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PDBsum entry 2vv6
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Signaling protein, transferase
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PDB id
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2vv6
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References listed in PDB file
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Key reference
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Title
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Changes in quaternary structure in the signaling mechanisms of pas domains.
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Authors
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R.A.Ayers,
K.Moffat.
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Ref.
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Biochemistry, 2008,
47,
12078-12086.
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PubMed id
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Abstract
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FixL from Bradyrhizobium japonicum is a PAS sensor protein in which two PAS
domains covalently linked to a histidine kinase domain are responsible for
regulating nitrogen fixation in an oxygen-dependent manner. The more C-terminal
PAS domain, denoted bjFixLH, contains a heme cofactor that binds diatomic
molecules such as carbon monoxide and oxygen and regulates the activity of the
FixL histidine kinase as part of a two-component signaling system. We present
the structures of ferric, deoxy, and carbon monoxide-bound bjFixLH in a new
space group ( P1) and at resolutions (1.5-1.8 A) higher than the resolutions of
those previously obtained. Interestingly, bjFixLH can form two different dimers
(in P1 and R32 crystal forms) in the same crystallization solution, where the
monomers in one dimer are rotated approximately 175 degrees relative to the
second. This suggests that PAS monomers are plastic and that two quite distinct
quaternary structures are closely similar in free energy. We use screw rotation
analysis to carry out a quantitative pairwise comparison of PAS quaternary
structures, which identifies five different relative orientations adopted by
isolated PAS monomers. We conclude that PAS monomer arrangement is
context-dependent and could differ depending on whether the PAS domains are
isolated or are part of a full-length protein. Structurally homologous residues
comprise a conserved dimer interface. Using network analysis, we find that the
architecture of the PAS dimer interface is continuous rather than modular; the
network of residues comprising the interface is strongly connected. A continuous
dimer interface is consistent with the low dimer-monomer dissociation
equilibrium constant. Finally, we quantitate quaternary structural changes
induced by carbon monoxide binding to a bjFixLH dimer, in which monomers rotate
by up to approximately 2 degrees relative to each other. We relate these changes
to those in other dimeric PAS domains and discuss the role of quaternary
structural changes in the signaling mechanisms of PAS sensor proteins.
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