of the N-terminal domain. (C) Comparison of the DNA
binding site sequences (iteron) of RepE and RepA initiator
protein of pPS10 plasmid. Conserved sequences with their
operator DNA sequence are boxed. The corresponding amino acid
residues of RepE and RepA in contact with the bases on the DNA
are indicated.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(1999,
18,
4597-4607)
copyright 1999.
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Secondary reference #1
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Title
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Crystallization and preliminary X-Ray diffraction studies of a replication initiator protein (repe54) of the mini-F plasmid complexed with iteron DNA.
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Authors
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H.Komori,
N.Sasai,
F.Matsunaga,
C.Wada,
K.Miki.
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Ref.
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J Biochem (tokyo), 1999,
125,
24-26.
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PubMed id
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