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PDBsum entry 2lbp
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Periplasmic binding protein
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PDB id
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2lbp
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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 of the l-Leucine-Binding protein refined at 2.4 a resolution and comparison with the leu/ile/val-Binding protein structure.
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Authors
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J.S.Sack,
S.D.Trakhanov,
I.H.Tsigannik,
F.A.Quiocho.
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Ref.
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J Mol Biol, 1989,
206,
193-207.
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PubMed id
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Abstract
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The three-dimensional X-ray structure of the leucine-binding protein (36,900 Mr
and 346 residues), an active transport component of Escherichia coli, has been
determined by the method of molecular replacement, using the refined structure
of the Leu/Ile/Val-binding protein (344 residues) as the model structure. The
two amino acid-binding proteins have 80% sequence identity and, although both
crystallize in the same space group, they have very different unit cell
dimensions. The rotation function yielded one significant peak, which
subsequently led to a single self-consistent translation function solution. The
model was first refined by the constrained least-squares method, with each of
the two domains of the molecule treated separately to allow for any small change
in the relative orientation of the two domains. The model was then modified in
order to reflect the 72 changes in amino acid side-chains and two insertions in
going from the Leu/Ile/Val-binding protein sequence to that of the
L-leucine-binding protein. Final structure refinement, using the restrained
least-squares technique, resulted in an R-factor of 0.20 for 13,797 reflections
to a resolution of 2.4 A. The model is comprised of 2600 protein atoms and 91
solvent molecules. The L-leucine-binding protein structure is, as expected, very
similar to the Leu/Ile/Val-binding protein structure; both are in the unliganded
conformation with the cleft between the two domains wide open and easily
accessible. The superimposing of the structures yields a root-mean-square
difference of 0.68 A in the alpha-carbon atoms of the 317 equivalent residues.
The five regions of the leucine-binding protein structure that differ by more
than 1.6 A from the Leu/Ile/Val-binding protein structure are far from the major
portion of the ligand-binding site, which is located in one domain of the
bilobate protein. Between the structures, there are three differences in the
amino acid side-chains that form the major portion of the substrate-binding
sites. These substitutions, by themselves, fail to clearly explain the
differences in the specificities for branched aliphatic amino acids.
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Secondary reference #1
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Title
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Periplasmic binding protein structure and function. Refined X-Ray structures of the leucine/isoleucine/valine-Binding protein and its complex with leucine.
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Authors
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J.S.Sack,
M.A.Saper,
F.A.Quiocho.
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Ref.
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J Mol Biol, 1989,
206,
171-191.
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PubMed id
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