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PDBsum entry 3orc
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Gene regulation/DNA
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PDB id
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3orc
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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 an engineered cro monomer bound nonspecifically to DNA: possible implications for nonspecific binding by the wild-Type protein.
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Authors
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R.A.Albright,
M.C.Mossing,
B.W.Matthews.
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Ref.
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Protein Sci, 1998,
7,
1485-1494.
[DOI no: ]
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PubMed id
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Abstract
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The structure has been determined at 3.0 A resolution of a complex of engineered
monomeric Cro repressor with a seven-base pair DNA fragment. Although the
sequence of the DNA corresponds to the consensus half-operator that is
recognized by each subunit of the wild-type Cro dimer, the complex that is
formed in the crystals by the isolated monomer appears to correspond to a
sequence-independent mode of association. The overall orientation of the protein
relative to the DNA is markedly different from that observed for Cro dimer bound
to a consensus operator. The recognition helix is rotated 48 degrees further out
of the major groove, while the turn region of the helix-turn-helix remains in
contact with the DNA backbone. All of the direct base-specific interactions seen
in the wild-type Cro-operator complex are lost. Virtually all of the ionic
interactions with the DNA backbone, however, are maintained, as is the subset of
contacts between the DNA backbone and a channel on the protein surface. Overall,
25% less surface area is buried at the protein DNA interface than for half of
the wild-type Cro-operator complex, and the contacts are more ionic in character
due to a reduction of hydrogen bonding and van der Waals interactions. Based on
this crystal structure, model building was used to develop a possible model for
the sequence-nonspecific interaction of the wild-type Cro dimer with DNA. In the
sequence-specific complex, the DNA is bent, the protein dimer undergoes a large
hinge-bending motion relative to the uncomplexed form, and the complex is
twofold symmetric. In contrast, in the proposed nonspecific complex the DNA is
straight, the protein retains a conformation similar to the apo form, and the
complex lacks twofold symmetry. The model is consistent with thermodynamic,
chemical, and mutagenic studies, and suggests that hinge bending of the Cro
dimer may be critical in permitting the transition from the binding of protein
at generic sites on the DNA to binding at high affinity operator sites.
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Figure 2.
Fig. 2. Stereo figure showing the electron density in the region where the sugar-phosphatebackbone oftheDNA (yellow)passes
through thechanelonthe surface of the Cro monomer(white).Thepart of theproteinshownincludesPhe58,whichpenetratesinto
thehydrophobic core, andtheC-terminalresidues(toAsn61).whichoccupytheminorgroove of he NA. Coefficients are 2F0 - F,
andphases are from the refmedmodel The map is contouredat lm.
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Figure 8.
Fig. 8. Comparison of thebinding f Crotooperator DNA withtheten-
tativemodel for the bindingtononcognate DNA. A: Themodelfornon-
specificbindingvewedperpendiculartothe DNA (c.f. Fig. 7A). The
right-handmonomer is alignedonthe DNA asinthecomplexof he
engineeredCromonomer.Theremainder ofthe dimerwasbuiltassuming
theconformation f wild-typeCr(Andersonet al., 1981;Ohlendorfet al.,
1998).Terecognitionhelices of bothmonomers,shown in red,arecose
to the DNA, butthe contactsaremade y opposite ends fthe helices,
and are not equivalent. B: Binding of wild-typeCrotooperator DNA (from
Albright & atthews,
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The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(1998,
7,
1485-1494)
copyright 1998.
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Secondary reference #1
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Title
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Refined structure of cro repressor protein from bacteriophage lambda suggests both flexibility and plasticity.
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Authors
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D.H.Ohlendorf,
D.E.Tronrud,
B.W.Matthews.
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Ref.
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J Mol Biol, 1998,
280,
129-136.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2. Ramachandran diagram, calculated using the
program of [Laskowski et al 1993], showing the backbone
conformational angles for the four Cro monomers. Glycine
residues are shown as triangles, non-glycine residues as
squares. Ser60 is toward the carboxy terminus of the molecule at
the point where the electron density becomes weak, indicative of
disorder.
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Figure 3.
Figure 3. Representative sections of the electron density
map following refinement. Coefficients are 2F[o]−F[c], where
F[o] are the observed amplitudes and F[c] are those calculated
from the refined model. Phases also are from the refined model.
(a) The region near cisPro59. The Figure includes the conserved
water molecule, labeled Sol. (b) The region where Phe58 of
monomer A (labeled A58) penetrates into the hydrophobic core of
monomer C and is surrounded by residues, including Leu7, Leu23,
Val25, Ile30, Arg38 and Ile40.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #2
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Title
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Crystal structure of lambda-Cro bound to a consensus operator at 3.0 a resolution.
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Authors
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R.A.Albright,
B.W.Matthews.
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Ref.
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J Mol Biol, 1998,
280,
137-151.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. DNA fragment used in the cocrystal. The overall
fragment is a 19 base-pair duplex with 5′ single
“sticky-ended” overhangs. The central 17 base-pairs
correspond to a consensus operator. The dot indicates the
pseudo-dyad axis of the operator. Regions in which the sequence
palindrome is strictly upheld are shaded. The circles indicate
the locations and the nomenclature used to identify the
phosphate groups that are directly contacted by Cro.
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Figure 8.
Figure 8. (a) Stereo view showing the flexible ball and
socket joint of Cro. The Phe-cisPro ball of one monomer (green)
is inserted into the hydrophobic socket of the other monomer
(blue). For simplicity, only the C^α main-chain trace is shown,
together with the side-chains that form the ball and socket. The
short, covalent, linker between the ball and socket is shown in
red, and hydrogen bonds between the β1 and β2 strands are
shown as broken lines. (b) Ball and socket as seen in the Fab
switch region of the immunoglobulin McPC603 ([Satow et al 1986];
Brookhaven accession code 2MCP). As in (a), the ball is shown in
green, the socket in blue and the covalent linker in red. All of
the immunoglobulin residues are from the heavy chain.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #3
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Title
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High-Resolution structure of an engineered cro monomer shows changes in conformation relative to the native dimer.
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Authors
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R.A.Albright,
M.C.Mossing,
B.W.Matthews.
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Ref.
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Biochemistry, 1996,
35,
735-742.
[DOI no: ]
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PubMed id
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Secondary reference #4
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Title
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Stable, Monomeric variants of lambda cro obtained by insertion of a designed beta-Hairpin sequence.
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Authors
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M.C.Mossing,
R.T.Sauer.
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Ref.
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Science, 1990,
250,
1712-1715.
[DOI no: ]
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PubMed id
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