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Enzyme class:
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Chains A, B, C, D:
E.C.?
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DOI no:
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Protein Sci
7:848-859
(1998)
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PubMed id:
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Thermodynamic and structural consequences of flexible loop deletion by circular permutation in the streptavidin-biotin system.
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V.Chu,
S.Freitag,
I.Le Trong,
R.E.Stenkamp,
P.S.Stayton.
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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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Selected figure(s)
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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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Figures were
selected
by the author.
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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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D.S.Cerutti,
I.Le Trong,
R.E.Stenkamp,
and
T.P.Lybrand
(2009).
Dynamics of the streptavidin-biotin complex in solution and in its crystal lattice: distinct behavior revealed by molecular simulations.
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J Phys Chem B,
113,
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J.A.Määttä,
S.H.Helppolainen,
V.P.Hytönen,
M.S.Johnson,
M.S.Kulomaa,
T.T.Airenne,
and
H.R.Nordlund
(2009).
Structural and functional characteristics of xenavidin, the first frog avidin from Xenopus tropicalis.
|
| |
BMC Struct Biol,
9,
63.
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PDB codes:
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R.Krishnan,
E.B.Walton,
and
K.J.Van Vliet
(2009).
Characterizing rare-event property distributions via replicate molecular dynamics simulations of proteins.
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J Mol Model,
15,
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Z.Qian,
J.R.Horton,
X.Cheng,
and
S.Lutz
(2009).
Structural redesign of lipase B from Candida antarctica by circular permutation and incremental truncation.
|
| |
J Mol Biol,
393,
191-201.
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PDB codes:
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J.A.Määttä,
T.T.Airenne,
H.R.Nordlund,
J.Jänis,
T.A.Paldanius,
P.Vainiotalo,
M.S.Johnson,
M.S.Kulomaa,
and
V.P.Hytönen
(2008).
Rational modification of ligand-binding preference of avidin by circular permutation and mutagenesis.
|
| |
Chembiochem,
9,
1124-1135.
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PDB code:
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L.Li,
J.J.Dantzer,
J.Nowacki,
B.J.O'Callaghan,
and
S.O.Meroueh
(2008).
PDBcal: a comprehensive dataset for receptor-ligand interactions with three-dimensional structures and binding thermodynamics from isothermal titration calorimetry.
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Chem Biol Drug Des,
71,
529-532.
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R.Krishnan,
B.Oommen,
E.B.Walton,
J.M.Maloney,
and
K.J.Van Vliet
(2008).
Modeling and simulation of chemomechanics at the cell-matrix interface.
|
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Cell Adh Migr,
2,
83-94.
|
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S.Y.Tseng,
C.C.Wang,
C.W.Lin,
C.L.Chen,
W.Y.Yu,
C.H.Chen,
C.Y.Wu,
and
C.H.Wong
(2008).
Glycan arrays on aluminum-coated glass slides.
|
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Chem Asian J,
3,
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A.Abyzov,
and
V.A.Ilyin
(2007).
A comprehensive analysis of non-sequential alignments between all protein structures.
|
| |
BMC Struct Biol,
7,
78.
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J.Carey,
S.Lindman,
M.Bauer,
and
S.Linse
(2007).
Protein reconstitution and three-dimensional domain swapping: benefits and constraints of covalency.
|
| |
Protein Sci,
16,
2317-2333.
|
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J.DeChancie,
and
K.N.Houk
(2007).
The origins of femtomolar protein-ligand binding: hydrogen-bond cooperativity and desolvation energetics in the biotin-(strept)avidin binding site.
|
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J Am Chem Soc,
129,
5419-5429.
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T.Young,
R.Abel,
B.Kim,
B.J.Berne,
and
R.A.Friesner
(2007).
Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding.
|
| |
Proc Natl Acad Sci U S A,
104,
808-813.
|
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Z.Qian,
C.J.Fields,
and
S.Lutz
(2007).
Investigating the structural and functional consequences of circular permutation on lipase B from Candida antarctica.
|
| |
Chembiochem,
8,
1989-1996.
|
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M.Howarth,
D.J.Chinnapen,
K.Gerrow,
P.C.Dorrestein,
M.R.Grandy,
N.L.Kelleher,
A.El-Husseini,
and
A.Y.Ting
(2006).
A monovalent streptavidin with a single femtomolar biotin binding site.
|
| |
Nat Methods,
3,
267-273.
|
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F.M.Aslan,
Y.Yu,
S.C.Mohr,
and
C.R.Cantor
(2005).
Engineered single-chain dimeric streptavidins with an unexpected strong preference for biotin-4-fluorescein.
|
| |
Proc Natl Acad Sci U S A,
102,
8507-8512.
|
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V.P.Hytönen,
H.R.Nordlund,
J.Hörhä,
T.K.Nyholm,
D.E.Hyre,
T.Kulomaa,
E.J.Porkka,
A.T.Marttila,
P.S.Stayton,
O.H.Laitinen,
and
M.S.Kulomaa
(2005).
Dual-affinity avidin molecules.
|
| |
Proteins,
61,
597-607.
|
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Y.Eisenberg-Domovich,
V.P.Hytönen,
M.Wilchek,
E.A.Bayer,
M.S.Kulomaa,
and
O.Livnah
(2005).
High-resolution crystal structure of an avidin-related protein: insight into high-affinity biotin binding and protein stability.
|
| |
Acta Crystallogr D Biol Crystallogr,
61,
528-538.
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PDB codes:
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B.A.Manjasetty,
J.Hennecke,
R.Glockshuber,
and
U.Heinemann
(2004).
Structure of circularly permuted DsbA(Q100T99): preserved global fold and local structural adjustments.
|
| |
Acta Crystallogr D Biol Crystallogr,
60,
304-309.
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PDB code:
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I.Le Trong,
S.Freitag,
L.A.Klumb,
V.Chu,
P.S.Stayton,
and
R.E.Stenkamp
(2003).
Structural studies of hydrogen bonds in the high-affinity streptavidin-biotin complex: mutations of amino acids interacting with the ureido oxygen of biotin.
|
| |
Acta Crystallogr D Biol Crystallogr,
59,
1567-1573.
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PDB codes:
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K.Kwon,
E.D.Streaker,
and
D.Beckett
(2002).
Binding specificity and the ligand dissociation process in the E. coli biotin holoenzyme synthetase.
|
| |
Protein Sci,
11,
558-570.
|
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S.K.Avrantinis,
R.L.Stafford,
X.Tian,
and
G.A.Weiss
(2002).
Dissecting the streptavidin-biotin interaction by phage-displayed shotgun scanning.
|
| |
Chembiochem,
3,
1229-1234.
|
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J.Clarkson,
D.N.Batchelder,
and
D.A.Smith
(2001).
UV resonance Raman study of streptavidin binding of biotin and 2-iminobiotin: comparison with avidin.
|
| |
Biopolymers,
62,
307-314.
|
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P.T.Beernink,
Y.R.Yang,
R.Graf,
D.S.King,
S.S.Shah,
and
H.K.Schachman
(2001).
Random circular permutation leading to chain disruption within and near alpha helices in the catalytic chains of aspartate transcarbamoylase: effects on assembly, stability, and function.
|
| |
Protein Sci,
10,
528-537.
|
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X.Ni,
and
H.K.Schachman
(2001).
In vivo assembly of aspartate transcarbamoylase from fragmented and circularly permuted catalytic polypeptide chains.
|
| |
Protein Sci,
10,
519-527.
|
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|
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D.E.Hyre,
I.Le Trong,
S.Freitag,
R.E.Stenkamp,
and
P.S.Stayton
(2000).
Ser45 plays an important role in managing both the equilibrium and transition state energetics of the streptavidin-biotin system.
|
| |
Protein Sci,
9,
878-885.
|
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PDB code:
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S.Freitag,
I.Le Trong,
L.A.Klumb,
P.S.Stayton,
and
R.E.Stenkamp
(1999).
Atomic resolution structure of biotin-free Tyr43Phe streptavidin: what is in the binding site?
|
| |
Acta Crystallogr D Biol Crystallogr,
55,
1118-1126.
|
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PDB code:
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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
