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PDBsum entry 2b5a
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Gene regulation
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PDB id
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2b5a
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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 the restriction-Modification system control element c.Bcll and mapping of its binding site.
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Authors
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M.R.Sawaya,
Z.Zhu,
F.Mersha,
S.H.Chan,
R.Dabur,
S.Y.Xu,
G.K.Balendiran.
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Ref.
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Structure, 2005,
13,
1837-1847.
[DOI no: ]
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PubMed id
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Abstract
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Protection from DNA invasion is afforded by restriction-modification systems in
many bacteria. The efficiency of protection depends crucially on the relative
expression levels of restriction versus methytransferase genes. This regulation
is provided by a controller protein, named C protein. Studies of the Bcll system
in E. coli suggest that C.Bcll functions as a negative regulator for M.Bcll
expression, implying that it plays a role in defense against foreign DNA during
virus infection. C.Bcll binds (Kd = 14.3 nM) to a 2-fold symmetric C box DNA
sequence that overlaps with the putative -35 promoter region upstream of the
bcllM and bcllC genes. The C.Bcll fold comprises five alpha helices: two helices
form a helix-turn-helix motif, and the remaining three helices form the
extensive dimer interface. The C.Bcll-DNA model proposed suggests that DNA
bending might play an important role in gene regulation, and that Glu27 and
Asp31 in C.Bcll might function critically in the regulation.
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Figure 6.
Figure 6. Structure of C Protein
(A) Ribbon diagram of
the C.BclI dimer, viewed from two orthogonal perspectives.
Secondary structural elements are labeled for molecule A. The
HTH motif is formed by helix B (red), loop 2 (green), and helix
C (recognition helix, blue). The remaining three helices
(yellow) form the dimer interface. The 2-fold symmetry axis is
indicated by the black ellipse and the vertical line.
(B)
Superposition of C.BclI (yellow) and C.Ahd1 (1y7y, orange), the
HTH3 family transcription factor (1y9q, green), the SinR
transcription regulator (1b0n, blue), cylr2 (1utx, red), and the
l repressor (1lmb, purple).
(C) Sequence alignment of
C.BclI with other C proteins and structure-based sequence
alignment with proteins shown in (B) (bottom). Residues involved
in dimer contacts are colored green in the C.BclI sequence.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2005,
13,
1837-1847)
copyright 2005.
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