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Contents |
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(+ 5 more)
60 a.a.
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66 a.a.
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* Residue conservation analysis
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PDB id:
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Translation
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Title:
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1.55 a crystal structure of the pleiotropic translational regulator, hfq
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Structure:
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Host factor for q beta. Chain: a, b, h, i, k, m, s, t, y, n, r, w. Synonym: hfq. Engineered: yes
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Source:
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Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Biol. unit:
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Dodecamer (from
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Resolution:
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1.55Å
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R-factor:
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0.237
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R-free:
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0.259
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Authors:
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M.A.Schumacher,R.F.Pearson,T.Moller,P.Valentin-Hansen,R.G.Brennan
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Key ref:
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M.A.Schumacher
et al.
(2002).
Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein.
EMBO J,
21,
3546-3556.
PubMed id:
DOI:
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Date:
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03-Jan-02
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Release date:
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10-Jul-02
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PROCHECK
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Headers
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References
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Enzyme class:
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Chains A, B, H, I, K, M, S, T, Y, N, R, W:
E.C.?
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DOI no:
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EMBO J
21:3546-3556
(2002)
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PubMed id:
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Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein.
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M.A.Schumacher,
R.F.Pearson,
T.Møller,
P.Valentin-Hansen,
R.G.Brennan.
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ABSTRACT
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In prokaryotes, Hfq regulates translation by modulating the structure of
numerous RNA molecules by binding preferentially to A/U-rich sequences. To
elucidate the mechanisms of target recognition and translation regulation by
Hfq, we determined the crystal structures of the Staphylococcus aureus Hfq and
an Hfq-RNA complex to 1.55 and 2.71 A resolution, respectively. The structures
reveal that Hfq possesses the Sm-fold previously observed only in eukaryotes and
archaea. However, unlike these heptameric Sm proteins, Hfq forms a
homo-hexameric ring. The Hfq-RNA structure reveals that the single-stranded
hepta-oligoribonucleotide binds in a circular conformation around a central
basic cleft, whereby Tyr42 residues from adjacent subunits stack with six of the
bases, and Gln8, outside the Sm motif, provides key protein-base contacts. Such
binding suggests a mechanism for Hfq function.
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Selected figure(s)
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Figure 1.
Figure 1 The structure of Hfq. (A) Structure of the Hfq monomer
shown as a ribbon diagram. Secondary structural elements are
labeled, as are the first (N) and last (C) residues observed.
Figures 1A−C, 2B−D, 3A, 4B and C and 6 were made with
Swiss-PdbViewer and rendered with POVRAY (Guex and Peitsch,
1997; POVRAY, Persistence of Vision Raytracer version 3.1
http://www.povray.org). (B) Structure of the Hfq hexamer with
each subunit colored differently. (C) The two Hfq hexamers in
the crystallographic asymmetric unit. This view is rotated
90° to (B) along the vertical axis in the plane of the
paper. Interactions between the two rings are made by residues
from the hydrophobic surface of each hexamer (see Figure 5B).
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Figure 6.
Figure 6 RNA recognition by Hfq. Cross-eyed stereo view of the
5' adenine- and uracil-binding pockets. Hydrogen bonds are shown
as black lines. All residues that contact the nucleotide are
located within the Sm1 and Sm2 motifs (shown as sticks), with
the exception of conserved residue Gln8, which is located on
helix  1
and colored according to atom type (blue, red and yellow for
nitrogen, oxygen and carbon).
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2002,
21,
3546-3556)
copyright 2002.
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Figures were
selected
by an automated process.
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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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|
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F.Geinguenaud,
V.Calandrini,
J.Teixeira,
C.Mayer,
J.Liquier,
C.Lavelle,
and
V.Arluison
(2011).
Conformational transition of DNA bound to Hfq probed by infrared spectroscopy.
|
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Phys Chem Chem Phys,
13,
1222-1229.
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|
|
|
|
|
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J.S.Nielsen,
M.H.Christiansen,
M.Bonde,
S.Gottschalk,
D.Frees,
L.E.Thomsen,
and
B.H.Kallipolitis
(2011).
Searching for small σB-regulated genes in Staphylococcus aureus.
|
| |
Arch Microbiol,
193,
23-34.
|
|
|
|
|
|
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K.Semrad
(2011).
Proteins with RNA chaperone activity: a world of diverse proteins with a common task-impediment of RNA misfolding.
|
| |
Biochem Res Int,
2011,
532908.
|
|
|
|
|
|
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S.Fischer,
J.Benz,
B.Späth,
A.Jellen-Ritter,
R.Heyer,
M.Dörr,
L.K.Maier,
C.Menzel-Hobeck,
M.Lehr,
K.Jantzer,
J.Babski,
J.Soppa,
and
A.Marchfelder
(2011).
Regulatory RNAs in Haloferax volcanii.
|
| |
Biochem Soc Trans,
39,
159-162.
|
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|
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|
|
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A.Boysen,
J.Møller-Jensen,
B.Kallipolitis,
P.Valentin-Hansen,
and
M.Overgaard
(2010).
Translational regulation of gene expression by an anaerobically induced small non-coding RNA in Escherichia coli.
|
| |
J Biol Chem,
285,
10690-10702.
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|
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C.Lorenz,
T.Gesell,
B.Zimmermann,
U.Schoeberl,
I.Bilusic,
L.Rajkowitsch,
C.Waldsich,
A.von Haeseler,
and
R.Schroeder
(2010).
Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts.
|
| |
Nucleic Acids Res,
38,
3794-3808.
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|
|
|
|
|
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E.Kühn-Hölsken,
C.Lenz,
A.Dickmanns,
H.H.Hsiao,
F.M.Richter,
B.Kastner,
R.Ficner,
and
H.Urlaub
(2010).
Mapping the binding site of snurportin 1 on native U1 snRNP by cross-linking and mass spectrometry.
|
| |
Nucleic Acids Res,
38,
5581-5593.
|
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|
|
|
|
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G.Bai,
A.Golubov,
E.A.Smith,
and
K.A.McDonough
(2010).
The importance of the small RNA chaperone Hfq for growth of epidemic Yersinia pestis, but not Yersinia pseudotuberculosis, with implications for plague biology.
|
| |
J Bacteriol,
192,
4239-4245.
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|
|
|
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|
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J.S.Hankins,
H.Denroche,
and
G.A.Mackie
(2010).
Interactions of the RNA-binding protein Hfq with cspA mRNA, encoding the major cold shock protein.
|
| |
J Bacteriol,
192,
2482-2490.
|
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|
|
|
|
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J.S.Nielsen,
L.K.Lei,
T.Ebersbach,
A.S.Olsen,
J.K.Klitgaard,
P.Valentin-Hansen,
and
B.H.Kallipolitis
(2010).
Defining a role for Hfq in Gram-positive bacteria: evidence for Hfq-dependent antisense regulation in Listeria monocytogenes.
|
| |
Nucleic Acids Res,
38,
907-919.
|
|
|
|
|
|
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K.Kobayashi,
I.Kikuno,
K.Kuroha,
K.Saito,
K.Ito,
R.Ishitani,
T.Inada,
and
O.Nureki
(2010).
Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1α complex.
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Proc Natl Acad Sci U S A,
107,
17575-17579.
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PDB codes:
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L.Barra-Bily,
S.P.Pandey,
A.Trautwetter,
C.Blanco,
and
G.C.Walker
(2010).
The Sinorhizobium meliloti RNA chaperone Hfq mediates symbiosis of S. meliloti and alfalfa.
|
| |
J Bacteriol,
192,
1710-1718.
|
|
|
|
|
|
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L.Jelsbak,
H.Ingmer,
L.Valihrach,
M.T.Cohn,
M.H.Christiansen,
B.H.Kallipolitis,
and
D.Frees
(2010).
The chaperone ClpX stimulates expression of Staphylococcus aureus protein A by Rot dependent and independent pathways.
|
| |
PLoS One,
5,
e12752.
|
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|
|
|
|
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M.C.Lybecker,
C.A.Abel,
A.L.Feig,
and
D.S.Samuels
(2010).
Identification and function of the RNA chaperone Hfq in the Lyme disease spirochete Borrelia burgdorferi.
|
| |
Mol Microbiol,
78,
622-635.
|
|
|
|
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|
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M.D.Daugherty,
D.S.Booth,
B.Jayaraman,
Y.Cheng,
and
A.D.Frankel
(2010).
HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes.
|
| |
Proc Natl Acad Sci U S A,
107,
12481-12486.
|
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|
|
|
|
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N.N.Salim,
and
A.L.Feig
(2010).
An upstream Hfq binding site in the fhlA mRNA leader region facilitates the OxyS-fhlA interaction.
|
| |
PLoS One,
5,
0.
|
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|
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R.P.Galão,
A.Chari,
I.Alves-Rodrigues,
D.Lobão,
A.Mas,
C.Kambach,
U.Fischer,
and
J.Díez
(2010).
LSm1-7 complexes bind to specific sites in viral RNA genomes and regulate their translation and replication.
|
| |
RNA,
16,
817-827.
|
|
|
|
|
|
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S.D.Stojanović,
B.L.Zarić,
and
S.D.Zarić
(2010).
Protein subunit interfaces: a statistical analysis of hot spots in Sm proteins.
|
| |
J Mol Model,
16,
1743-1751.
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|
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T.Soper,
P.Mandin,
N.Majdalani,
S.Gottesman,
and
S.A.Woodson
(2010).
Positive regulation by small RNAs and the role of Hfq.
|
| |
Proc Natl Acad Sci U S A,
107,
9602-9607.
|
|
|
|
|
|
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Y.Liu,
N.Wu,
J.Dong,
Y.Gao,
X.Zhang,
C.Mu,
N.Shao,
and
G.Yang
(2010).
Hfq is a global regulator that controls the pathogenicity of Staphylococcus aureus.
|
| |
PLoS One,
5,
0.
|
|
|
|
|
|
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A.Bøggild,
M.Overgaard,
P.Valentin-Hansen,
and
D.E.Brodersen
(2009).
Cyanobacteria contain a structural homologue of the Hfq protein with altered RNA-binding properties.
|
| |
FEBS J,
276,
3904-3915.
|
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PDB codes:
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A.Jousselin,
L.Metzinger,
and
B.Felden
(2009).
On the facultative requirement of the bacterial RNA chaperone, Hfq.
|
| |
Trends Microbiol,
17,
399-405.
|
|
|
|
|
|
|
A.M.Hansen,
and
J.B.Kaper
(2009).
Hfq affects the expression of the LEE pathogenicity island in enterohaemorrhagic Escherichia coli.
|
| |
Mol Microbiol,
73,
446-465.
|
|
|
|
|
|
|
C.Ansong,
H.Yoon,
S.Porwollik,
H.Mottaz-Brewer,
B.O.Petritis,
N.Jaitly,
J.N.Adkins,
M.McClelland,
F.Heffron,
and
R.D.Smith
(2009).
Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation.
|
| |
PLoS ONE,
4,
e4809.
|
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|
|
|
|
|
D.Das,
P.Kozbial,
H.L.Axelrod,
M.D.Miller,
D.McMullan,
S.S.Krishna,
P.Abdubek,
C.Acosta,
T.Astakhova,
P.Burra,
D.Carlton,
C.Chen,
H.J.Chiu,
T.Clayton,
M.C.Deller,
L.Duan,
Y.Elias,
M.A.Elsliger,
D.Ernst,
C.Farr,
J.Feuerhelm,
A.Grzechnik,
S.K.Grzechnik,
J.Hale,
G.W.Han,
L.Jaroszewski,
K.K.Jin,
H.A.Johnson,
H.E.Klock,
M.W.Knuth,
A.Kumar,
D.Marciano,
A.T.Morse,
K.D.Murphy,
E.Nigoghossian,
A.Nopakun,
L.Okach,
S.Oommachen,
J.Paulsen,
C.Puckett,
R.Reyes,
C.L.Rife,
N.Sefcovic,
S.Sudek,
H.Tien,
C.Trame,
C.V.Trout,
H.van den Bedem,
D.Weekes,
A.White,
Q.Xu,
K.O.Hodgson,
J.Wooley,
A.M.Deacon,
A.Godzik,
S.A.Lesley,
and
I.A.Wilson
(2009).
Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution.
|
| |
Proteins,
75,
296-307.
|
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PDB code:
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D.Schilling,
and
U.Gerischer
(2009).
The Acinetobacter baylyi Hfq gene encodes a large protein with an unusual C terminus.
|
| |
J Bacteriol,
191,
5553-5562.
|
|
|
|
|
|
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E.Diestra,
B.Cayrol,
V.Arluison,
and
C.Risco
(2009).
Cellular electron microscopy imaging reveals the localization of the Hfq protein close to the bacterial membrane.
|
| |
PLoS One,
4,
e8301.
|
|
|
|
|
|
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J.F.Hopkins,
S.Panja,
S.A.McNeil,
and
S.A.Woodson
(2009).
Effect of salt and RNA structure on annealing and strand displacement by Hfq.
|
| |
Nucleic Acids Res,
37,
6205-6213.
|
|
|
|
|
|
|
K.L.Anderson,
and
P.M.Dunman
(2009).
Messenger RNA Turnover Processes in Escherichia coli, Bacillus subtilis, and Emerging Studies in Staphylococcus aureus.
|
| |
Int J Microbiol,
2009,
525491.
|
|
|
|
|
|
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S.C.Pulvermacher,
L.T.Stauffer,
and
G.V.Stauffer
(2009).
Role of the Escherichia coli Hfq protein in GcvB regulation of oppA and dppA mRNAs.
|
| |
Microbiology,
155,
115-123.
|
|
|
|
|
|
|
S.Veretnik,
C.Wills,
P.Youkharibache,
R.E.Valas,
and
P.E.Bourne
(2009).
Sm/Lsm genes provide a glimpse into the early evolution of the spliceosome.
|
| |
PLoS Comput Biol,
5,
e1000315.
|
|
|
|
|
|
|
T.M.Link,
P.Valentin-Hansen,
and
R.G.Brennan
(2009).
Structure of Escherichia coli Hfq bound to polyriboadenylate RNA.
|
| |
Proc Natl Acad Sci U S A,
106,
19292-19297.
|
|
|
PDB code:
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|
|
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A.Chowdhury,
and
S.Tharun
(2008).
lsm1 mutations impairing the ability of the Lsm1p-7p-Pat1p complex to preferentially bind to oligoadenylated RNA affect mRNA decay in vivo.
|
| |
RNA,
14,
2149-2158.
|
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|
|
|
|
|
A.S.Attia,
J.L.Sedillo,
W.Wang,
W.Liu,
C.A.Brautigam,
W.Winkler,
and
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(2008).
Moraxella catarrhalis expresses an unusual Hfq protein.
|
| |
Infect Immun,
76,
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|
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|
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L.Rajkowitsch,
E.Sonnleitner,
R.Schroeder,
and
U.Bläsi
(2008).
The C-terminal domain of Escherichia coli Hfq is required for regulation.
|
| |
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36,
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|
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|
D.G.Scofield,
and
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(2008).
Evolutionary diversification of the Sm family of RNA-associated proteins.
|
| |
Mol Biol Evol,
25,
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|
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|
F.Tritschler,
A.Eulalio,
S.Helms,
S.Schmidt,
M.Coles,
O.Weichenrieder,
E.Izaurralde,
and
V.Truffault
(2008).
Similar modes of interaction enable Trailer Hitch and EDC3 to associate with DCP1 and Me31B in distinct protein complexes.
|
| |
Mol Cell Biol,
28,
6695-6708.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Graille,
M.Chaillet,
and
H.van Tilbeurgh
(2008).
Structure of yeast Dom34: a protein related to translation termination factor Erf1 and involved in No-Go decay.
|
| |
J Biol Chem,
283,
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|
|
|
PDB codes:
|
|
|
|
|
|
|
|
R.Russell
(2008).
RNA misfolding and the action of chaperones.
|
| |
Front Biosci,
13,
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|
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|
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C.Chevalier,
P.Romby,
and
T.Geissmann
(2008).
RNA switches regulate initiation of translation in bacteria.
|
| |
Biol Chem,
389,
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|
|
|
|
|
|
|
T.Lee,
and
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(2008).
The RNA binding protein Hfq interacts specifically with tRNAs.
|
| |
RNA,
14,
514-523.
|
|
|
|
|
|
|
A.Chowdhury,
J.Mukhopadhyay,
and
S.Tharun
(2007).
The decapping activator Lsm1p-7p-Pat1p complex has the intrinsic ability to distinguish between oligoadenylated and polyadenylated RNAs.
|
| |
RNA,
13,
998.
|
|
|
|
|
|
|
C.Bohn,
C.Rigoulay,
and
P.Bouloc
(2007).
No detectable effect of RNA-binding protein Hfq absence in Staphylococcus aureus.
|
| |
BMC Microbiol,
7,
10.
|
|
|
|
|
|
|
F.Tritschler,
A.Eulalio,
V.Truffault,
M.D.Hartmann,
S.Helms,
S.Schmidt,
M.Coles,
E.Izaurralde,
and
O.Weichenrieder
(2007).
A divergent Sm fold in EDC3 proteins mediates DCP1 binding and P-body targeting.
|
| |
Mol Cell Biol,
27,
8600-8611.
|
|
|
PDB codes:
|
|
|
|
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|
|
|
J.S.Nielsen,
A.Bøggild,
C.B.Andersen,
G.Nielsen,
A.Boysen,
D.E.Brodersen,
and
P.Valentin-Hansen
(2007).
An Hfq-like protein in archaea: crystal structure and functional characterization of the Sm protein from Methanococcus jannaschii.
|
| |
RNA,
13,
2213-2223.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
K.C.Tu,
and
B.L.Bassler
(2007).
Multiple small RNAs act additively to integrate sensory information and control quorum sensing in Vibrio harveyi.
|
| |
Genes Dev,
21,
221-233.
|
|
|
|
|
|
|
K.H.Chin,
S.K.Ruan,
A.H.Wang,
and
S.H.Chou
(2007).
XC5848, an ORFan protein from Xanthomonas campestris, adopts a novel variant of Sm-like motif.
|
| |
Proteins,
68,
1006-1010.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
L.Rajkowitsch,
and
R.Schroeder
(2007).
Dissecting RNA chaperone activity.
|
| |
RNA,
13,
2053-2060.
|
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|
|
|
|
|
R.G.Brennan,
and
T.M.Link
(2007).
Hfq structure, function and ligand binding.
|
| |
Curr Opin Microbiol,
10,
125-133.
|
|
|
|
|
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Acta Crystallogr D Biol Crystallogr,
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PDB codes:
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RNA,
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Genetics,
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T.L.McNealy,
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The Hfq homolog in Legionella pneumophila demonstrates regulation by LetA and RpoS and interacts with the global regulator CsrA.
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J Bacteriol,
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The Gemin6-Gemin7 heterodimer from the survival of motor neurons complex has an Sm protein-like structure.
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Structure,
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PDB code:
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G.Storz,
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The RNA-binding protein Hfq of Listeria monocytogenes: role in stress tolerance and virulence.
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J Bacteriol,
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Structural and functional analysis of ataxin-2 and ataxin-3.
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Eur J Biochem,
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P.J.Mikulecky,
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Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs.
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Nat Struct Mol Biol,
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The bacterial Sm-like protein Hfq: a key player in RNA transactions.
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Mol Microbiol,
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| |
RNA,
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PDB code:
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V.Anantharaman,
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Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability.
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The C-terminal domain of Escherichia coli Hfq increases the stability of the hexamer.
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Eur J Biochem,
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Homomeric ring assemblies of eukaryotic Sm proteins have affinity for both RNA and DNA. Crystal structure of an oligomeric complex of yeast SmF.
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J Biol Chem,
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PDB codes:
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B.Vecerek,
I.Moll,
T.Afonyushkin,
V.Kaberdin,
and
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Interaction of the RNA chaperone Hfq with mRNAs: direct and indirect roles of Hfq in iron metabolism of Escherichia coli.
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Mol Microbiol,
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C.C.Brescia,
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Identification of the Hfq-binding site on DsrA RNA: Hfq binds without altering DsrA secondary structure.
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RNA,
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C.Mura,
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Structure and assembly of an augmented Sm-like archaeal protein 14-mer.
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Proc Natl Acad Sci U S A,
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PDB code:
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C.Sauter,
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Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli.
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Nucleic Acids Res,
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PDB code:
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RNA chaperone activity of the Sm-like Hfq protein.
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RNA,
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Hfq affects the length and the frequency of short oligo(A) tails at the 3' end of Escherichia coli rpsO mRNAs.
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Nucleic Acids Res,
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Crystal structures of the Pyrococcus abyssi Sm core and its complex with RNA. Common features of RNA binding in archaea and eukarya.
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J Biol Chem,
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PDB codes:
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|
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T.M.Gruber,
and
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Multiple sigma subunits and the partitioning of bacterial transcription space.
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Accumulation of glucose 6-phosphate or fructose 6-phosphate is responsible for destabilization of glucose transporter mRNA in Escherichia coli.
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J Biol Chem,
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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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