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PDBsum entry 3dzd
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Transcription regulator
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PDB id
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3dzd
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References listed in PDB file
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Key reference
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Title
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Structure and regulatory mechanism of aquifex aeolicus ntrc4: variability and evolution in bacterial transcriptional regulation.
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Authors
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J.D.Batchelor,
M.Doucleff,
C.J.Lee,
K.Matsubara,
S.De carlo,
J.Heideker,
M.H.Lamers,
J.G.Pelton,
D.E.Wemmer.
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Ref.
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J Mol Biol, 2008,
384,
1058-1075.
[DOI no: ]
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PubMed id
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Abstract
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Genetic changes lead gradually to altered protein function, making deduction of
the molecular basis for activity from a sequence difficult. Comparative studies
provide insights into the functional consequences of specific changes. Here we
present structural and biochemical studies of NtrC4, a sigma-54 activator from
Aquifex aeolicus, and compare it with NtrC1 (a paralog) and NtrC (a homolog from
Salmonella enterica) to provide insight into how a substantial change in
regulatory mechanism may have occurred. Activity assays show that assembly of
NtrC4's active oligomer is repressed by the N-terminal receiver domain, and that
BeF3- addition (mimicking phosphorylation) removes this repression. Observation
of assembly without activation for NtrC4 indicates that it is much less strongly
repressed than NtrC1. The crystal structure of the unactivated receiver-ATPase
domain combination shows a partially disrupted interface. NMR structures of the
regulatory domain show that its activation mechanism is very similar to that of
NtrC1. The crystal structure of the NtrC4 DNA-binding domain shows that it is
dimeric and more similar in structure to NtrC than NtrC1. Electron microscope
images of the ATPase-DNA-binding domain combination show formation of oligomeric
rings. Sequence alignments provide insights into the distribution of activation
mechanisms in this family of proteins.
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Figure 6.
Fig. 6. Ribbon diagram of the crystal structure of the
dimeric DNA-binding domain of NtrC4.
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Figure 10.
Fig. 10. The receiver domain dimer interface for NtrC4 is
shown. (a) The active dimer interface showing side chains of
K93, D98, I92, V89, A88, and V85. (b) The unactivated dimer
interface showing side chains of H115, R108, Y97, and D98. (c)
The active receiver dimer showing side chains of Y97, H115, V89,
and I92. (d) The unactivated receiver dimer showing the same
side chains as (c).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2008,
384,
1058-1075)
copyright 2008.
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