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PDBsum entry 2vbz
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DNA binding protein
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PDB id
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2vbz
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Contents |
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* Residue conservation analysis
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Nucleic Acids Res
35:7324-7335
(2007)
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PubMed id:
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Mechanistic insights from the crystal structures of a feast/famine regulatory protein from Mycobacterium tuberculosis H37Rv.
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T.Shrivastava,
R.Ramachandran.
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ABSTRACT
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Rv3291c gene from Mycobacterium tuberculosis codes for a transcriptional
regulator belonging to the (leucine responsive regulatory protein/regulator of
asparigine synthase C gene product) Lrp/AsnC-family. We have identified a novel
effector-binding site from crystal structures of the apo protein, complexes with
a variety of amino acid effectors, X-ray based ligand screening and qualitative
fluorescence spectroscopy experiments. The new effector site is in addition to
the structural characterization of another distinct site in the protein
conserved in the related AsnC-family of regulators. The structures reveal that
the ligand-binding loops of two crystallographically independent subunits adopt
different conformations to generate two distinct effector-binding sites. A
change in the conformation of the binding site loop 100-106 in the B subunit is
apparently necessary for octameric association and also allows the loop to
interact with a bound ligand in the newly identified effector-binding site.
There are four sites of each kind in the octamer and the protein preferentially
binds to aromatic amino acids. While amino acids like Phe, Tyr and Trp exhibit
binding to only one site, His exhibits binding to both sites. Binding of Phe is
accompanied by a conformational change of 3.7 A in the 75-83 loop, which is
advantageously positioned to control formation of higher oligomers. Taken
together, the present studies suggest an elegant control mechanism for global
transcription regulation involving binding of ligands to the two sites,
individually or collectively.
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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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E.Peeters,
S.V.Albers,
A.Vassart,
A.J.Driessen,
and
D.Charlier
(2009).
Ss-LrpB, a transcriptional regulator from Sulfolobus solfataricus, regulates a gene cluster with a pyruvate ferredoxin oxidoreductase-encoding operon and permease genes.
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Mol Microbiol,
71,
972-988.
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M.Yamada,
S.A.Ishijima,
and
M.Suzuki
(2009).
Interactions between the archaeal transcription repressor FL11 and its coregulators lysine and arginine.
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Proteins,
74,
520-525.
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PDB codes:
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T.Kumarevel,
N.Nakano,
K.Ponnuraj,
S.C.Gopinath,
K.Sakamoto,
A.Shinkai,
P.K.Kumar,
and
S.Yokoyama
(2008).
Crystal structure of glutamine receptor protein from Sulfolobus tokodaii strain 7 in complex with its effector L-glutamine: implications of effector binding in molecular association and DNA binding.
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Nucleic Acids Res,
36,
4808-4820.
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PDB codes:
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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
codes are
shown on the right.
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Links
