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PDBsum entry 2qdf
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Membrane protein, protein transport
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PDB id
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2qdf
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Contents |
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* Residue conservation analysis
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DOI no:
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Science
317:961-964
(2007)
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PubMed id:
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Structure and function of an essential component of the outer membrane protein assembly machine.
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S.Kim,
J.C.Malinverni,
P.Sliz,
T.J.Silhavy,
S.C.Harrison,
D.Kahne.
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ABSTRACT
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Integral beta-barrel proteins are found in the outer membranes of mitochondria,
chloroplasts, and Gram-negative bacteria. The machine that assembles these
proteins contains an integral membrane protein, called YaeT in Escherichia coli,
which has one or more polypeptide transport-associated (POTRA) domains. The
crystal structure of a periplasmic fragment of YaeT reveals the POTRA domain
fold and suggests a model for how POTRA domains can bind different peptide
sequences, as required for a machine that handles numerous beta-barrel protein
precursors. Analysis of POTRA domain deletions shows which are essential and
provides a view of the spatial organization of this assembly machine.
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Selected figure(s)
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Figure 1.
Fig. 1. Diagram of bacterial outer membrane protein (OMP)
biogenesis.
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Figure 2.
Fig. 2. Structure of YaeT. (A) Domain organization. (B) X-ray
structure of YaeT[21-351]. POTRA domains P1 to P4 are colored
yellow, green, blue, and red, respectively. The eight residues
from P5 are colored gray. The missing electron density in the P3
domain is represented by a dashed line. (C) Ribbon diagram of a
POTRA domain (P2) with side chains of the conserved residues
shown. (D) Sequence alignments of POTRA domains from selected
members of the YaeT/Omp85, Sam50, and Toc75 families, found in
Gram-negative bacteria, mitochondria, and chloroplasts or
cyanobacteria, respectively [adapted from Sánchez-Pulido
et al. (14)]. Conserved residues are highlighted (28). The
intensity of the orange color reflects the level of conservation
in physicochemical properties. (E) X-ray structure of the dimer.
The POTRA domains in one monomer are colored as in (B); the
other monomer is purple. (F) Dimer interface showing the
C-terminal residue contacts of one monomer (gray) to the P2
(light green) and P3 (light blue) domains of the other monomer.
Labels represent hydrophobic residues. L, Leu; Y, Tyr; F, Phe;
V, Val; I, Ile; T, Thr.
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The above figures are
reprinted
by permission from the AAAs:
Science
(2007,
317,
961-964)
copyright 2007.
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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.L.Leyton,
A.E.Rossiter,
and
I.R.Henderson
(2012).
From self sufficiency to dependence: mechanisms and factors important for autotransporter biogenesis.
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Nat Rev Microbiol,
10,
213-225.
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J.Selkrig,
K.Mosbahi,
C.T.Webb,
M.J.Belousoff,
A.J.Perry,
T.J.Wells,
F.Morris,
D.L.Leyton,
M.Totsika,
M.D.Phan,
N.Celik,
M.Kelly,
C.Oates,
E.L.Hartland,
R.M.Robins-Browne,
S.H.Ramarathinam,
A.W.Purcell,
M.A.Schembri,
R.A.Strugnell,
I.R.Henderson,
D.Walker,
and
T.Lithgow
(2012).
Discovery of an archetypal protein transport system in bacterial outer membranes.
|
| |
Nat Struct Mol Biol,
19,
506.
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E.Freinkman,
S.S.Chng,
and
D.Kahne
(2011).
The complex that inserts lipopolysaccharide into the bacterial outer membrane forms a two-protein plug-and-barrel.
|
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Proc Natl Acad Sci U S A,
108,
2486-2491.
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|
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|
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E.Schleiff,
and
T.Becker
(2011).
Common ground for protein translocation: access control for mitochondria and chloroplasts.
|
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Nat Rev Mol Cell Biol,
12,
48-59.
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E.Schleiff,
U.G.Maier,
and
T.Becker
(2011).
Omp85 in eukaryotic systems: one protein family with distinct functions.
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Biol Chem,
392,
21-27.
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G.Chimalakonda,
N.Ruiz,
S.S.Chng,
R.A.Garner,
D.Kahne,
and
T.J.Silhavy
(2011).
Lipoprotein LptE is required for the assembly of LptD by the beta-barrel assembly machine in the outer membrane of Escherichia coli.
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Proc Natl Acad Sci U S A,
108,
2492-2497.
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K.Imai,
N.Fujita,
M.M.Gromiha,
and
P.Horton
(2011).
Eukaryote-wide sequence analysis of mitochondrial β-barrel outer membrane proteins.
|
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BMC Genomics,
12,
79.
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T.Endo,
S.Kawano,
and
K.Yamano
(2011).
BamE structure: the assembly of β-barrel proteins in the outer membranes of bacteria and mitochondria.
|
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EMBO Rep,
12,
94-95.
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|
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|
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T.J.Knowles,
D.F.Browning,
M.Jeeves,
R.Maderbocus,
S.Rajesh,
P.Sridhar,
E.Manoli,
D.Emery,
U.Sommer,
A.Spencer,
D.L.Leyton,
D.Squire,
R.R.Chaudhuri,
M.R.Viant,
A.F.Cunningham,
I.R.Henderson,
and
M.Overduin
(2011).
Structure and function of BamE within the outer membrane and the β-barrel assembly machine.
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EMBO Rep,
12,
123-128.
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PDB code:
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V.Karuppiah,
J.L.Berry,
and
J.P.Derrick
(2011).
Outer membrane translocons: structural insights into channel formation.
|
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Trends Microbiol,
19,
40-48.
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A.Ebie Tan,
N.K.Burgess,
D.S.DeAndrade,
J.D.Marold,
and
K.G.Fleming
(2010).
Self-association of unfolded outer membrane proteins.
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Macromol Biosci,
10,
763-767.
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C.L.Hagan,
S.Kim,
and
D.Kahne
(2010).
Reconstitution of outer membrane protein assembly from purified components.
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Science,
328,
890-892.
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C.S.Hayes,
S.K.Aoki,
and
D.A.Low
(2010).
Bacterial contact-dependent delivery systems.
|
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Annu Rev Genet,
44,
71-90.
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|
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|
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D.Bennion,
E.S.Charlson,
E.Coon,
and
R.Misra
(2010).
Dissection of β-barrel outer membrane protein assembly pathways through characterizing BamA POTRA 1 mutants of Escherichia coli.
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Mol Microbiol,
77,
1153-1171.
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|
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|
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D.M.Walther,
M.P.Bos,
D.Rapaport,
and
J.Tommassen
(2010).
The mitochondrial porin, VDAC, has retained the ability to be assembled in the bacterial outer membrane.
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Mol Biol Evol,
27,
887-895.
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|
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|
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|
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J.Tommassen
(2010).
Assembly of outer-membrane proteins in bacteria and mitochondria.
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Microbiology,
156,
2587-2596.
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|
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K.Anwari,
S.Poggio,
A.Perry,
X.Gatsos,
S.H.Ramarathinam,
N.A.Williamson,
N.Noinaj,
S.Buchanan,
K.Gabriel,
A.W.Purcell,
C.Jacobs-Wagner,
and
T.Lithgow
(2010).
A modular BAM complex in the outer membrane of the alpha-proteobacterium Caulobacter crescentus.
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PLoS One,
5,
e8619.
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L.Bullmann,
R.Haarmann,
O.Mirus,
R.Bredemeier,
F.Hempel,
U.G.Maier,
and
E.Schleiff
(2010).
Filling the gap, evolutionarily conserved Omp85 in plastids of chromalveolates.
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J Biol Chem,
285,
6848-6856.
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P.Z.Gatzeva-Topalova,
L.R.Warner,
A.Pardi,
and
M.C.Sousa
(2010).
Structure and flexibility of the complete periplasmic domain of BamA: the protein insertion machine of the outer membrane.
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Structure,
18,
1492-1501.
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PDB code:
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T.Arnold,
K.Zeth,
and
D.Linke
(2010).
Omp85 from the thermophilic cyanobacterium Thermosynechococcus elongatus differs from proteobacterial Omp85 in structure and domain composition.
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J Biol Chem,
285,
18003-18015.
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PDB code:
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T.J.Silhavy,
D.Kahne,
and
S.Walker
(2010).
The bacterial cell envelope.
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Cold Spring Harb Perspect Biol,
2,
a000414.
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T.M.Voegel,
J.G.Warren,
A.Matsumoto,
M.M.Igo,
and
B.C.Kirkpatrick
(2010).
Localization and characterization of Xylella fastidiosa haemagglutinin adhesins.
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Microbiology,
156,
2172-2179.
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T.R.Lenhart,
and
D.R.Akins
(2010).
Borrelia burgdorferi locus BB0795 encodes a BamA orthologue required for growth and efficient localization of outer membrane proteins.
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Mol Microbiol,
75,
692-709.
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U.Lehr,
M.Schütz,
P.Oberhettinger,
F.Ruiz-Perez,
J.W.Donald,
T.Palmer,
D.Linke,
I.R.Henderson,
and
I.B.Autenrieth
(2010).
C-terminal amino acid residues of the trimeric autotransporter adhesin YadA of Yersinia enterocolitica are decisive for its recognition and assembly by BamA.
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Mol Microbiol,
78,
932-946.
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A.C.Meli,
M.Kondratova,
V.Molle,
L.Coquet,
A.V.Kajava,
and
N.Saint
(2009).
EtpB is a pore-forming outer membrane protein showing TpsB protein features involved in the two-partner secretion system.
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J Membr Biol,
230,
143-154.
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A.Chacinska,
C.M.Koehler,
D.Milenkovic,
T.Lithgow,
and
N.Pfanner
(2009).
Importing mitochondrial proteins: machineries and mechanisms.
|
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Cell,
138,
628-644.
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|
|
|
|
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C.S.Hayes,
and
D.A.Low
(2009).
Signals of growth regulation in bacteria.
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Curr Opin Microbiol,
12,
667-673.
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|
|
|
|
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D.M.Walther,
D.Rapaport,
and
J.Tommassen
(2009).
Biogenesis of beta-barrel membrane proteins in bacteria and eukaryotes: evolutionary conservation and divergence.
|
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Cell Mol Life Sci,
66,
2789-2804.
|
|
|
|
|
|
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E.B.Volokhina,
F.Beckers,
J.Tommassen,
and
M.P.Bos
(2009).
The beta-barrel outer membrane protein assembly complex of Neisseria meningitidis.
|
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J Bacteriol,
191,
7074-7085.
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|
|
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|
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F.Jacob-Dubuisson,
V.Villeret,
B.Clantin,
A.S.Delattre,
and
N.Saint
(2009).
First structural insights into the TpsB/Omp85 superfamily.
|
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Biol Chem,
390,
675-684.
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|
|
|
|
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J.Brockmeyer,
S.Spelten,
T.Kuczius,
M.Bielaszewska,
and
H.Karch
(2009).
Structure and function relationship of the autotransport and proteolytic activity of EspP from Shiga toxin-producing Escherichia coli.
|
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PLoS One,
4,
e6100.
|
|
|
|
|
|
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J.J.Díaz-Mejía,
M.Babu,
and
A.Emili
(2009).
Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome.
|
| |
FEMS Microbiol Rev,
33,
66-97.
|
|
|
|
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|
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M.G.Blango,
and
M.A.Mulvey
(2009).
Bacterial landlines: contact-dependent signaling in bacterial populations.
|
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Curr Opin Microbiol,
12,
177-181.
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R.Ieva,
and
H.D.Bernstein
(2009).
Interaction of an autotransporter passenger domain with BamA during its translocation across the bacterial outer membrane.
|
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Proc Natl Acad Sci U S A,
106,
19120-19125.
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S.K.Aoki,
J.S.Webb,
B.A.Braaten,
and
D.A.Low
(2009).
Contact-dependent growth inhibition causes reversible metabolic downregulation in Escherichia coli.
|
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J Bacteriol,
191,
1777-1786.
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|
|
|
|
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S.Masson,
T.Kern,
A.Le Gouëllec,
C.Giustini,
J.P.Simorre,
P.Callow,
T.Vernet,
F.Gabel,
and
A.Zapun
(2009).
Central domain of DivIB caps the C-terminal regions of the FtsL/DivIC coiled-coil rod.
|
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J Biol Chem,
284,
27687-27700.
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|
|
|
|
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T.A.Walton,
C.M.Sandoval,
C.A.Fowler,
A.Pardi,
and
M.C.Sousa
(2009).
The cavity-chaperone Skp protects its substrate from aggregation but allows independent folding of substrate domains.
|
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Proc Natl Acad Sci U S A,
106,
1772-1777.
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|
|
|
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|
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T.Becker,
M.Gebert,
N.Pfanner,
and
M.van der Laan
(2009).
Biogenesis of mitochondrial membrane proteins.
|
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Curr Opin Cell Biol,
21,
484-493.
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|
|
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|
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T.J.Knowles,
A.Scott-Tucker,
M.Overduin,
and
I.R.Henderson
(2009).
Membrane protein architects: the role of the BAM complex in outer membrane protein assembly.
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Nat Rev Microbiol,
7,
206-214.
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F.van den Ent,
T.M.Vinkenvleugel,
A.Ind,
P.West,
D.Veprintsev,
N.Nanninga,
T.den Blaauwen,
and
J.Löwe
(2008).
Structural and mutational analysis of the cell division protein FtsQ.
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Mol Microbiol,
68,
110-123.
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PDB codes:
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H.J.Wu,
A.H.Wang,
and
M.P.Jennings
(2008).
Discovery of virulence factors of pathogenic bacteria.
|
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Curr Opin Chem Biol,
12,
93.
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|
|
|
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|
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J.Nesper,
A.Brosig,
P.Ringler,
G.J.Patel,
S.A.Müller,
J.H.Kleinschmidt,
W.Boos,
K.Diederichs,
and
W.Welte
(2008).
Omp85(Tt) from Thermus thermophilus HB27: an ancestral type of the Omp85 protein family.
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J Bacteriol,
190,
4568-4575.
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K.M.Watts,
and
D.A.Hunstad
(2008).
Components of SurA required for outer membrane biogenesis in uropathogenic Escherichia coli.
|
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PLoS ONE,
3,
e3359.
|
|
|
|
|
|
|
N.C.Grassly,
and
C.Fraser
(2008).
Mathematical models of infectious disease transmission.
|
| |
Nat Rev Microbiol,
6,
477-487.
|
|
|
|
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P.Vuong,
D.Bennion,
J.Mantei,
D.Frost,
and
R.Misra
(2008).
Analysis of YfgL and YaeT interactions through bioinformatics, mutagenesis, and biochemistry.
|
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J Bacteriol,
190,
1507-1517.
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P.Z.Gatzeva-Topalova,
T.A.Walton,
and
M.C.Sousa
(2008).
Crystal structure of YaeT: conformational flexibility and substrate recognition.
|
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Structure,
16,
1873-1881.
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PDB code:
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S.K.Aoki,
J.C.Malinverni,
K.Jacoby,
B.Thomas,
R.Pamma,
B.N.Trinh,
S.Remers,
J.Webb,
B.A.Braaten,
T.J.Silhavy,
and
D.A.Low
(2008).
Contact-dependent growth inhibition requires the essential outer membrane protein BamA (YaeT) as the receptor and the inner membrane transport protein AcrB.
|
| |
Mol Microbiol,
70,
323-340.
|
|
|
|
|
|
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S.Ruer,
G.Ball,
A.Filloux,
and
S.de Bentzmann
(2008).
The 'P-usher', a novel protein transporter involved in fimbrial assembly and TpsA secretion.
|
| |
EMBO J,
27,
2669-2680.
|
|
|
|
|
|
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T.J.Knowles,
M.Jeeves,
S.Bobat,
F.Dancea,
D.McClelland,
T.Palmer,
M.Overduin,
and
I.R.Henderson
(2008).
Fold and function of polypeptide transport-associated domains responsible for delivering unfolded proteins to membranes.
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Mol Microbiol,
68,
1216-1227.
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PDB code:
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W.A.Kaserer,
X.Jiang,
Q.Xiao,
D.C.Scott,
M.Bauler,
D.Copeland,
S.M.Newton,
and
P.E.Klebba
(2008).
Insight from TonB hybrid proteins into the mechanism of iron transport through the outer membrane.
|
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J Bacteriol,
190,
4001-4016.
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X.Gatsos,
A.J.Perry,
K.Anwari,
P.Dolezal,
P.P.Wolynec,
V.A.Likić,
A.W.Purcell,
S.K.Buchanan,
and
T.Lithgow
(2008).
Protein secretion and outer membrane assembly in Alphaproteobacteria.
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FEMS Microbiol Rev,
32,
995.
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Y.Tashiro,
N.Nomura,
R.Nakao,
H.Senpuku,
R.Kariyama,
H.Kumon,
S.Kosono,
H.Watanabe,
T.Nakajima,
and
H.Uchiyama
(2008).
Opr86 is essential for viability and is a potential candidate for a protective antigen against biofilm formation by Pseudomonas aeruginosa.
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J Bacteriol,
190,
3969-3978.
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E.Papanikou,
S.Karamanou,
and
A.Economou
(2007).
Bacterial protein secretion through the translocase nanomachine.
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Nat Rev Microbiol,
5,
839-851.
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M.P.Bos,
V.Robert,
and
J.Tommassen
(2007).
Functioning of outer membrane protein assembly factor Omp85 requires a single POTRA domain.
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EMBO Rep,
8,
1149-1154.
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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
code is
shown on the right.
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