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PDBsum entry 1swf
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Biotin-binding protein
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PDB id
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1swf
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Thermodynamic and structural consequences of flexible loop deletion by circular permutation in the streptavidin-Biotin system.
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Authors
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V.Chu,
S.Freitag,
I.Le trong,
R.E.Stenkamp,
P.S.Stayton.
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Ref.
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Protein Sci, 1998,
7,
848-859.
[DOI no: ]
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PubMed id
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Abstract
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A circularly permuted streptavidin (CP51/46) has been designed to remove the
flexible polypeptide loop that undergoes an open to closed conformational change
when biotin is bound. The original termini have been joined by a tetrapeptide
linker, and four loop residues have been removed, resulting in the creation of
new N- and C-termini. Isothermal titration calorimetric studies show that the
association constant has been reduced approximately six orders of magnitude
below that of wild-type streptavidin to 10(7) M(-1). The deltaH degrees of
biotin association for CP51/46 is reduced by 11.1 kcal/mol. Crystal structures
of CP51/46 and its biotin complex show no significant alterations in the binding
site upon removal of the loop. A hydrogen bond between Ser45 and Ser52 found in
the absence of biotin is broken in the closed conformation as the side-chain
hydroxyl of Ser45 moves to hydrogen bond to a ureido nitrogen of biotin. This is
true in both the wild-type and CP51/46 forms of the protein, and the hydrogen
bonding interaction might thus help nucleate closure of the loop. The reduced
entropic cost of binding biotin to CP51/46 is consistent with the removal of
this loop and a reduction in entropic costs associated with loop closure and
immobilization. The reduced enthalpic contribution to the free energy of binding
is not readily explainable in terms of the molecular structure, as the binding
contacts are nearly entirely conserved, and only small differences in solvent
accessible surfaces are observed relative to wild-type streptavidin.
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Figure 3.
Fig. 3. A: MOLSCRIPT (Kraulis, 991)stereoviewofthetetramericcircularlypermutedstreptavidin CP51/46. subunits2(green)
and3(cyan),theengineeredloopsextendawayfromtheglobulr structure and are stabilized by crystal packinginteractions.
B: MOLSCRIPTstereoview o themutant-biotincomplex. n subunit 3 (cyan)thenewconnectingloopadoptsadifferentconfor-
mationmoreintegratedinthe p barrelstructureand also stabilized y crystal packin.
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Figure 8.
ig. 8. Superposition of thestreptavidinCP51/46unboundstructure(blue)andteCP51/46-biotincomplex(red)intheregion of the
iningsite (for ubunit 1 inthetetramer). A: Thetryptophan sidechainsthatmediatehydrophobicinteractionswithbitishowonly
inor deviatinsfromtheunboundstructure. B: Hydrogenbondinginteractionswithbiotin.
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The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(1998,
7,
848-859)
copyright 1998.
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Secondary reference #1
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Title
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Thermodynamic and structural consequences of flexible loop deletion by circular permutation in the streptavidin-Biotin system.
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Authors
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V.Chu,
S.Freitag,
I.Le trong,
R.E.Stenkamp,
P.S.Stayton.
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Ref.
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Protein Sci, 1998,
7,
848-859.
[DOI no: ]
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PubMed id
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Note: In the PDB file this reference is
annotated as "TO BE PUBLISHED". The citation details given above have
been manually determined.
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Figure 3.
Fig. 3. A: MOLSCRIPT (Kraulis, 991)stereoviewofthetetramericcircularlypermutedstreptavidin CP51/46. subunits2(green)
and3(cyan),theengineeredloopsextendawayfromtheglobulr structure and are stabilized by crystal packinginteractions.
B: MOLSCRIPTstereoview o themutant-biotincomplex. n subunit 3 (cyan)thenewconnectingloopadoptsadifferentconfor-
mationmoreintegratedinthe p barrelstructureand also stabilized y crystal packin.
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Figure 8.
ig. 8. Superposition of thestreptavidinCP51/46unboundstructure(blue)andteCP51/46-biotincomplex(red)intheregion of the
iningsite (for ubunit 1 inthetetramer). A: Thetryptophan sidechainsthatmediatehydrophobicinteractionswithbitishowonly
inor deviatinsfromtheunboundstructure. B: Hydrogenbondinginteractionswithbiotin.
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by the Protein Society
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Secondary reference #2
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Title
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Structural studies of the streptavidin binding loop.
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Authors
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S.Freitag,
I.Le trong,
L.Klumb,
P.S.Stayton,
R.E.Stenkamp.
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Ref.
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Protein Sci, 1997,
6,
1157-1166.
[DOI no: ]
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PubMed id
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Figure 2.
Fig. 2. he four observed crystal forms of ligand-free (top) and biotin-
bound (bottom) streptavidin are depicted schematically to illustrate the
behavior f [he loop (residues 45 S2) relative lo the biotin
binding site. The circles represent the streptavidin tetramer subunits with
the binding sites (missing ectors). I and 2 . and 3 and 4. respec-
tively, build the dimer pairs. Subunit 1 and 4. and 2 and 3, respectively,
donate rp 120 to each others binding site. The curved lines over the
binding sites trace the loop with dotted lines representing
disordered conformations. Triangles in the binding sites symbolize biotin.
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Figure 3.
Fig. 3. Ca representation of asuperposition of thebindinglooprgion in subunit 2 of structure4II(ligand free) on subunit 2
structure (biotin bound). Thi plotillustratestherelativeopen(red,unbound)and closed black,biotin-bound)conformations of te
inding loops.
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by the Protein Society
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