 |
PDBsum entry 1omp
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Periplasmic binding protein
|
PDB id
|
|
|
|
1omp
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Biochemistry
31:10657-10663
(1992)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis.
|
|
A.J.Sharff,
L.E.Rodseth,
J.C.Spurlino,
F.A.Quiocho.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The periplasmic maltodextrin binding protein of Escherichia coli serves as an
initial receptor for the active transport of and chemotaxis toward
maltooligosaccharides. The three-dimensional structure of the binding protein
complexed with maltose has been previously reported [Spurlino, J. C., Lu, G.-Y.,
& Quiocho, F. A. (1991) J. Biol. Chem. 266, 5202-5219]. Here we report the
structure of the unliganded form of the binding protein refined to 1.8-A
resolution. This structure, combined with that for the liganded form, provides
the first crystallographic evidence that a major ligand-induced conformational
change occurs in a periplasmic binding protein. The unliganded structure shows a
rigid-body "hinge-bending" between the two globular domains by approximately 35
degrees, relative to the maltose-bound structure, opening the sugar binding site
groove located between the two domains. In addition, there is an 8 degrees twist
of one domain relative to the other domain. The conformational changes observed
between this structure and the maltose-bound structure are consistent with
current models of maltose/maltodextrin transport and maltose chemotaxis and
solidify a mechanism for receptor differentiation between the ligand-free and
ligand-bound forms in signal transduction.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
B.C.Chu,
and
H.J.Vogel
(2011).
A structural and functional analysis of type III periplasmic and substrate binding proteins: their role in bacterial siderophore and heme transport.
|
| |
Biol Chem,
392,
39-52.
|
|
|
|
|
|
|
G.M.Clore
(2011).
Exploring sparsely populated states of macromolecules by diamagnetic and paramagnetic NMR relaxation.
|
| |
Protein Sci,
20,
229-246.
|
|
|
|
|
|
|
J.R.Perilla,
O.Beckstein,
E.J.Denning,
and
T.B.Woolf
(2011).
Computing ensembles of transitions from stable states: Dynamic importance sampling.
|
| |
J Comput Chem,
32,
196-209.
|
|
|
|
|
|
|
S.S.Rizk,
M.Paduch,
J.H.Heithaus,
E.M.Duguid,
A.Sandstrom,
and
A.A.Kossiakoff
(2011).
Allosteric control of ligand-binding affinity using engineered conformation-specific effector proteins.
|
| |
Nat Struct Mol Biol,
18,
437-442.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
E.Bordignon,
M.Grote,
and
E.Schneider
(2010).
The maltose ATP-binding cassette transporter in the 21st century--towards a structural dynamic perspective on its mode of action.
|
| |
Mol Microbiol,
77,
1354-1366.
|
|
|
|
|
|
|
G.A.Bermejo,
M.P.Strub,
C.Ho,
and
N.Tjandra
(2010).
Ligand-free open-closed transitions of periplasmic binding proteins: the case of glutamine-binding protein.
|
| |
Biochemistry,
49,
1893-1902.
|
|
|
|
|
|
|
I.H.Walker,
P.C.Hsieh,
and
P.D.Riggs
(2010).
Mutations in maltose-binding protein that alter affinity and solubility properties.
|
| |
Appl Microbiol Biotechnol,
88,
187-197.
|
|
|
|
|
|
|
S.Fushinobu
(2010).
Unique sugar metabolic pathways of bifidobacteria.
|
| |
Biosci Biotechnol Biochem,
74,
2374-2384.
|
|
|
|
|
|
|
A.D.Gould,
P.G.Telmer,
and
B.H.Shilton
(2009).
Stimulation of the maltose transporter ATPase by unliganded maltose binding protein.
|
| |
Biochemistry,
48,
8051-8061.
|
|
|
|
|
|
|
A.K.Mittermaier,
and
L.E.Kay
(2009).
Observing biological dynamics at atomic resolution using NMR.
|
| |
Trends Biochem Sci,
34,
601-611.
|
|
|
|
|
|
|
B.Lomenick,
R.Hao,
N.Jonai,
R.M.Chin,
M.Aghajan,
S.Warburton,
J.Wang,
R.P.Wu,
F.Gomez,
J.A.Loo,
J.A.Wohlschlegel,
T.M.Vondriska,
J.Pelletier,
H.R.Herschman,
J.Clardy,
C.F.Clarke,
and
J.Huang
(2009).
Target identification using drug affinity responsive target stability (DARTS).
|
| |
Proc Natl Acad Sci U S A,
106,
21984-21989.
|
|
|
|
|
|
|
C.Oswald,
S.H.Smits,
M.Höing,
E.Bremer,
and
L.Schmitt
(2009).
Structural analysis of the choline-binding protein ChoX in a semi-closed and ligand-free conformation.
|
| |
Biol Chem,
390,
1163-1170.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.S.Kim,
B.Pierre,
M.Ostermeier,
L.L.Looger,
and
J.R.Kim
(2009).
Enzyme stabilization by domain insertion into a thermophilic protein.
|
| |
Protein Eng Des Sel,
22,
615-623.
|
|
|
|
|
|
|
C.S.Souza,
L.C.Ferreira,
L.Thomas,
J.A.Barbosa,
and
A.Balan
(2009).
Crystallization, data collection and data processing of maltose-binding protein (MalE) from the phytopathogen Xanthomonas axonopodis pv. citri.
|
| |
Acta Crystallogr Sect F Struct Biol Cryst Commun,
65,
105-107.
|
|
|
|
|
|
|
G.Grasso,
A.I.Bush,
R.D'Agata,
E.Rizzarelli,
and
G.Spoto
(2009).
Enzyme solid-state support assays: a surface plasmon resonance and mass spectrometry coupled study of immobilized insulin degrading enzyme.
|
| |
Eur Biophys J,
38,
407-414.
|
|
|
|
|
|
|
G.M.Clore,
and
J.Iwahara
(2009).
Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes.
|
| |
Chem Rev,
109,
4108-4139.
|
|
|
|
|
|
|
I.Iijima,
and
T.Hohsaka
(2009).
Position-specific incorporation of fluorescent non-natural amino acids into maltose-binding protein for detection of ligand binding by FRET and fluorescence quenching.
|
| |
Chembiochem,
10,
999.
|
|
|
|
|
|
|
M.J.Cuneo,
L.S.Beese,
and
H.W.Hellinga
(2009).
Structural analysis of semi-specific oligosaccharide recognition by a cellulose-binding protein of thermotoga maritima reveals adaptations for functional diversification of the oligopeptide periplasmic binding protein fold.
|
| |
J Biol Chem,
284,
33217-33223.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Tonelli,
L.R.Masterson,
G.Cornilescu,
J.L.Markley,
and
G.Veglia
(2009).
One-sample approach to determine the relative orientations of proteins in ternary and binary complexes from residual dipolar coupling measurements.
|
| |
J Am Chem Soc,
131,
14138-14139.
|
|
|
|
|
|
|
N.Matsumoto,
M.Yamada,
Y.Kurakata,
H.Yoshida,
S.Kamitori,
A.Nishikawa,
and
T.Tonozuka
(2009).
Crystal structures of open and closed forms of cyclo/maltodextrin-binding protein.
|
| |
FEBS J,
276,
3008-3019.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
P.Ragunathan,
B.Spellerberg,
and
K.Ponnuraj
(2009).
Structure of laminin-binding adhesin (Lmb) from Streptococcus agalactiae.
|
| |
Acta Crystallogr D Biol Crystallogr,
65,
1262-1269.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.Shi,
A.Proteau,
J.Wagner,
Q.Cui,
E.O.Purisima,
A.Matte,
and
M.Cygler
(2009).
Trapping open and closed forms of FitE: a group III periplasmic binding protein.
|
| |
Proteins,
75,
598-609.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.L.Davidson,
E.Dassa,
C.Orelle,
and
J.Chen
(2008).
Structure, function, and evolution of bacterial ATP-binding cassette systems.
|
| |
Microbiol Mol Biol Rev,
72,
317.
|
|
|
|
|
|
|
A.Paciaroni,
A.Orecchini,
E.Cornicchi,
M.Marconi,
C.Petrillo,
M.Haertlein,
M.Moulin,
H.Schober,
M.Tarek,
and
F.Sacchetti
(2008).
Fingerprints of amorphous icelike behavior in the vibrational density of states of protein hydration water.
|
| |
Phys Rev Lett,
101,
148104.
|
|
|
|
|
|
|
E.J.Levin,
N.L.Elsen,
K.D.Seder,
J.G.McCoy,
B.G.Fox,
and
G.N.Phillips
(2008).
X-ray structure of a soluble Rieske-type ferredoxin from Mus musculus.
|
| |
Acta Crystallogr D Biol Crystallogr,
64,
933-940.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
G.M.Clore
(2008).
Visualizing lowly-populated regions of the free energy landscape of macromolecular complexes by paramagnetic relaxation enhancement.
|
| |
Mol Biosyst,
4,
1058-1069.
|
|
|
|
|
|
|
K.Murata,
S.Kawai,
B.Mikami,
and
W.Hashimoto
(2008).
Superchannel of bacteria: biological significance and new horizons.
|
| |
Biosci Biotechnol Biochem,
72,
265-277.
|
|
|
|
|
|
|
L.A.Yatsunyk,
J.A.Easton,
L.R.Kim,
S.A.Sugarbaker,
B.Bennett,
R.M.Breece,
I.I.Vorontsov,
D.L.Tierney,
M.W.Crowder,
and
A.C.Rosenzweig
(2008).
Structure and metal binding properties of ZnuA, a periplasmic zinc transporter from Escherichia coli.
|
| |
J Biol Inorg Chem,
13,
271-288.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.J.Cuneo,
L.S.Beese,
and
H.W.Hellinga
(2008).
Ligand-induced conformational changes in a thermophilic ribose-binding protein.
|
| |
BMC Struct Biol,
8,
50.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.J.Cuneo,
Y.Tian,
M.Allert,
and
H.W.Hellinga
(2008).
The backbone structure of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein is essentially identical to its mesophilic E. coli homolog.
|
| |
BMC Struct Biol,
8,
20.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.Suzuki,
J.Wada,
T.Katayama,
S.Fushinobu,
T.Wakagi,
H.Shoun,
H.Sugimoto,
A.Tanaka,
H.Kumagai,
H.Ashida,
M.Kitaoka,
and
K.Yamamoto
(2008).
Structural and thermodynamic analyses of solute-binding Protein from Bifidobacterium longum specific for core 1 disaccharide and lacto-N-biose I.
|
| |
J Biol Chem,
283,
13165-13173.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
V.Laux,
P.Callow,
D.I.Svergun,
P.A.Timmins,
V.T.Forsyth,
and
M.Haertlein
(2008).
Selective deuteration of tryptophan and methionine residues in maltose binding protein: a model system for neutron scattering.
|
| |
Eur Biophys J,
37,
815-822.
|
|
|
|
|
|
|
B.R.Chandra,
M.Yogavel,
and
A.Sharma
(2007).
Structural analysis of ABC-family periplasmic zinc binding protein provides new insights into mechanism of ligand uptake and release.
|
| |
J Mol Biol,
367,
970-982.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.Tang,
C.D.Schwieters,
and
G.M.Clore
(2007).
Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR.
|
| |
Nature,
449,
1078-1082.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.G.Su,
X.Jiao,
T.G.Sun,
C.H.Li,
W.Z.Chen,
and
C.X.Wang
(2007).
Analysis of domain movements in glutamine-binding protein with simple models.
|
| |
Biophys J,
92,
1326-1335.
|
|
|
|
|
|
|
J.Liang,
J.R.Kim,
J.T.Boock,
T.J.Mansell,
and
M.Ostermeier
(2007).
Ligand binding and allostery can emerge simultaneously.
|
| |
Protein Sci,
16,
929-937.
|
|
|
|
|
|
|
M.L.Daus,
S.Berendt,
S.Wuttge,
and
E.Schneider
(2007).
Maltose binding protein (MalE) interacts with periplasmic loops P2 and P1 respectively of the MalFG subunits of the maltose ATP binding cassette transporter (MalFGK(2)) from Escherichia coli/Salmonella during the transport cycle.
|
| |
Mol Microbiol,
66,
1107-1122.
|
|
|
|
|
|
|
M.L.Oldham,
D.Khare,
F.A.Quiocho,
A.L.Davidson,
and
J.Chen
(2007).
Crystal structure of a catalytic intermediate of the maltose transporter.
|
| |
Nature,
450,
515-521.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.S.Prajapati,
M.Das,
S.Sreeramulu,
M.Sirajuddin,
S.Srinivasan,
V.Krishnamurthy,
R.Ranjani,
C.Ramakrishnan,
and
R.Varadarajan
(2007).
Thermodynamic effects of proline introduction on protein stability.
|
| |
Proteins,
66,
480-491.
|
|
|
|
|
|
|
T.Tonozuka,
A.Sogawa,
M.Yamada,
N.Matsumoto,
H.Yoshida,
S.Kamitori,
K.Ichikawa,
M.Mizuno,
A.Nishikawa,
and
Y.Sakano
(2007).
Structural basis for cyclodextrin recognition by Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein.
|
| |
FEBS J,
274,
2109-2120.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.Müller,
E.Severi,
C.Mulligan,
A.G.Watts,
D.J.Kelly,
K.S.Wilson,
A.J.Wilkinson,
and
G.H.Thomas
(2006).
Conservation of structure and mechanism in primary and secondary transporters exemplified by SiaP, a sialic acid binding virulence factor from Haemophilus influenzae.
|
| |
J Biol Chem,
281,
22212-22222.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
I.L.Medintz,
and
J.R.Deschamps
(2006).
Maltose-binding protein: a versatile platform for prototyping biosensing.
|
| |
Curr Opin Biotechnol,
17,
17-27.
|
|
|
|
|
|
|
M.G.Sandros,
V.Shete,
and
D.E.Benson
(2006).
Selective, reversible, reagentless maltose biosensing with core-shell semiconducting nanoparticles.
|
| |
Analyst,
131,
229-235.
|
|
|
|
|
|
|
M.Ying,
and
T.Flatmark
(2006).
Binding of the viral immunogenic octapeptide VSV8 to native glucose-regulated protein Grp94 (gp96) and its inhibition by the physiological ligands ATP and Ca2+.
|
| |
FEBS J,
273,
513-522.
|
|
|
|
|
|
|
A.Pang,
Y.Arinaminpathy,
M.S.Sansom,
and
P.C.Biggin
(2005).
Comparative molecular dynamics--similar folds and similar motions?
|
| |
Proteins,
61,
809-822.
|
|
|
|
|
|
|
K.D.Krewulak,
C.M.Shepherd,
and
H.J.Vogel
(2005).
Molecular dynamics simulations of the periplasmic ferric-hydroxamate binding protein FhuD.
|
| |
Biometals,
18,
375-386.
|
|
|
|
|
|
|
K.Deuschle,
S.Okumoto,
M.Fehr,
L.L.Looger,
L.Kozhukh,
and
W.B.Frommer
(2005).
Construction and optimization of a family of genetically encoded metabolite sensors by semirational protein engineering.
|
| |
Protein Sci,
14,
2304-2314.
|
|
|
|
|
|
|
T.Stockner,
H.J.Vogel,
and
D.P.Tieleman
(2005).
A salt-bridge motif involved in ligand binding and large-scale domain motions of the maltose-binding protein.
|
| |
Biophys J,
89,
3362-3371.
|
|
|
|
|
|
|
W.Hashimoto,
K.Momma,
Y.Maruyama,
M.Yamasaki,
B.Mikami,
and
K.Murata
(2005).
Structure and function of bacterial super-biosystem responsible for import and depolymerization of macromolecules.
|
| |
Biosci Biotechnol Biochem,
69,
673-692.
|
|
|
|
|
|
|
W.Zhang,
J.S.Olson,
and
G.N.Phillips
(2005).
Biophysical and kinetic characterization of HemAT, an aerotaxis receptor from Bacillus subtilis.
|
| |
Biophys J,
88,
2801-2814.
|
|
|
|
|
|
|
A.J.Bordner,
and
R.A.Abagyan
(2004).
Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations.
|
| |
Proteins,
57,
400-413.
|
|
|
|
|
|
|
A.Schiefner,
G.Holtmann,
K.Diederichs,
W.Welte,
and
E.Bremer
(2004).
Structural basis for the binding of compatible solutes by ProX from the hyperthermophilic archaeon Archaeoglobus fulgidus.
|
| |
J Biol Chem,
279,
48270-48281.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
C.F.Higgins,
and
K.J.Linton
(2004).
The ATP switch model for ABC transporters.
|
| |
Nat Struct Mol Biol,
11,
918-926.
|
|
|
|
|
|
|
D.B.Sherman,
S.Zhang,
J.B.Pitner,
and
A.Tropsha
(2004).
Evaluation of the relative stability of liganded versus ligand-free protein conformations using Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method.
|
| |
Proteins,
56,
828-838.
|
|
|
|
|
|
|
G.Guntas,
S.F.Mitchell,
and
M.Ostermeier
(2004).
A molecular switch created by in vitro recombination of nonhomologous genes.
|
| |
Chem Biol,
11,
1483-1487.
|
|
|
|
|
|
|
M.I.Austermuhle,
J.A.Hall,
C.S.Klug,
and
A.L.Davidson
(2004).
Maltose-binding protein is open in the catalytic transition state for ATP hydrolysis during maltose transport.
|
| |
J Biol Chem,
279,
28243-28250.
|
|
|
|
|
|
|
M.S.Sujatha,
and
P.V.Balaji
(2004).
Identification of common structural features of binding sites in galactose-specific proteins.
|
| |
Proteins,
55,
44-65.
|
|
|
|
|
|
|
M.T.Sebulsky,
C.D.Speziali,
B.H.Shilton,
D.R.Edgell,
and
D.E.Heinrichs
(2004).
FhuD1, a ferric hydroxamate-binding lipoprotein in Staphylococcus aureus: a case of gene duplication and lateral transfer.
|
| |
J Biol Chem,
279,
53152-53159.
|
|
|
|
|
|
|
R.F.Fischetti,
D.J.Rodi,
D.B.Gore,
and
L.Makowski
(2004).
Wide-angle X-ray solution scattering as a probe of ligand-induced conformational changes in proteins.
|
| |
Chem Biol,
11,
1431-1443.
|
|
|
|
|
|
|
R.W.Roberts
(2004).
Engineering switches, genetically.
|
| |
Chem Biol,
11,
1475-1476.
|
|
|
|
|
|
|
W.Hashimoto,
M.Yamasaki,
T.Itoh,
K.Momma,
B.Mikami,
and
K.Murata
(2004).
Super-channel in bacteria: structural and functional aspects of a novel biosystem for the import and depolymerization of macromolecules.
|
| |
J Biosci Bioeng,
98,
399-413.
|
|
|
|
|
|
|
D.R.Smyth,
M.K.Mrozkiewicz,
W.J.McGrath,
P.Listwan,
and
B.Kobe
(2003).
Crystal structures of fusion proteins with large-affinity tags.
|
| |
Protein Sci,
12,
1313-1322.
|
|
|
|
|
|
|
D.Rinaldo,
and
M.J.Field
(2003).
A computational study of the open and closed forms of the N-lobe human serum transferrin apoprotein.
|
| |
Biophys J,
85,
3485-3501.
|
|
|
|
|
|
|
F.A.Saul,
M.Mourez,
B.Vulliez-Le Normand,
N.Sassoon,
G.A.Bentley,
and
J.M.Betton
(2003).
Crystal structure of a defective folding protein.
|
| |
Protein Sci,
12,
577-585.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
N.K.Karpowich,
H.H.Huang,
P.C.Smith,
and
J.F.Hunt
(2003).
Crystal structures of the BtuF periplasmic-binding protein for vitamin B12 suggest a functionally important reduction in protein mobility upon ligand binding.
|
| |
J Biol Chem,
278,
8429-8434.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
O.Millet,
R.P.Hudson,
and
L.E.Kay
(2003).
The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy.
|
| |
Proc Natl Acad Sci U S A,
100,
12700-12705.
|
|
|
|
|
|
|
P.G.Telmer,
and
B.H.Shilton
(2003).
Insights into the conformational equilibria of maltose-binding protein by analysis of high affinity mutants.
|
| |
J Biol Chem,
278,
34555-34567.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
R.Ruíz,
S.Marqués,
and
J.L.Ramos
(2003).
Leucines 193 and 194 at the N-terminal domain of the XylS protein, the positive transcriptional regulator of the TOL meta-cleavage pathway, are involved in dimerization.
|
| |
J Bacteriol,
185,
3036-3041.
|
|
|
|
|
|
|
R.S.Prajapati,
G.M.Lingaraju,
K.Bacchawat,
A.Surolia,
and
R.Varadarajan
(2003).
Thermodynamic effects of replacements of Pro residues in helix interiors of maltose-binding protein.
|
| |
Proteins,
53,
863-871.
|
|
|
|
|
|
|
W.Zhang,
and
G.N.Phillips
(2003).
Crystallization and X-ray diffraction analysis of the sensor domain of the HemAT aerotactic receptor.
|
| |
Acta Crystallogr D Biol Crystallogr,
59,
749-751.
|
|
|
|
|
|
|
Y.Mishima,
K.Momma,
W.Hashimoto,
B.Mikami,
and
K.Murata
(2003).
Crystal structure of AlgQ2, a macromolecule (alginate)-binding protein of Sphingomonas sp. A1, complexed with an alginate tetrasaccharide at 1.6-A resolution.
|
| |
J Biol Chem,
278,
6552-6559.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.L.Davidson
(2002).
Mechanism of coupling of transport to hydrolysis in bacterial ATP-binding cassette transporters.
|
| |
J Bacteriol,
184,
1225-1233.
|
|
|
|
|
|
|
B.Ma,
M.Shatsky,
H.J.Wolfson,
and
R.Nussinov
(2002).
Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations.
|
| |
Protein Sci,
11,
184-197.
|
|
|
|
|
|
|
M.Fehr,
W.B.Frommer,
and
S.Lalonde
(2002).
Visualization of maltose uptake in living yeast cells by fluorescent nanosensors.
|
| |
Proc Natl Acad Sci U S A,
99,
9846-9851.
|
|
|
|
|
|
|
M.Wojciechowski,
and
J.Skolnick
(2002).
Docking of small ligands to low-resolution and theoretically predicted receptor structures.
|
| |
J Comput Chem,
23,
189-197.
|
|
|
|
|
|
|
R.M.de Lorimier,
J.J.Smith,
M.A.Dwyer,
L.L.Looger,
K.M.Sali,
C.D.Paavola,
S.S.Rizk,
S.Sadigov,
D.W.Conrad,
L.Loew,
and
H.W.Hellinga
(2002).
Construction of a fluorescent biosensor family.
|
| |
Protein Sci,
11,
2655-2675.
|
|
|
|
|
|
|
C.M.Bruns,
D.S.Anderson,
K.G.Vaughan,
P.A.Williams,
A.J.Nowalk,
D.E.McRee,
and
T.A.Mietzner
(2001).
Crystallographic and biochemical analyses of the metal-free Haemophilus influenzae Fe3+-binding protein.
|
| |
Biochemistry,
40,
15631-15637.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Chen,
S.Sharma,
F.A.Quiocho,
and
A.L.Davidson
(2001).
Trapping the transition state of an ATP-binding cassette transporter: evidence for a concerted mechanism of maltose transport.
|
| |
Proc Natl Acad Sci U S A,
98,
1525-1530.
|
|
|
|
|
|
|
J.D.Fox,
R.B.Kapust,
and
D.S.Waugh
(2001).
Single amino acid substitutions on the surface of Escherichia coli maltose-binding protein can have a profound impact on the solubility of fusion proteins.
|
| |
Protein Sci,
10,
622-630.
|
|
|
|
|
|
|
J.Mendieta,
G.Ramírez,
and
F.Gago
(2001).
Molecular dynamics simulations of the conformational changes of the glutamate receptor ligand-binding core in the presence of glutamate and kainate.
|
| |
Proteins,
44,
460-469.
|
|
|
|
|
|
|
J.P.Arié,
N.Sassoon,
and
J.M.Betton
(2001).
Chaperone function of FkpA, a heat shock prolyl isomerase, in the periplasm of Escherichia coli.
|
| |
Mol Microbiol,
39,
199-210.
|
|
|
|
|
|
|
J.S.Marvin,
and
H.W.Hellinga
(2001).
Manipulation of ligand binding affinity by exploitation of conformational coupling.
|
| |
Nat Struct Biol,
8,
795-798.
|
|
|
|
|
|
|
W.Hashimoto,
K.Momma,
Y.Mishima,
B.Mikami,
and
K.Murata
(2001).
Super-channel in bacteria: function and structure of a macromolecule import system mediated by a pit-dependent ABC transporter.
|
| |
Biosci Biotechnol Biochem,
65,
1949-1956.
|
|
|
|
|
|
|
Y.Mishima,
K.Momma,
W.Hashimoto,
B.Mikami,
and
K.Murata
(2001).
Super-channel in bacteria: function and structure of the macromolecule import system mediated by a pit-dependent ABC transporter.
|
| |
FEMS Microbiol Lett,
204,
215-221.
|
|
|
|
|
|
|
D.I.Kreimer,
H.Malak,
J.R.Lakowicz,
S.Trakhanov,
E.Villar,
and
V.L.Shnyrov
(2000).
Thermodynamics and dynamics of histidine-binding protein, the water-soluble receptor of histidine permease. Implications for the transport of high and low affinity ligands.
|
| |
Eur J Biochem,
267,
4242-4252.
|
|
|
|
|
|
|
D.Yin,
X.Yang,
Y.Hu,
K.Kuczera,
R.L.Schowen,
R.T.Borchardt,
and
T.C.Squier
(2000).
Substrate binding stabilizes S-adenosylhomocysteine hydrolase in a closed conformation.
|
| |
Biochemistry,
39,
9811-9818.
|
|
|
|
|
|
|
E.M.Brown
(2000).
The extracellular Ca2+-sensing receptor: central mediator of systemic calcium homeostasis.
|
| |
Annu Rev Nutr,
20,
507-533.
|
|
|
|
|
|
|
N.Chattopadhyay
(2000).
Biochemistry, physiology and pathophysiology of the extracellular calcium-sensing receptor.
|
| |
Int J Biochem Cell Biol,
32,
789-804.
|
|
|
|
|
|
|
X.Liu,
J.Yang,
A.M.Ghazi,
and
T.K.Frey
(2000).
Characterization of the zinc binding activity of the rubella virus nonstructural protease.
|
| |
J Virol,
74,
5949-5956.
|
|
|
|
|
|
|
C.Brunkhorst,
C.Andersen,
and
E.Schneider
(1999).
Acarbose, a pseudooligosaccharide, is transported but not metabolized by the maltose-maltodextrin system of Escherichia coli.
|
| |
J Bacteriol,
181,
2612-2619.
|
|
|
|
|
|
|
K.Döring,
T.Surrey,
P.Nollert,
and
F.Jähnig
(1999).
Effects of ligand binding on the internal dynamics of maltose-binding protein.
|
| |
Eur J Biochem,
266,
477-483.
|
|
|
|
|
|
|
S.Hayward
(1999).
Structural principles governing domain motions in proteins.
|
| |
Proteins,
36,
425-435.
|
|
|
|
|
|
|
S.Sheshadri,
G.M.Lingaraju,
and
R.Varadarajan
(1999).
Denaturant mediated unfolding of both native and molten globule states of maltose binding protein are accompanied by large deltaCp's.
|
| |
Protein Sci,
8,
1689-1695.
|
|
|
|
|
|
|
Y.Zhang,
P.J.Gardina,
A.S.Kuebler,
H.S.Kang,
J.A.Christopher,
and
M.D.Manson
(1999).
Model of maltose-binding protein/chemoreceptor complex supports intrasubunit signaling mechanism.
|
| |
Proc Natl Acad Sci U S A,
96,
939-944.
|
|
|
|
|
|
|
B.Sandak,
R.Nussinov,
and
H.J.Wolfson
(1998).
A method for biomolecular structural recognition and docking allowing conformational flexibility.
|
| |
J Comput Biol,
5,
631-654.
|
|
|
|
|
|
|
D.G.Vassylyev,
H.Tomitori,
K.Kashiwagi,
K.Morikawa,
and
K.Igarashi
(1998).
Crystal structure and mutational analysis of the Escherichia coli putrescine receptor. Structural basis for substrate specificity.
|
| |
J Biol Chem,
273,
17604-17609.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.G.Vassylyev,
T.Kashiwagi,
H.Tomitori,
K.Kashiwagi,
K.Igarashi,
and
K.Morikawa
(1998).
Crystallization and preliminary X-ray analysis of the periplasmic receptor (PotF) of the putrescine transport system in Escherichia coli.
|
| |
Acta Crystallogr D Biol Crystallogr,
54,
132-134.
|
|
|
|
|
|
|
D.M.Lawson,
C.E.Williams,
L.A.Mitchenall,
and
R.N.Pau
(1998).
Ligand size is a major determinant of specificity in periplasmic oxyanion-binding proteins: the 1.2 A resolution crystal structure of Azotobacter vinelandii ModA.
|
| |
Structure,
6,
1529-1539.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.M.Betton,
N.Sassoon,
M.Hofnung,
and
M.Laurent
(1998).
Degradation versus aggregation of misfolded maltose-binding protein in the periplasm of Escherichia coli.
|
| |
J Biol Chem,
273,
8897-8902.
|
|
|
|
|
|
|
M.Pajatsch,
M.Gerhart,
R.Peist,
R.Horlacher,
W.Boos,
and
A.Böck
(1998).
The periplasmic cyclodextrin binding protein CymE from Klebsiella oxytoca and its role in maltodextrin and cyclodextrin transport.
|
| |
J Bacteriol,
180,
2630-2635.
|
|
|
|
|
|
|
M.S.Jurica,
and
B.L.Stoddard
(1998).
Mind your B's and R's: bacterial chemotaxis, signal transduction and protein recognition.
|
| |
Structure,
6,
809-813.
|
|
|
|
|
|
|
N.Campobasso,
C.A.Costello,
C.Kinsland,
T.P.Begley,
and
S.E.Ealick
(1998).
Crystal structure of thiaminase-I from Bacillus thiaminolyticus at 2.0 A resolution.
|
| |
Biochemistry,
37,
15981-15989.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
S.Raffy,
N.Sassoon,
M.Hofnung,
and
J.M.Betton
(1998).
Tertiary structure-dependence of misfolding substitutions in loops of the maltose-binding protein.
|
| |
Protein Sci,
7,
2136-2142.
|
|
|
|
|
|
|
W.Boos,
and
H.Shuman
(1998).
Maltose/maltodextrin system of Escherichia coli: transport, metabolism, and regulation.
|
| |
Microbiol Mol Biol Rev,
62,
204-229.
|
|
|
|
|
|
|
B.X.Yan,
and
Y.Q.Sun
(1997).
Glycine residues provide flexibility for enzyme active sites.
|
| |
J Biol Chem,
272,
3190-3194.
|
|
|
|
|
|
|
C.Ganesh,
A.N.Shah,
C.P.Swaminathan,
A.Surolia,
and
R.Varadarajan
(1997).
Thermodynamic characterization of the reversible, two-state unfolding of maltose binding protein, a large two-domain protein.
|
| |
Biochemistry,
36,
5020-5028.
|
|
|
|
|
|
|
D.Chamberlain,
B.P.O'Hara,
S.A.Wilson,
L.H.Pearl,
and
S.J.Perkins
(1997).
Oligomerization of the amide sensor protein AmiC by x-ray and neutron scattering and molecular modeling.
|
| |
Biochemistry,
36,
8020-8029.
|
|
|
|
|
|
|
F.A.Quiocho,
J.C.Spurlino,
and
L.E.Rodseth
(1997).
Extensive features of tight oligosaccharide binding revealed in high-resolution structures of the maltodextrin transport/chemosensory receptor.
|
| |
Structure,
5,
997.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
F.A.Saul,
B.Vulliez-le Normand,
F.Lema,
and
G.A.Bentley
(1997).
Crystal structure of a recombinant form of the maltodextrin-binding protein carrying an inserted sequence of a B-cell epitope from the preS2 region of hepatitis B virus.
|
| |
Proteins,
27,
1-8.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
G.E.Arnold,
and
R.L.Ornstein
(1997).
Protein hinge bending as seen in molecular dynamics simulations of native and M61 mutant T4 lysozymes.
|
| |
Biopolymers,
41,
533-544.
|
|
|
|
|
|
|
G.Richarme,
and
T.D.Caldas
(1997).
Chaperone properties of the bacterial periplasmic substrate-binding proteins.
|
| |
J Biol Chem,
272,
15607-15612.
|
|
|
|
|
|
|
J.A.Hall,
K.Gehring,
and
H.Nikaido
(1997).
Two modes of ligand binding in maltose-binding protein of Escherichia coli. Correlation with the structure of ligands and the structure of binding protein.
|
| |
J Biol Chem,
272,
17605-17609.
|
|
|
|
|
|
|
J.A.Hall,
T.E.Thorgeirsson,
J.Liu,
Y.K.Shin,
and
H.Nikaido
(1997).
Two modes of ligand binding in maltose-binding protein of Escherichia coli. Electron paramagnetic resonance study of ligand-induced global conformational changes by site-directed spin labeling.
|
| |
J Biol Chem,
272,
17610-17614.
|
|
|
|
|
|
|
J.J.Falke,
R.B.Bass,
S.L.Butler,
S.A.Chervitz,
and
M.A.Danielson
(1997).
The two-component signaling pathway of bacterial chemotaxis: a molecular view of signal transduction by receptors, kinases, and adaptation enzymes.
|
| |
Annu Rev Cell Dev Biol,
13,
457-512.
|
|
|
|
|
|
|
J.M.Betton,
J.P.Jacob,
M.Hofnung,
and
J.K.Broome-Smith
(1997).
Creating a bifunctional protein by insertion of beta-lactamase into the maltodextrin-binding protein.
|
| |
Nat Biotechnol,
15,
1276-1279.
|
|
|
|
|
|
|
J.S.Marvin,
E.E.Corcoran,
N.A.Hattangadi,
J.V.Zhang,
S.A.Gere,
and
H.W.Hellinga
(1997).
The rational design of allosteric interactions in a monomeric protein and its applications to the construction of biosensors.
|
| |
Proc Natl Acad Sci U S A,
94,
4366-4371.
|
|
|
|
|
|
|
J.Trewhella
(1997).
Insights into biomolecular function from small-angle scattering.
|
| |
Curr Opin Struct Biol,
7,
702-708.
|
|
|
|
|
|
|
S.H.Sleigh,
J.R.Tame,
E.J.Dodson,
and
A.J.Wilkinson
(1997).
Peptide binding in OppA, the crystal structures of the periplasmic oligopeptide binding protein in the unliganded form and in complex with lysyllysine.
|
| |
Biochemistry,
36,
9747-9758.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
S.Szmelcman,
N.Sassoon,
and
M.Hofnung
(1997).
Residues in the alpha helix 7 of the bacterial maltose binding protein which are important in interactions with the Mal FGK2 complex.
|
| |
Protein Sci,
6,
628-636.
|
|
|
|
|
|
|
T.B.Woolf
(1997).
Molecular dynamics of individual alpha-helices of bacteriorhodopsin in dimyristol phosphatidylocholine. I. Structure and dynamics.
|
| |
Biophys J,
73,
2376-2392.
|
|
|
|
|
|
|
T.E.Blank,
M.P.Woods,
C.M.Lebo,
P.Xin,
and
J.E.Hopper
(1997).
Novel Gal3 proteins showing altered Gal80p binding cause constitutive transcription of Gal4p-activated genes in Saccharomyces cerevisiae.
|
| |
Mol Cell Biol,
17,
2566-2575.
|
|
|
|
|
|
|
V.Novokhatny,
and
K.Ingham
(1997).
Thermodynamics of maltose binding protein unfolding.
|
| |
Protein Sci,
6,
141-146.
|
|
|
|
|
|
|
A.Wolf,
K.C.Lee,
J.F.Kirsch,
and
G.F.Ames
(1996).
Ligand-dependent conformational plasticity of the periplasmic histidine-binding protein HisJ. Involvement in transport specificity.
|
| |
J Biol Chem,
271,
21243-21250.
|
|
|
|
|
|
|
F.A.Quiocho,
and
P.S.Ledvina
(1996).
Atomic structure and specificity of bacterial periplasmic receptors for active transport and chemotaxis: variation of common themes.
|
| |
Mol Microbiol,
20,
17-25.
|
|
|
|
|
|
|
G.F.Ames,
C.E.Liu,
A.K.Joshi,
and
K.Nikaido
(1996).
Liganded and unliganded receptors interact with equal affinity with the membrane complex of periplasmic permeases, a subfamily of traffic ATPases.
|
| |
J Biol Chem,
271,
14264-14270.
|
|
|
|
|
|
|
G.V.Louie,
P.D.Brownlie,
R.Lambert,
J.B.Cooper,
T.L.Blundell,
S.P.Wood,
V.N.Malashkevich,
A.Hädener,
M.J.Warren,
and
P.M.Shoolingin-Jordan
(1996).
The three-dimensional structure of Escherichia coli porphobilinogen deaminase at 1.76-A resolution.
|
| |
Proteins,
25,
48-78.
|
|
|
|
|
|
|
M.A.Danielson,
and
J.J.Falke
(1996).
Use of 19F NMR to probe protein structure and conformational changes.
|
| |
Annu Rev Biophys Biomol Struct,
25,
163-195.
|
|
|
|
|
|
|
S.Sugiyama,
Y.Matsuo,
K.Maenaka,
D.G.Vassylyev,
M.Matsushima,
K.Kashiwagi,
K.Igarashi,
and
K.Morikawa
(1996).
The 1.8-A X-ray structure of the Escherichia coli PotD protein complexed with spermidine and the mechanism of polyamine binding.
|
| |
Protein Sci,
5,
1984-1990.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
Y.Zhang,
D.E.Mannering,
A.L.Davidson,
N.Yao,
and
M.D.Manson
(1996).
Maltose-binding protein containing an interdomain disulfide bridge confers a dominant-negative phenotype for transport and chemotaxis.
|
| |
J Biol Chem,
271,
17881-17889.
|
|
|
|
|
|
|
A.M.Stock,
and
S.L.Mowbray
(1995).
Bacterial chemotaxis: a field in motion.
|
| |
Curr Opin Struct Biol,
5,
744-751.
|
|
|
|
|
|
|
A.Wolf,
E.W.Shaw,
B.H.Oh,
H.De Bondt,
A.K.Joshi,
and
G.F.Ames
(1995).
Structure/function analysis of the periplasmic histidine-binding protein. Mutations decreasing ligand binding alter the properties of the conformational change and of the closed form.
|
| |
J Biol Chem,
270,
16097-16106.
|
|
|
|
|
|
|
C.L.Careaga,
J.Sutherland,
J.Sabeti,
and
J.J.Falke
(1995).
Large amplitude twisting motions of an interdomain hinge: a disulfide trapping study of the galactose-glucose binding protein.
|
| |
Biochemistry,
34,
3048-3055.
|
|
|
|
|
|
|
J.R.Tame,
E.J.Dodson,
G.Murshudov,
C.F.Higgins,
and
A.J.Wilkinson
(1995).
The crystal structures of the oligopeptide-binding protein OppA complexed with tripeptide and tetrapeptide ligands.
|
| |
Structure,
3,
1395-1406.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.A.Schumacher,
K.Y.Choi,
F.Lu,
H.Zalkin,
and
R.G.Brennan
(1995).
Mechanism of corepressor-mediated specific DNA binding by the purine repressor.
|
| |
Cell,
83,
147-155.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.D.Paulsen,
and
R.L.Ornstein
(1995).
Dramatic differences in the motions of the mouth of open and closed cytochrome P450BM-3 by molecular dynamics simulations.
|
| |
Proteins,
21,
237-243.
|
|
|
|
|
|
|
S.Trakhanov,
and
F.A.Quiocho
(1995).
Influence of divalent cations in protein crystallization.
|
| |
Protein Sci,
4,
1914-1919.
|
|
|
|
|
|
|
W.R.Cannon,
J.M.Briggs,
J.Shen,
J.A.McCammon,
and
F.A.Quiocho
(1995).
Conservative and nonconservative mutations in proteins: anomalous mutations in a transport receptor analyzed by free energy and quantum chemical calculations.
|
| |
Protein Sci,
4,
387-393.
|
|
|
|
|
|
|
A.Vrielink,
W.Rüger,
H.P.Driessen,
and
P.S.Freemont
(1994).
Crystal structure of the DNA modifying enzyme beta-glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose.
|
| |
EMBO J,
13,
3413-3422.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
B.Schwermann,
K.Pfau,
B.Liliensiek,
M.Schleyer,
T.Fischer,
and
E.P.Bakker
(1994).
Purification, properties and structural aspects of a thermoacidophilic alpha-amylase from Alicyclobacillus acidocaldarius atcc 27009. Insight into acidostability of proteins.
|
| |
Eur J Biochem,
226,
981-991.
|
|
|
|
|
|
|
J.Jäger,
S.J.Smerdon,
J.Wang,
D.C.Boisvert,
and
T.A.Steitz
(1994).
Comparison of three different crystal forms shows HIV-1 reverse transcriptase displays an internal swivel motion.
|
| |
Structure,
2,
869-876.
|
|
|
|
|
|
|
K.M.Covitz,
C.H.Panagiotidis,
L.I.Hor,
M.Reyes,
N.A.Treptow,
and
H.A.Shuman
(1994).
Mutations that alter the transmembrane signalling pathway in an ATP binding cassette (ABC) transporter.
|
| |
EMBO J,
13,
1752-1759.
|
|
|
|
|
|
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
code is
shown on the right.
|
|
Links
