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PDBsum entry 2avi
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Biotin binding protein
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PDB id
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2avi
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Contents |
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* Residue conservation analysis
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DOI no:
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Proc Natl Acad Sci U S A
90:5076-5080
(1993)
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PubMed id:
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Three-dimensional structures of avidin and the avidin-biotin complex.
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O.Livnah,
E.A.Bayer,
M.Wilchek,
J.L.Sussman.
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ABSTRACT
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The crystal structures of a deglycosylated form of the egg-white glycoprotein
avidin and of its complex with biotin have been determined to 2.6 and 3.0 A,
respectively. The structures reveal the amino acid residues critical for
stabilization of the tetrameric assembly and for the exceptionally tight binding
of biotin. Each monomer is an eight-stranded antiparallel beta-barrel,
remarkably similar to that of the genetically distinct bacterial analog
streptavidin. As in streptavidin, binding of biotin involves a highly stabilized
network of polar and hydrophobic interactions. There are, however, some
differences. The presence of additional hydrophobic and hydrophilic groups in
the binding site of avidin (which are missing in streptavidin) may account for
its higher affinity constant. Two amino acid substitutions are proposed to be
responsible for its susceptibility to denaturation relative to streptavidin.
Unexpectedly, a residual N-acetylglucosamine moiety was detected in the
deglycosylated avidin monomer by difference Fourier synthesis.
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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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C.P.Wilson,
C.Boglio,
L.Ma,
S.L.Cockroft,
and
S.J.Webb
(2011).
Palladium(II)-Mediated Assembly of Biotinylated Ion Channels.
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Chemistry,
17,
3465-3473.
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J.A.Määttä,
Y.Eisenberg-Domovich,
H.R.Nordlund,
R.Hayouka,
M.S.Kulomaa,
O.Livnah,
and
V.P.Hytönen
(2011).
Chimeric avidin shows stability against harsh chemical conditions--biochemical analysis and 3D structure.
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Biotechnol Bioeng,
108,
481-490.
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PDB code:
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J.Leppiniemi,
J.A.Määttä,
H.Hammaren,
M.Soikkeli,
M.Laitaoja,
J.Jänis,
M.S.Kulomaa,
and
V.P.Hytönen
(2011).
Bifunctional avidin with covalently modifiable ligand binding site.
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PLoS One,
6,
e16576.
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J.M.Teulon,
Y.Delcuze,
M.Odorico,
S.W.Chen,
P.Parot,
and
J.L.Pellequer
(2011).
Single and multiple bonds in (strept)avidin-biotin interactions.
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J Mol Recognit,
24,
490-502.
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J.Wiklander,
B.C.Karlsson,
T.Aastrup,
and
I.A.Nicholls
(2011).
Towards a synthetic avidin mimic.
|
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Anal Bioanal Chem,
400,
1397-1404.
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N.A.Filenko,
C.Kolar,
J.T.West,
S.A.Smith,
Y.I.Hassan,
G.E.Borgstahl,
J.Zempleni,
and
Y.L.Lyubchenko
(2011).
The role of histone h4 biotinylation in the structure of nucleosomes.
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PLoS One,
6,
e16299.
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S.L.Carrier,
C.M.Kownacki,
and
Z.D.Schultz
(2011).
Protein-ligand binding investigated by a single nanoparticle TERS approach.
|
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Chem Commun (Camb),
47,
2065-2067.
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T.Konry,
I.Smolina,
J.M.Yarmush,
D.Irimia,
and
M.L.Yarmush
(2011).
Ultrasensitive detection of low-abundance surface-marker protein using isothermal rolling circle amplification in a microfluidic nanoliter platform.
|
| |
Small,
7,
395-400.
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B.M.Barth,
R.Sharma,
E.I.AltinoÄŸlu,
T.T.Morgan,
S.S.Shanmugavelandy,
J.M.Kaiser,
C.McGovern,
G.L.Matters,
J.P.Smith,
M.Kester,
and
J.H.Adair
(2010).
Bioconjugation of calcium phosphosilicate composite nanoparticles for selective targeting of human breast and pancreatic cancers in vivo.
|
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ACS Nano,
4,
1279-1287.
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K.Aita,
T.Temma,
Y.Shimizu,
Y.Kuge,
K.Seki,
and
H.Saji
(2010).
Synthesis of a new NIR fluorescent Nd complex labeling agent.
|
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J Fluoresc,
20,
225-234.
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T.Hianik,
X.Wang,
V.Tashlitsky,
T.Oretskaya,
S.Ponikova,
M.Antalík,
J.S.Ellis,
and
M.Thompson
(2010).
Interaction of cationic surfactants with DNA detected by spectroscopic and acoustic wave techniques.
|
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Analyst,
135,
980-986.
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A.Fürstenberg,
O.Kel,
J.Gradinaru,
T.R.Ward,
D.Emery,
G.Bollot,
J.Mareda,
and
E.Vauthey
(2009).
Site-dependent excited-state dynamics of a fluorescent probe bound to avidin and streptavidin.
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Chemphyschem,
10,
1517-1532.
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A.Kussrow,
E.Kaltgrad,
M.L.Wolfenden,
M.J.Cloninger,
M.G.Finn,
and
D.J.Bornhop
(2009).
Measurement of monovalent and polyvalent carbohydrate-lectin binding by back-scattering interferometry.
|
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Anal Chem,
81,
4889-4897.
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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.
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BMC Struct Biol,
9,
63.
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PDB codes:
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J.J.Panek,
T.R.Ward,
A.Jezierska,
and
M.Novic
(2009).
Effects of tryptophan residue fluorination on streptavidin stability and biotin-streptavidin interactions via molecular dynamics simulations.
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J Mol Model,
15,
257-266.
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M.Reffay,
Y.Gambin,
H.Benabdelhak,
G.Phan,
N.Taulier,
A.Ducruix,
R.S.Hodges,
and
W.Urbach
(2009).
Tracking membrane protein association in model membranes.
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PLoS ONE,
4,
e5035.
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M.U.Kaikkonen,
H.P.Lesch,
J.Pikkarainen,
J.K.Räty,
T.Vuorio,
T.Huhtala,
M.Taavitsainen,
T.Laitinen,
P.Tuunanen,
O.Gröhn,
A.Närvänen,
K.J.Airenne,
and
S.Ylä-Herttuala
(2009).
(Strept)avidin-displaying lentiviruses as versatile tools for targeting and dual imaging of gene delivery.
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Gene Ther,
16,
894-904.
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S.M.Burrows,
and
D.Pappas
(2009).
Comparison of methods to classify and quantify free and bound states of complexes using single molecule fluorescence anisotropy.
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Analyst,
134,
1911-1921.
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Y.Takakura,
M.Tsunashima,
J.Suzuki,
S.Usami,
Y.Kakuta,
N.Okino,
M.Ito,
and
T.Yamamoto
(2009).
Tamavidins--novel avidin-like biotin-binding proteins from the Tamogitake mushroom.
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FEBS J,
276,
1383-1397.
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PDB code:
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H.Jung,
T.Yang,
M.D.Lasagna,
J.Shi,
G.D.Reinhart,
and
P.S.Cremer
(2008).
Impact of hapten presentation on antibody binding at lipid membrane interfaces.
|
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Biophys J,
94,
3094-3103.
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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.
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Chembiochem,
9,
1124-1135.
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PDB code:
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N.Borovok,
N.Iram,
D.Zikich,
J.Ghabboun,
G.I.Livshits,
D.Porath,
and
A.B.Kotlyar
(2008).
Assembling of G-strands into novel tetra-molecular parallel G4-DNA nanostructures using avidin-biotin recognition.
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Nucleic Acids Res,
36,
5050-5060.
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R.Barattin,
and
N.Voyer
(2008).
Chemical modifications of AFM tips for the study of molecular recognition events.
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Chem Commun (Camb),
(),
1513-1532.
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R.Hayouka,
Y.Eisenberg-Domovich,
V.P.Hytönen,
J.A.Määttä,
H.R.Nordlund,
M.S.Kulomaa,
M.Wilchek,
E.A.Bayer,
and
O.Livnah
(2008).
Critical importance of loop conformation to avidin-enhanced hydrolysis of an active biotin ester.
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Acta Crystallogr D Biol Crystallogr,
64,
302-308.
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PDB codes:
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X.Ai,
A.Semesi,
A.Yee,
C.H.Arrowsmith,
W.Y.Choy,
and
S.S.Li
(2008).
The hypothetical protein Atu4866 from Agrobacterium tumefaciens adopts a streptavidin-like fold.
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Protein Sci,
17,
154-158.
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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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M.V.Rekharsky,
T.Mori,
C.Yang,
Y.H.Ko,
N.Selvapalam,
H.Kim,
D.Sobransingh,
A.E.Kaifer,
S.Liu,
L.Isaacs,
W.Chen,
S.Moghaddam,
M.K.Gilson,
K.Kim,
and
Y.Inoue
(2007).
A synthetic host-guest system achieves avidin-biotin affinity by overcoming enthalpy-entropy compensation.
|
| |
Proc Natl Acad Sci U S A,
104,
20737-20742.
|
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V.P.Hytönen,
J.A.Määttä,
E.A.Niskanen,
J.Huuskonen,
K.J.Helttunen,
K.K.Halling,
H.R.Nordlund,
K.Rissanen,
M.S.Johnson,
T.A.Salminen,
M.S.Kulomaa,
O.H.Laitinen,
and
T.T.Airenne
(2007).
Structure and characterization of a novel chicken biotin-binding protein A (BBP-A).
|
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BMC Struct Biol,
7,
8.
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PDB codes:
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A.Bonsted,
B.Ã.˜.Engesaeter,
A.Høgset,
G.M.Maelandsmo,
L.Prasmickaite,
C.D'Oliveira,
W.E.Hennink,
J.H.van Steenis,
and
K.Berg
(2006).
Photochemically enhanced transduction of polymer-complexed adenovirus targeted to the epidermal growth factor receptor.
|
| |
J Gene Med,
8,
286-297.
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D.J.Estes,
S.R.Lopez,
A.O.Fuller,
and
M.Mayer
(2006).
Triggering and visualizing the aggregation and fusion of lipid membranes in microfluidic chambers.
|
| |
Biophys J,
91,
233-243.
|
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D.Teoli,
L.Parisi,
N.Realdon,
M.Guglielmi,
A.Rosato,
and
M.Morpurgo
(2006).
Wet sol-gel derived silica for controlled release of proteins.
|
| |
J Control Release,
116,
295-303.
|
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M.E.Davis,
P.C.Hsieh,
T.Takahashi,
Q.Song,
S.Zhang,
R.D.Kamm,
A.J.Grodzinsky,
P.Anversa,
and
R.T.Lee
(2006).
Local myocardial insulin-like growth factor 1 (IGF-1) delivery with biotinylated peptide nanofibers improves cell therapy for myocardial infarction.
|
| |
Proc Natl Acad Sci U S A,
103,
8155-8160.
|
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M.Seki
(2006).
Biological significance and development of practical synthesis of biotin.
|
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Med Res Rev,
26,
434-482.
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P.Hidalgo-Fernández,
E.Ayet,
I.Canal,
and
J.A.Farrera
(2006).
Avidin and streptavidin ligands based on the glycoluril bicyclic system.
|
| |
Org Biomol Chem,
4,
3147-3154.
|
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S.Rauf,
D.Zhou,
C.Abell,
D.Klenerman,
and
D.J.Kang
(2006).
Building three-dimensional nanostructures with active enzymes by surface templated layer-by-layer assembly.
|
| |
Chem Commun (Camb),
(),
1721-1723.
|
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|
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E.A.Niskanen,
V.P.Hytönen,
A.Grapputo,
H.R.Nordlund,
M.S.Kulomaa,
and
O.H.Laitinen
(2005).
Chicken genome analysis reveals novel genes encoding biotin-binding proteins related to avidin family.
|
| |
BMC Genomics,
6,
41.
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F.Pincet,
and
J.Husson
(2005).
The solution to the streptavidin-biotin paradox: the influence of history on the strength of single molecular bonds.
|
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Biophys J,
89,
4374-4381.
|
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J.Auerswald,
D.Widmer,
N.F.de Rooij,
A.Sigrist,
T.Staubli,
T.Stöckli,
and
H.F.Knapp
(2005).
Fast immobilization of probe beads by dielectrophoresis-controlled adhesion in a versatile microfluidic platform for affinity assay.
|
| |
Electrophoresis,
26,
3697-3705.
|
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|
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T.R.Ward
(2005).
Artificial metalloenzymes for enantioselective catalysis based on the noncovalent incorporation of organometallic moieties in a host protein.
|
| |
Chemistry,
11,
3798-3804.
|
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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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V.P.Hytönen,
J.A.Määttä,
H.Kidron,
K.K.Halling,
J.Hörhä,
T.Kulomaa,
T.K.Nyholm,
M.S.Johnson,
T.A.Salminen,
M.S.Kulomaa,
and
T.T.Airenne
(2005).
Avidin related protein 2 shows unique structural and functional features among the avidin protein family.
|
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BMC Biotechnol,
5,
28.
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PDB code:
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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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F.Meiser,
C.Cortez,
and
F.Caruso
(2004).
Biofunctionalization of fluorescent rare-earth-doped lanthanum phosphate colloidal nanoparticles.
|
| |
Angew Chem Int Ed Engl,
43,
5954-5957.
|
|
|
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|
|
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L.Dreesen,
Y.Sartenaer,
C.Humbert,
A.A.Mani,
C.Méthivier,
C.M.Pradier,
P.A.Thiry,
and
A.Peremans
(2004).
Probing ligand-protein recognition with sum-frequency generation spectroscopy: the avidin-biocytin case.
|
| |
Chemphyschem,
5,
1719-1725.
|
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|
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M.Morpurgo,
A.Radu,
E.A.Bayer,
and
M.Wilchek
(2004).
DNA condensation by high-affinity interaction with avidin.
|
| |
J Mol Recognit,
17,
558-566.
|
|
|
|
|
|
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M.Wilchek,
and
M.Wilchek
(2004).
My life with affinity.
|
| |
Protein Sci,
13,
3066-3070.
|
|
|
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|
|
N.R.Cook,
P.E.Row,
and
H.W.Davidson
(2004).
Lysosome associated membrane protein 1 (Lamp1) traffics directly from the TGN to early endosomes.
|
| |
Traffic,
5,
685-699.
|
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|
S.Nayak,
and
L.A.Lyon
(2004).
Ligand-functionalized core/shell microgels with permselective shells.
|
| |
Angew Chem Int Ed Engl,
43,
6706-6709.
|
|
|
|
|
|
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Y.Eisenberg-Domovich,
Y.Pazy,
O.Nir,
B.Raboy,
E.A.Bayer,
M.Wilchek,
and
O.Livnah
(2004).
Structural elements responsible for conversion of streptavidin to a pseudoenzyme.
|
| |
Proc Natl Acad Sci U S A,
101,
5916-5921.
|
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PDB codes:
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A.Hirano,
M.Wakabayashi,
Y.Matsuno,
and
M.Sugawara
(2003).
A single-channel sensor based on gramicidin controlled by molecular recognition at bilayer lipid membranes containing receptor.
|
| |
Biosens Bioelectron,
18,
973-983.
|
|
|
|
|
|
|
E.Zahavy,
M.Fisher,
A.Bromberg,
and
U.Olshevsky
(2003).
Detection of frequency resonance energy transfer pair on double-labeled microsphere and Bacillus anthracis spores by flow cytometry.
|
| |
Appl Environ Microbiol,
69,
2330-2339.
|
|
|
|
|
|
|
L.B.Ujam,
R.H.Clemmitt,
S.A.Clarke,
R.A.Brooks,
N.Rushton,
and
H.A.Chase
(2003).
Isolation of monocytes from human peripheral blood using immuno-affinity expanded-bed adsorption.
|
| |
Biotechnol Bioeng,
83,
554-566.
|
|
|
|
|
|
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T.I.Rokitskaya,
E.A.Kotova,
and
Y.N.Antonenko
(2003).
Tandem gramicidin channels cross-linked by streptavidin.
|
| |
J Gen Physiol,
121,
463-476.
|
|
|
|
|
|
|
I.Harvey,
P.Garneau,
and
J.Pelletier
(2002).
Forced engagement of a RNA/protein complex by a chemical inducer of dimerization to modulate gene expression.
|
| |
Proc Natl Acad Sci U S A,
99,
1882-1887.
|
|
|
|
|
|
|
L.Oddershede,
J.K.Dreyer,
S.Grego,
S.Brown,
and
K.Berg-Sørensen
(2002).
The motion of a single molecule, the lambda-receptor, in the bacterial outer membrane.
|
| |
Biophys J,
83,
3152-3161.
|
|
|
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|
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P.Caliceti,
M.Chinol,
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Where a reference describes a PDB structure, the PDB
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