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PDBsum entry 3clc
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Transcription regulator/DNA
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PDB id
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3clc
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Contents |
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* Residue conservation analysis
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PDB id:
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Transcription regulator/DNA
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Title:
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Crystal structure of the restriction-modification controller protein c.Esp1396i tetramer in complex with its natural 35 base-pair operator
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Structure:
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Regulatory protein. Chain: a, b, c, d. Engineered: yes. 35-mer. Chain: e. Engineered: yes. Other_details: operator DNA. 35-mer. Chain: f.
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Source:
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Enterobacter sp.. Strain: rfl1396. Gene: esp1396ic. Expressed in: escherichia coli. Synthetic: yes. Other_details: chemically synthesised DNA. Other_details: chemically synthesised DNA
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Resolution:
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2.80Å
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R-factor:
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0.209
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R-free:
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0.239
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Authors:
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J.E.Mcgeehan,S.D.Streeter,S.J.Thresh,N.Ball,R.B.Ravelli,G.G.Kneale
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Key ref:
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J.E.McGeehan
et al.
(2008).
Structural analysis of the genetic switch that regulates the expression of restriction-modification genes.
Nucleic Acids Res,
36,
4778-4787.
PubMed id:
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Date:
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18-Mar-08
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Release date:
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29-Jul-08
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PROCHECK
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Headers
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References
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Q8GGH0
(Q8GGH0_9ENTR) -
Regulatory protein from Enterobacter sp. RFL1396
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Seq:
Struc:
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79 a.a.
76 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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A-T-G-T-G-A-C-T-T-A-T-A-G-T-C-C-G-T-G-T-G-A-T-T-A-T-A-G-T-C-A-A-C-A-T
35 bases
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A-T-G-T-T-G-A-C-T-A-T-A-A-T-C-A-C-A-C-G-G-A-C-T-A-T-A-A-G-T-C-A-C-A-T
35 bases
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Nucleic Acids Res
36:4778-4787
(2008)
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PubMed id:
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Structural analysis of the genetic switch that regulates the expression of restriction-modification genes.
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J.E.McGeehan,
S.D.Streeter,
S.J.Thresh,
N.Ball,
R.B.Ravelli,
G.G.Kneale.
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ABSTRACT
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Controller (C) proteins regulate the timing of the expression of restriction and
modification (R-M) genes through a combination of positive and negative feedback
circuits. A single dimer bound to the operator switches on transcription of the
C-gene and the endonuclease gene; at higher concentrations, a second dimer bound
adjacently switches off these genes. Here we report the first structure of a C
protein-DNA operator complex, consisting of two C protein dimers bound to the
native 35 bp operator sequence of the R-M system Esp1396I. The structure reveals
a role for both direct and indirect DNA sequence recognition. The structure of
the DNA in the complex is highly distorted, with severe compression of the minor
groove resulting in a 50 degrees bend within each operator site, together with a
large expansion of the major groove in the centre of the DNA sequence.
Cooperative binding between dimers governs the concentration-dependent
activation-repression switch and arises, in part, from the interaction of Glu25
and Arg35 side chains at the dimer-dimer interface. Competition between Arg35
and an equivalent residue of the sigma(70) subunit of RNA polymerase for the
Glu25 site underpins the switch from activation to repression of the
endonuclease gene.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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D.Chaix,
M.L.Ferguson,
C.Atmanene,
A.Van Dorsselaer,
S.Sanglier-Cianférani,
C.A.Royer,
and
N.Declerck
(2010).
Physical basis of the inducer-dependent cooperativity of the Central glycolytic genes Repressor/DNA complex.
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Nucleic Acids Res,
38,
5944-5957.
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K.Ishikawa,
E.Fukuda,
and
I.Kobayashi
(2010).
Conflicts targeting epigenetic systems and their resolution by cell death: novel concepts for methyl-specific and other restriction systems.
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DNA Res,
17,
325-342.
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M.K.Kaw,
and
R.M.Blumenthal
(2010).
Translational independence between overlapping genes for a restriction endonuclease and its transcriptional regulator.
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BMC Mol Biol,
11,
87.
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T.Massad,
K.Skaar,
H.Nilsson,
P.Damberg,
P.Henriksson-Peltola,
E.Haggård-Ljungquist,
M.Högbom,
and
P.Stenmark
(2010).
Crystal structure of the P2 C-repressor: a binder of non-palindromic direct DNA repeats.
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Nucleic Acids Res,
38,
7778-7790.
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PDB code:
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E.Bogdanova,
M.Zakharova,
S.Streeter,
J.Taylor,
T.Heyduk,
G.Kneale,
and
K.Severinov
(2009).
Transcription regulation of restriction-modification system Esp1396I.
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Nucleic Acids Res,
37,
3354-3366.
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I.Mruk,
and
R.M.Blumenthal
(2009).
Tuning the relative affinities for activating and repressing operators of a temporally regulated restriction-modification system.
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Nucleic Acids Res,
37,
983-998.
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N.Ball,
S.D.Streeter,
G.G.Kneale,
and
J.E.McGeehan
(2009).
Structure of the restriction-modification controller protein C.Esp1396I.
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Acta Crystallogr D Biol Crystallogr,
65,
900-905.
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PDB codes:
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S.D.Streeter,
J.E.McGeehan,
and
G.G.Kneale
(2009).
Overexpression, purification and preliminary X-ray diffraction analysis of the controller protein C.Csp231I from Citrobacter sp. RFL231.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
65,
898-901.
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V.Sorokin,
K.Severinov,
and
M.S.Gelfand
(2009).
Systematic prediction of control proteins and their DNA binding sites.
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Nucleic Acids Res,
37,
441-451.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
