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PDBsum entry 1al3
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Transcription regulation
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PDB id
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1al3
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References listed in PDB file
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Key reference
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Title
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The structure of the cofactor-Binding fragment of the lysr family member, Cysb: a familiar fold with a surprising subunit arrangement.
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Authors
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R.Tyrrell,
K.H.Verschueren,
E.J.Dodson,
G.N.Murshudov,
C.Addy,
A.J.Wilkinson.
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Ref.
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Structure, 1997,
5,
1017-1032.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: CysB is a tetrameric protein of identical subunits (M(r) = 36,000)
which controls the expression of genes associated with the biosynthesis of
cysteine in bacteria. CysB is both an activator and a repressor of transcription
whose activity is responsive to the inducer N-acetylserine; thiosulphate and
sulphide act as anti-inducers. CysB is a member of the LysR family of
prokaryotic transcriptional regulatory proteins which share sequence
similarities over approximately 280 residues including a putative
helix-turn-helix DNA-binding motif at their N terminus. The aims of the present
study were to explore further the complex molecular biology and curious ligand
binding properties of CysB and to provide structural insights into the LysR
family of proteins. RESULTS: The crystal structure of a dimeric chymotryptic
fragment of Klebsiella aerogenes CysB comprising residues 88-324, has been
solved by multiple isomorphous replacement and multi-crystal averaging and
refined against data extending to 1.8 A resolution. The protein comprises two
alpha/beta domains (I and II) connected by two short segments of polypeptide.
The two domains enclose a cavity lined by polar sidechains, including those of
two residues whose mutation is associated with constitutive expression of the
cysteine regulon. A sulphate anion and a number of well ordered water molecules
have been modelled into discrete electron-density peaks within this cavity. In
the dimer, strands beta B from domain I and strands beta G from domain II come
together so that a pair of antiparallel symmetry-related 11-stranded twisted
beta-pleated sheets is formed. CONCLUSIONS: The overall structure of
CysB(88-324) is strikingly similar to those of the periplasmic substrate-binding
proteins. A similar fold has also been observed in the cofactor-binding domain
of Lac repressor, implying a structural relationship between the Lac repressor
and LysR families of proteins. In contrast to Lac repressor, in CysB the twofold
axis of symmetry that relates the monomers in the dimer is perpendicular rather
than parallel to the long axis of the cofactor-binding domain. This seems likely
to place the DNA-binding domains at opposite extremes of the molecule possibly
accounting for CysB's extended DNA footprints.
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Figure 1.
Figure 1. Schematic diagram of the CysB-binding sites (CBS)
at the cysJIH, cysK cysP and cysB promoters. The boxes represent
19 base pair sequences believed to represent half-sites to which
a single subunit binds [3]. At activation sites (purple),
N-acetylserine stimulates CysB binding and activates
transcription. N-acetylserine also stimulates binding to the
accessory sites (white). N-acetylserine inhibits binding to
CBS-B (red) partially relieving repression at the cysB promoter.
The cofactor also diminishes binding to the accessory site
CBS-K2 (green). Finally, N-acetylserine can also influence the
extent of bending induced by binding at the cysK and cysP
promoters. Bending at points indicated by arrows is induced by
binding to both the activation site and to either half-site K2c
or P3b (orange). N-acetylserine prevents binding at the latter
and simultaneously stimulates binding at the activation sites.
(The figure is adapted from Colyer and Kredich [27].)
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1997,
5,
1017-1032)
copyright 1997.
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