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PDBsum entry 2g7b
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Transport protein
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PDB id
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2g7b
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References listed in PDB file
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Key reference
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Title
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Protein design: reengineering cellular retinoic acid binding protein ii into a rhodopsin protein mimic.
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Authors
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C.Vasileiou,
S.Vaezeslami,
R.M.Crist,
M.Rabago-Smith,
J.H.Geiger,
B.Borhan.
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Ref.
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J Am Chem Soc, 2007,
129,
6140-6148.
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PubMed id
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Abstract
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Rational redesign of the binding pocket of Cellular Retinoic Acid Binding
Protein II (CRABPII) has provided a mutant that can bind retinal as a protonated
Schiff base, mimicking the binding observed in rhodopsin. The reengineering was
accomplished through a series of choreographed manipulations to ultimately
orient the reactive species (the epsilon-amino group of Lys132 and the carbonyl
of retinal) in the proper geometry for imine formation. The guiding principle
was to achieve the appropriate Bürgi-Dunitz trajectory for the reaction to
ensue. Through crystallographic analysis of protein mutants incapable of forming
the requisite Schiff base, a highly ordered water molecule was identified as a
key culprit in orienting retinal in a nonconstructive manner. Removal of the
ordered water, along with placing reinforcing mutations to favor the desired
orientation of retinal, led to a triple mutant CRABPII protein capable of
nanomolar binding of retinal as a protonated Schiff base. The high-resolution
crystal structure of all-trans-retinal bound to the CRABPII triple mutant (1.2 A
resolution) unequivocally illustrates the imine formed between retinal and the
protein.
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Added reference #1*
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Title
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Structural analysis of site-directed mutants of cellular retinoic acid-binding protein II addresses the relationship between structural integrity and ligand binding.
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Authors
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S.Vaezeslami,
X.Jia,
C.Vasileiou,
B.Borhan,
J.H.Geiger.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2008,
64,
1228-1239.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1 (a) RA in the pocket of WT-CRABPII; (b)
hydrogen-bonding interactions of the carboxylate group of RA
with the residues inside the pocket. The distances are in
angstroms.
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Figure 5.
Figure 5 (a) Overlaid structures of R132K:Y134F-RA (brown) and
WT CRABPII-RA (yellow); (b) water-mediated interaction between
Arg111 deep inside the cavity and Ala36 located on the loop
connecting  2
to  B
in R132K:Y134F-RA. The distances are in ansgtroms.
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by the IUCr
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*Note, "added" references are those not in the PDB file but
which have either been obtained from the journal or suggested by the
author(s).
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Secondary reference #1
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Title
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Determining crystal structures of proteins and protein complexes by x-Ray crystallography: x-Ray crystallographic studies of the mutants of cellular retinoic acid binding protein type ii toward designing a mimic of rhodopsin
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Author
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S.Vaezeslami.
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Ref.
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thesis ...
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