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PDBsum entry 1csp
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Transcription regulation
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PDB id
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1csp
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Contents |
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* Residue conservation analysis
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Nature
364:164-168
(1993)
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PubMed id:
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Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein.
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H.Schindelin,
M.A.Marahiel,
U.Heinemann.
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ABSTRACT
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The cold-shock response in both Escherichia coli and Bacillus subtilis is
induced by an abrupt downshift in growth temperature. It leads to the increased
production of the major cold-shock proteins, CS7.4 and CspB, respectively. CS7.4
is a transcriptional activator of two genes. CS7.4 and CspB share 43 per cent
sequence identity with the nucleic acid-binding domain of the eukaryotic
gene-regulatory Y-box factors. This cold-shock domain is conserved from bacteria
to man and contains the RNA-binding RNP1 sequence motif. As a prototype of the
cold-shock domain, the structure of CspB has been determined here from two
crystal forms. In both, CspB is present as an antiparallel five-stranded
beta-barrel. Three consecutive beta-strands, the central one containing the RNP1
motif, create a surface rich in aromatic and basic residues that are presumably
involved in nucleic acid binding. Preferential binding of CspB to
single-stranded DNA is observed in gel retardation experiments.
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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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O.Blifernez,
L.Wobbe,
K.Niehaus,
and
O.Kruse
(2011).
Protein arginine methylation modulates light-harvesting antenna translation in Chlamydomonas reinhardtii.
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Plant J,
65,
119-130.
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G.Panicker,
N.Mojib,
T.Nakatsuji,
J.Aislabie,
and
A.K.Bej
(2010).
Occurrence and distribution of capB in Antarctic microorganisms and study of its structure and regulation in the Antarctic biodegradative Pseudomonas sp. 30/3.
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Extremophiles,
14,
171-183.
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H.Balhesteros,
R.R.Mazzon,
C.A.da Silva,
E.A.Lang,
and
M.V.Marques
(2010).
CspC and CspD are essential for Caulobacter crescentus stationary phase survival.
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Arch Microbiol,
192,
747-758.
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A.L.Stewart,
and
M.L.Waters
(2009).
Structural effects on ss- and dsDNA recognition by a beta-hairpin peptide.
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Chembiochem,
10,
539-544.
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H.Fu,
G.R.Grimsley,
A.Razvi,
J.M.Scholtz,
and
C.N.Pace
(2009).
Increasing protein stability by improving beta-turns.
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Proteins,
77,
491-498.
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J.D.Bloom,
and
M.J.Glassman
(2009).
Inferring stabilizing mutations from protein phylogenies: application to influenza hemagglutinin.
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PLoS Comput Biol,
5,
e1000349.
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P.K.Latha,
R.Soni,
M.Khan,
S.S.Marla,
and
R.Goel
(2009).
Exploration of Csp genes from temperate and glacier soils of the Indian Himalayas and in silico analysis of encoding proteins.
|
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Curr Microbiol,
58,
343-348.
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S.Phadtare,
and
K.Severinov
(2009).
Comparative analysis of changes in gene expression due to RNA melting activities of translation initiation factor IF1 and a cold shock protein of the CspA family.
|
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Genes Cells,
14,
1227-1239.
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C.D.Geierhaas,
X.Salvatella,
J.Clarke,
and
M.Vendruscolo
(2008).
Characterisation of transition state structures for protein folding using 'high', 'medium' and 'low' {Phi}-values.
|
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Protein Eng Des Sel,
21,
215-222.
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M.Sackewitz,
S.von Einem,
G.Hause,
M.Wunderlich,
F.X.Schmid,
and
E.Schwarz
(2008).
A folded and functional protein domain in an amyloid-like fibril.
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Protein Sci,
17,
1044-1054.
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V.Chaikam,
and
D.Karlson
(2008).
Functional characterization of two cold shock domain proteins from Oryza sativa.
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Plant Cell Environ,
31,
995.
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Y.Lin,
L.J.Lin,
P.Sriratana,
K.Coleman,
T.Ha,
M.Spies,
and
I.K.Cann
(2008).
Engineering of functional replication protein a homologs based on insights into the evolution of oligonucleotide/oligosaccharide-binding folds.
|
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J Bacteriol,
190,
5766-5780.
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A.Verma,
and
W.Wenzel
(2007).
Protein structure prediction by all-atom free-energy refinement.
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BMC Struct Biol,
7,
12.
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D.Nashchekin,
S.Masich,
T.Soop,
A.Kukalev,
E.Kovrigina,
O.Nashchekina,
and
B.Daneholt
(2007).
Two splicing isoforms of the Y-box protein ctYB-1 appear on the same mRNA molecule.
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FEBS J,
274,
202-211.
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H.P.Morgan,
P.Estibeiro,
M.A.Wear,
K.E.Max,
U.Heinemann,
L.Cubeddu,
M.P.Gallagher,
P.J.Sadler,
and
M.D.Walkinshaw
(2007).
Sequence specificity of single-stranded DNA-binding proteins: a novel DNA microarray approach.
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Nucleic Acids Res,
35,
e75.
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J.Will,
A.Kyas,
W.S.Sheldrick,
and
D.Wolters
(2007).
Identification of (eta6-arene)ruthenium(II) protein binding sites in E. coli cells by combined multidimensional liquid chromatography and ESI tandem mass spectrometry: specific binding of [(eta6-p-cymene)RuCl2 (DMSO)] to stress-regulated proteins and to helicases.
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J Biol Inorg Chem,
12,
883-894.
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K.E.Max,
M.Zeeb,
R.Bienert,
J.Balbach,
and
U.Heinemann
(2007).
Common mode of DNA binding to cold shock domains. Crystal structure of hexathymidine bound to the domain-swapped form of a major cold shock protein from Bacillus caldolyticus.
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FEBS J,
274,
1265-1279.
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PDB code:
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M.J.Kim,
Y.K.Lee,
H.K.Lee,
and
H.Im
(2007).
Characterization of cold-shock protein A of Antarctic Streptomyces sp. AA8321.
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Protein J,
26,
51-59.
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S.Phadtare,
T.Kazakov,
M.Bubunenko,
D.L.Court,
T.Pestova,
and
K.Severinov
(2007).
Transcription antitermination by translation initiation factor IF1.
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J Bacteriol,
189,
4087-4093.
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D.Johnston,
C.Tavano,
S.Wickner,
and
N.Trun
(2006).
Specificity of DNA binding and dimerization by CspE from Escherichia coli.
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J Biol Chem,
281,
40208-40215.
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K.Hunger,
C.L.Beckering,
F.Wiegeshoff,
P.L.Graumann,
and
M.A.Marahiel
(2006).
Cold-induced putative DEAD box RNA helicases CshA and CshB are essential for cold adaptation and interact with cold shock protein B in Bacillus subtilis.
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J Bacteriol,
188,
240-248.
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K.Nakaminami,
D.T.Karlson,
and
R.Imai
(2006).
Functional conservation of cold shock domains in bacteria and higher plants.
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Proc Natl Acad Sci U S A,
103,
10122-10127.
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M.Zeeb,
K.E.Max,
U.Weininger,
C.Löw,
H.Sticht,
and
J.Balbach
(2006).
Recognition of T-rich single-stranded DNA by the cold shock protein Bs-CspB in solution.
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Nucleic Acids Res,
34,
4561-4571.
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PDB code:
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X.Huang,
and
H.X.Zhou
(2006).
Similarity and difference in the unfolding of thermophilic and mesophilic cold shock proteins studied by molecular dynamics simulations.
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Biophys J,
91,
2451-2463.
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Y.Qiu,
S.Kathariou,
and
D.M.Lubman
(2006).
Proteomic analysis of cold adaptation in a Siberian permafrost bacterium--Exiguobacterium sibiricum 255-15 by two-dimensional liquid separation coupled with mass spectrometry.
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Proteomics,
6,
5221-5233.
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J.L.Ramos,
M.Martínez-Bueno,
A.J.Molina-Henares,
W.Terán,
K.Watanabe,
X.Zhang,
M.T.Gallegos,
R.Brennan,
and
R.Tobes
(2005).
The TetR family of transcriptional repressors.
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Microbiol Mol Biol Rev,
69,
326-356.
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V.G.Eijsink,
S.Gåseidnes,
T.V.Borchert,
and
B.van den Burg
(2005).
Directed evolution of enzyme stability.
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Biomol Eng,
22,
21-30.
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A.Jung,
C.Bamann,
W.Kremer,
H.R.Kalbitzer,
and
E.Brunner
(2004).
High-temperature solution NMR structure of TmCsp.
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Protein Sci,
13,
342-350.
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B.N.Dominy,
H.Minoux,
and
C.L.Brooks
(2004).
An electrostatic basis for the stability of thermophilic proteins.
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Proteins,
57,
128-141.
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O.Guvench,
and
C.L.Brooks
(2004).
Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations.
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J Comput Chem,
25,
1005-1014.
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R.Bienert,
M.Zeeb,
L.Dostál,
A.Feske,
C.Magg,
K.Max,
H.Welfle,
J.Balbach,
and
U.Heinemann
(2004).
Single-stranded DNA bound to bacterial cold-shock proteins: preliminary crystallographic and Raman analysis.
|
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Acta Crystallogr D Biol Crystallogr,
60,
755-757.
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G.Felix,
and
T.Boller
(2003).
Molecular sensing of bacteria in plants. The highly conserved RNA-binding motif RNP-1 of bacterial cold shock proteins is recognized as an elicitor signal in tobacco.
|
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J Biol Chem,
278,
6201-6208.
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H.X.Zhou,
and
F.Dong
(2003).
Electrostatic contributions to the stability of a thermophilic cold shock protein.
|
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Biophys J,
84,
2216-2222.
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M.P.Nekrasov,
M.P.Ivshina,
K.G.Chernov,
E.A.Kovrigina,
V.M.Evdokimova,
A.A.Thomas,
J.W.Hershey,
and
L.P.Ovchinnikov
(2003).
The mRNA-binding protein YB-1 (p50) prevents association of the eukaryotic initiation factor eIF4G with mRNA and inhibits protein synthesis at the initiation stage.
|
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J Biol Chem,
278,
13936-13943.
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M.S.Bae,
E.J.Cho,
E.Y.Choi,
and
O.K.Park
(2003).
Analysis of the Arabidopsis nuclear proteome and its response to cold stress.
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Plant J,
36,
652-663.
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M.Torrez,
M.Schultehenrich,
and
D.R.Livesay
(2003).
Conferring thermostability to mesophilic proteins through optimized electrostatic surfaces.
|
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Biophys J,
85,
2845-2853.
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M.Zeeb,
and
J.Balbach
(2003).
Single-stranded DNA binding of the cold-shock protein CspB from Bacillus subtilis: NMR mapping and mutational characterization.
|
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Protein Sci,
12,
112-123.
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S.Phadtare,
J.Hwang,
K.Severinov,
and
M.Inouye
(2003).
CspB and CspL, thermostable cold-shock proteins from Thermotoga maritima.
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Genes Cells,
8,
801-810.
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D.Perl,
and
F.X.Schmid
(2002).
Some like it hot: the molecular determinants of protein thermostability.
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Chembiochem,
3,
39-44.
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H.Delbrück,
G.Ziegelin,
E.Lanka,
and
U.Heinemann
(2002).
An Src homology 3-like domain is responsible for dimerization of the repressor protein KorB encoded by the promiscuous IncP plasmid RP4.
|
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J Biol Chem,
277,
4191-4198.
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PDB codes:
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H.X.Zhou
(2002).
Toward the physical basis of thermophilic proteins: linking of enriched polar interactions and reduced heat capacity of unfolding.
|
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Biophys J,
83,
3126-3133.
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M.C.Nonato,
J.Widom,
and
J.Clardy
(2002).
Crystal structure of the N-terminal segment of human eukaryotic translation initiation factor 2alpha.
|
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J Biol Chem,
277,
17057-17061.
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PDB code:
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M.H.Weber,
I.Fricke,
N.Doll,
and
M.A.Marahiel
(2002).
CSDBase: an interactive database for cold shock domain-containing proteins and the bacterial cold shock response.
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Nucleic Acids Res,
30,
375-378.
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M.H.Weber,
and
M.A.Marahiel
(2002).
Coping with the cold: the cold shock response in the Gram-positive soil bacterium Bacillus subtilis.
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Philos Trans R Soc Lond B Biol Sci,
357,
895-907.
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S.F.Falsone,
M.Weichel,
R.Crameri,
M.Breitenbach,
and
A.J.Kungl
(2002).
Unfolding and double-stranded DNA binding of the cold shock protein homologue Cla h 8 from Cladosporium herbarum.
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J Biol Chem,
277,
16512-16516.
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A.T.Alexandrescu,
D.R.Snyder,
and
F.Abildgaard
(2001).
NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of crystallographic resolution on comparisons of hydrogen bond lengths.
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Protein Sci,
10,
1856-1868.
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K.Yamanaka,
W.Zheng,
E.Crooke,
Y.H.Wang,
and
M.Inouye
(2001).
CspD, a novel DNA replication inhibitor induced during the stationary phase in Escherichia coli.
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Mol Microbiol,
39,
1572-1584.
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M.H.Weber,
C.L.Beckering,
and
M.A.Marahiel
(2001).
Complementation of cold shock proteins by translation initiation factor IF1 in vivo.
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J Bacteriol,
183,
7381-7386.
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V.Agrawal,
and
R.K.Kishan
(2001).
Functional evolution of two subtly different (similar) folds.
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BMC Struct Biol,
1,
5.
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W.Kremer,
B.Schuler,
S.Harrieder,
M.Geyer,
W.Gronwald,
C.Welker,
R.Jaenicke,
and
H.R.Kalbitzer
(2001).
Solution NMR structure of the cold-shock protein from the hyperthermophilic bacterium Thermotoga maritima.
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Eur J Biochem,
268,
2527-2539.
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PDB code:
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X.Manival,
L.Ghisolfi-Nieto,
G.Joseph,
P.Bouvet,
and
M.Erard
(2001).
RNA-binding strategies common to cold-shock domain- and RNA recognition motif-containing proteins.
|
| |
Nucleic Acids Res,
29,
2223-2233.
|
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M.A.Swairjo,
A.J.Morales,
C.C.Wang,
A.R.Ortiz,
and
P.Schimmel
(2000).
Crystal structure of trbp111: a structure-specific tRNA-binding protein.
|
| |
EMBO J,
19,
6287-6298.
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PDB codes:
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M.Pelletier,
M.M.Miller,
and
L.K.Read
(2000).
RNA-binding properties of the mitochondrial Y-box protein RBP16.
|
| |
Nucleic Acids Res,
28,
1266-1275.
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N.Wang,
K.Yamanaka,
and
M.Inouye
(2000).
Acquisition of double-stranded DNA-binding ability in a hybrid protein between Escherichia coli CspA and the cold shock domain of human YB-1.
|
| |
Mol Microbiol,
38,
526-534.
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S.Derzelle,
B.Hallet,
K.P.Francis,
T.Ferain,
J.Delcour,
and
P.Hols
(2000).
Changes in cspL, cspP, and cspC mRNA abundance as a function of cold shock and growth phase in Lactobacillus plantarum.
|
| |
J Bacteriol,
182,
5105-5113.
|
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A.Danchin
(1999).
From protein sequence to function.
|
| |
Curr Opin Struct Biol,
9,
363-367.
|
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C.Welker,
G.Böhm,
H.Schurig,
and
R.Jaenicke
(1999).
Cloning, overexpression, purification, and physicochemical characterization of a cold shock protein homolog from the hyperthermophilic bacterium Thermotoga maritima.
|
| |
Protein Sci,
8,
394-403.
|
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K.Neuhaus,
K.P.Francis,
S.Rapposch,
A.Görg,
and
S.Scherer
(1999).
Pathogenic Yersinia species carry a novel, cold-inducible major cold shock protein tandem gene duplication producing both bicistronic and monocistronic mRNA.
|
| |
J Bacteriol,
181,
6449-6455.
|
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M.Gross,
D.K.Wilkins,
M.C.Pitkeathly,
E.W.Chung,
C.Higham,
A.Clark,
and
C.M.Dobson
(1999).
Formation of amyloid fibrils by peptides derived from the bacterial cold shock protein CspB.
|
| |
Protein Sci,
8,
1350-1357.
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M.Jacob,
G.Holtermann,
D.Perl,
J.Reinstein,
T.Schindler,
M.A.Geeves,
and
F.X.Schmid
(1999).
Microsecond folding of the cold shock protein measured by a pressure-jump technique.
|
| |
Biochemistry,
38,
2882-2891.
|
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M.M.Lopez,
K.Yutani,
and
G.I.Makhatadze
(1999).
Interactions of the major cold shock protein of Bacillus subtilis CspB with single-stranded DNA templates of different base composition.
|
| |
J Biol Chem,
274,
33601-33608.
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S.L.Hunt,
J.J.Hsuan,
N.Totty,
and
R.J.Jackson
(1999).
unr, a cellular cytoplasmic RNA-binding protein with five cold-shock domains, is required for internal initiation of translation of human rhinovirus RNA.
|
| |
Genes Dev,
13,
437-448.
|
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T.Schindler,
P.L.Graumann,
D.Perl,
S.Ma,
F.X.Schmid,
and
M.A.Marahiel
(1999).
The family of cold shock proteins of Bacillus subtilis. Stability and dynamics in vitro and in vivo.
|
| |
J Biol Chem,
274,
3407-3413.
|
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|
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V.M.Evdokimova,
and
L.P.Ovchinnikov
(1999).
Translational regulation by Y-box transcription factor: involvement of the major mRNA-associated protein, p50.
|
| |
Int J Biochem Cell Biol,
31,
139-149.
|
|
|
|
|
|
|
A.Nambiar,
S.K.Swamynathan,
J.C.Kandala,
and
R.V.Guntaka
(1998).
Characterization of the DNA-binding domain of the avian Y-box protein, chkYB-2, and mutational analysis of its single-strand binding motif in the Rous sarcoma virus enhancer.
|
| |
J Virol,
72,
900-909.
|
|
|
|
|
|
|
D.Perl,
C.Welker,
T.Schindler,
K.Schröder,
M.A.Marahiel,
R.Jaenicke,
and
F.X.Schmid
(1998).
Conservation of rapid two-state folding in mesophilic, thermophilic and hyperthermophilic cold shock proteins.
|
| |
Nat Struct Biol,
5,
229-235.
|
|
|
|
|
|
|
G.Varani,
and
K.Nagai
(1998).
RNA recognition by RNP proteins during RNA processing.
|
| |
Annu Rev Biophys Biomol Struct,
27,
407-445.
|
|
|
|
|
|
|
H.A.Thieringer,
P.G.Jones,
and
M.Inouye
(1998).
Cold shock and adaptation.
|
| |
Bioessays,
20,
49-57.
|
|
|
|
|
|
|
K.L.Reid,
H.M.Rodriguez,
B.J.Hillier,
and
L.M.Gregoret
(1998).
Stability and folding properties of a model beta-sheet protein, Escherichia coli CspA.
|
| |
Protein Sci,
7,
470-479.
|
|
|
|
|
|
|
M.R.Wada,
Y.Ohtani,
Y.Shibata,
K.J.Tanaka,
N.Tanimoto,
and
T.Nishikata
(1998).
An alternatively spliced gene encoding a Y-box protein showing maternal expression and tissue-specific zygotic expression in the ascidian embryo.
|
| |
Dev Growth Differ,
40,
631-640.
|
|
|
|
|
|
|
N.N.Alexandrov,
and
R.Luethy
(1998).
Alignment algorithm for homology modeling and threading.
|
| |
Protein Sci,
7,
254-258.
|
|
|
|
|
|
|
P.L.Graumann,
and
M.A.Marahiel
(1998).
A superfamily of proteins that contain the cold-shock domain.
|
| |
Trends Biochem Sci,
23,
286-290.
|
|
|
|
|
|
|
Y.G.Gao,
S.Y.Su,
H.Robinson,
S.Padmanabhan,
L.Lim,
B.S.McCrary,
S.P.Edmondson,
J.W.Shriver,
and
A.H.Wang
(1998).
The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA.
|
| |
Nat Struct Biol,
5,
782-786.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.Basu,
B.Dong,
A.R.Krainer,
and
C.C.Howe
(1997).
The intracisternal A-particle proximal enhancer-binding protein activates transcription and is identical to the RNA- and DNA-binding protein p54nrb/NonO.
|
| |
Mol Cell Biol,
17,
677-686.
|
|
|
|
|
|
|
C.Chothia,
T.Hubbard,
S.Brenner,
H.Barns,
and
A.Murzin
(1997).
Protein folds in the all-beta and all-alpha classes.
|
| |
Annu Rev Biophys Biomol Struct,
26,
597-627.
|
|
|
|
|
|
|
D.Suck
(1997).
Common fold, common function, common origin?
|
| |
Nat Struct Biol,
4,
161-165.
|
|
|
|
|
|
|
E.G.Moss,
R.C.Lee,
and
V.Ambros
(1997).
The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA.
|
| |
Cell,
88,
637-646.
|
|
|
|
|
|
|
G.S.Prasad,
R.Radhakrishnan,
D.T.Mitchell,
C.A.Earhart,
M.M.Dinges,
W.J.Cook,
P.M.Schlievert,
and
D.H.Ohlendorf
(1997).
Refined structures of three crystal forms of toxic shock syndrome toxin-1 and of a tetramutant with reduced activity.
|
| |
Protein Sci,
6,
1220-1227.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
H.A.Thieringer,
K.Singh,
H.Trivedi,
and
M.Inouye
(1997).
Identification and developmental characterization of a novel Y-box protein from Drosophila melanogaster.
|
| |
Nucleic Acids Res,
25,
4764-4770.
|
|
|
|
|
|
|
H.Hosaka,
A.Nakagawa,
I.Tanaka,
N.Harada,
K.Sano,
M.Kimura,
M.Yao,
and
S.Wakatsuki
(1997).
Ribosomal protein S7: a new RNA-binding motif with structural similarities to a DNA architectural factor.
|
| |
Structure,
5,
1199-1208.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.A.Kercher,
P.Lu,
and
M.Lewis
(1997).
Lac repressor-operator complex.
|
| |
Curr Opin Struct Biol,
7,
76-85.
|
|
|
|
|
|
|
M.Bycroft,
T.J.Hubbard,
M.Proctor,
S.M.Freund,
and
A.G.Murzin
(1997).
The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold.
|
| |
Cell,
88,
235-242.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.Jacob,
T.Schindler,
J.Balbach,
and
F.X.Schmid
(1997).
Diffusion control in an elementary protein folding reaction.
|
| |
Proc Natl Acad Sci U S A,
94,
5622-5627.
|
|
|
|
|
|
|
M.Sette,
P.van Tilborg,
R.Spurio,
R.Kaptein,
M.Paci,
C.O.Gualerzi,
and
R.Boelens
(1997).
The structure of the translational initiation factor IF1 from E.coli contains an oligomer-binding motif.
|
| |
EMBO J,
16,
1436-1443.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.Quevillon,
F.Agou,
J.C.Robinson,
and
M.Mirande
(1997).
The p43 component of the mammalian multi-synthetase complex is likely to be the precursor of the endothelial monocyte-activating polypeptide II cytokine.
|
| |
J Biol Chem,
272,
32573-32579.
|
|
|
|
|
|
|
V.Michel,
I.Lehoux,
G.Depret,
P.Anglade,
J.Labadie,
and
M.Hebraud
(1997).
The cold shock response of the psychrotrophic bacterium Pseudomonas fragi involves four low-molecular-mass nucleic acid-binding proteins.
|
| |
J Bacteriol,
179,
7331-7342.
|
|
|
|
|
|
|
X.Manival,
Y.Yang,
M.P.Strub,
M.Kochoyan,
M.Steinmetz,
and
S.Aymerich
(1997).
From genetic to structural characterization of a new class of RNA-binding domain within the SacY/BglG family of antiterminator proteins.
|
| |
EMBO J,
16,
5019-5029.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.E.Hodel,
P.D.Gershon,
X.Shi,
and
F.A.Quiocho
(1996).
The 1.85 A structure of vaccinia protein VP39: a bifunctional enzyme that participates in the modification of both mRNA ends.
|
| |
Cell,
85,
247-256.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
B.Mayr,
T.Kaplan,
S.Lechner,
and
S.Scherer
(1996).
Identification and purification of a family of dimeric major cold shock protein homologs from the psychrotrophic Bacillus cereus WSBC 10201.
|
| |
J Bacteriol,
178,
2916-2925.
|
|
|
|
|
|
|
B.Thammavongs,
D.Corroler,
J.M.Panoff,
Y.Auffray,
and
P.Boutibonnes
(1996).
Physiological response of Enterococcus faecalis JH2-2 to cold shock: growth at low temperatures and freezing/thawing challenge.
|
| |
Lett Appl Microbiol,
23,
398-402.
|
|
|
|
|
|
|
G.Parisi,
J.Echave,
D.Ghiringhelli,
and
V.Romanowski
(1996).
Computational characterisation of potential RNA-binding sites in arenavirus nucleocapsid proteins.
|
| |
Virus Genes,
13,
247-254.
|
|
|
|
|
|
|
H.S.Subramanya,
A.J.Doherty,
S.R.Ashford,
and
D.B.Wigley
(1996).
Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7.
|
| |
Cell,
85,
607-615.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
K.Matsumoto,
F.Meric,
and
A.P.Wolffe
(1996).
Translational repression dependent on the interaction of the Xenopus Y-box protein FRGY2 with mRNA. Role of the cold shock domain, tail domain, and selective RNA sequence recognition.
|
| |
J Biol Chem,
271,
22706-22712.
|
|
|
|
|
|
|
P.Graumann,
K.Schröder,
R.Schmid,
and
M.A.Marahiel
(1996).
Cold shock stress-induced proteins in Bacillus subtilis.
|
| |
J Bacteriol,
178,
4611-4619.
|
|
|
|
|
|
|
P.Graumann,
and
M.A.Marahiel
(1996).
A case of convergent evolution of nucleic acid binding modules.
|
| |
Bioessays,
18,
309-315.
|
|
|
|
|
|
|
T.Schindler,
and
F.X.Schmid
(1996).
Thermodynamic properties of an extremely rapid protein folding reaction.
|
| |
Biochemistry,
35,
16833-16842.
|
|
|
|
|
|
|
D.J.DeAngelo,
J.DeFalco,
L.Rybacki,
and
G.Childs
(1995).
The embryonic enhancer-binding protein SSAP contains a novel DNA-binding domain which has homology to several RNA-binding proteins.
|
| |
Mol Cell Biol,
15,
1254-1264.
|
|
|
|
|
|
|
I.W.Mattaj,
and
K.Nagai
(1995).
Recruiting proteins to the RNA world.
|
| |
Nat Struct Biol,
2,
518-522.
|
|
|
|
|
|
|
K.Nagai,
C.Oubridge,
N.Ito,
J.Avis,
and
P.Evans
(1995).
The RNP domain: a sequence-specific RNA-binding domain involved in processing and transport of RNA.
|
| |
Trends Biochem Sci,
20,
235-240.
|
|
|
|
|
|
|
K.Schröder,
P.Graumann,
A.Schnuchel,
T.A.Holak,
and
M.A.Marahiel
(1995).
Mutational analysis of the putative nucleic acid-binding surface of the cold-shock domain, CspB, revealed an essential role of aromatic and basic residues in binding of single-stranded DNA containing the Y-box motif.
|
| |
Mol Microbiol,
16,
699-708.
|
|
|
|
|
|
|
L.R.Kowalski,
K.Kondo,
and
M.Inouye
(1995).
Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae.
|
| |
Mol Microbiol,
15,
341-353.
|
|
|
|
|
|
|
M.Bycroft,
S.Grünert,
A.G.Murzin,
M.Proctor,
and
D.St Johnston
(1995).
NMR solution structure of a dsRNA binding domain from Drosophila staufen protein reveals homology to the N-terminal domain of ribosomal protein S5.
|
| |
EMBO J,
14,
3563-3571.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
P.Bouvet,
K.Matsumoto,
and
A.P.Wolffe
(1995).
Sequence-specific RNA recognition by the Xenopus Y-box proteins. An essential role for the cold shock domain.
|
| |
J Biol Chem,
270,
28297-28303.
|
|
|
|
|
|
|
R.H.Folmer,
M.Nilges,
R.N.Konings,
and
C.W.Hilbers
(1995).
Solution structure of the single-stranded DNA binding protein of the filamentous Pseudomonas phage Pf3: similarity to other proteins binding to single-stranded nucleic acids.
|
| |
EMBO J,
14,
4132-4142.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.Kudo,
M.G.Mattei,
and
M.Fukuda
(1995).
Characterization of the gene for dbpA, a family member of the nucleic-acid-binding proteins containing a cold-shock domain.
|
| |
Eur J Biochem,
231,
72-82.
|
|
|
|
|
|
|
T.Schindler,
M.Herrler,
M.A.Marahiel,
and
F.X.Schmid
(1995).
Extremely rapid protein folding in the absence of intermediates.
|
| |
Nat Struct Biol,
2,
663-673.
|
|
|
|
|
|
|
A.P.Stassen,
R.H.Folmer,
C.W.Hilbers,
and
R.N.Konings
(1994).
Single-stranded DNA binding protein encoded by the filamentous bacteriophage M13: structural and functional characteristics.
|
| |
Mol Biol Rep,
20,
109-127.
|
|
|
|
|
|
|
A.P.Wolffe
(1994).
Structural and functional properties of the evolutionarily ancient Y-box family of nucleic acid binding proteins.
|
| |
Bioessays,
16,
245-251.
|
|
|
|
|
|
|
A.Teplyakov,
G.Obmolova,
K.S.Wilson,
K.Ishii,
H.Kaji,
T.Samejima,
and
I.Kuranova
(1994).
Crystal structure of inorganic pyrophosphatase from Thermus thermophilus.
|
| |
Protein Sci,
3,
1098-1107.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
E.Fabre,
W.C.Boelens,
C.Wimmer,
I.W.Mattaj,
and
E.C.Hurt
(1994).
Nup145p is required for nuclear export of mRNA and binds homopolymeric RNA in vitro via a novel conserved motif.
|
| |
Cell,
78,
275-289.
|
|
|
|
|
|
|
G.I.Makhatadze,
and
M.A.Marahiel
(1994).
Effect of pH and phosphate ions on self-association properties of the major cold-shock protein from Bacillus subtilis.
|
| |
Protein Sci,
3,
2144-2147.
|
|
|
|
|
|
|
H.Jacquemin-Sablon,
G.Triqueneaux,
S.Deschamps,
M.le Maire,
J.Doniger,
and
F.Dautry
(1994).
Nucleic acid binding and intracellular localization of unr, a protein with five cold shock domains.
|
| |
Nucleic Acids Res,
22,
2643-2650.
|
|
|
|
|
|
|
H.Schindelin,
W.Jiang,
M.Inouye,
and
U.Heinemann
(1994).
Crystal structure of CspA, the major cold shock protein of Escherichia coli.
|
| |
Proc Natl Acad Sci U S A,
91,
5119-5123.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.M.Valpuesta,
and
J.L.Carrascosa
(1994).
Structure of viral connectors and their function in bacteriophage assembly and DNA packaging.
|
| |
Q Rev Biophys,
27,
107-155.
|
|
|
|
|
|
|
J.Muñoz-Dorado,
K.Kondo,
M.Inouye,
and
H.Sone
(1994).
Identification of cis- and trans-acting elements involved in the expression of cold shock-inducible TIP1 gene of yeast Saccharomyces cerevisiae.
|
| |
Nucleic Acids Res,
22,
560-568.
|
|
|
|
|
|
|
K.Newkirk,
W.Feng,
W.Jiang,
R.Tejero,
S.D.Emerson,
M.Inouye,
and
G.T.Montelione
(1994).
Solution NMR structure of the major cold shock protein (CspA) from Escherichia coli: identification of a binding epitope for DNA.
|
| |
Proc Natl Acad Sci U S A,
91,
5114-5118.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
K.Yamanaka,
T.Mitani,
T.Ogura,
H.Niki,
and
S.Hiraga
(1994).
Cloning, sequencing, and characterization of multicopy suppressors of a mukB mutation in Escherichia coli.
|
| |
Mol Microbiol,
13,
301-312.
|
|
|
|
|
|
|
M.Ladomery,
and
J.Sommerville
(1994).
Binding of Y-box proteins to RNA: involvement of different protein domains.
|
| |
Nucleic Acids Res,
22,
5582-5589.
|
|
|
|
|
|
|
M.Sugita,
and
M.Sugiura
(1994).
The existence of eukaryotic ribonucleoprotein consensus sequence-type RNA-binding proteins in a prokaryote, Synechococcus 6301.
|
| |
Nucleic Acids Res,
22,
25-31.
|
|
|
|
|
|
|
N.Sato
(1994).
A cold-regulated cyanobacterial gene cluster encodes RNA-binding protein and ribosomal protein S21.
|
| |
Plant Mol Biol,
24,
819-823.
|
|
|
|
|
|
|
P.A.Tucker,
D.Tsernoglou,
A.D.Tucker,
F.E.Coenjaerts,
H.Leenders,
and
P.C.van der Vliet
(1994).
Crystal structure of the adenovirus DNA binding protein reveals a hook-on model for cooperative DNA binding.
|
| |
EMBO J,
13,
2994-3002.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
P.G.Jones,
and
M.Inouye
(1994).
The cold-shock response--a hot topic.
|
| |
Mol Microbiol,
11,
811-818.
|
|
|
|
|
|
|
S.J.Lee,
A.Xie,
W.Jiang,
J.P.Etchegaray,
P.G.Jones,
and
M.Inouye
(1994).
Family of the major cold-shock protein, CspA (CS7.4), of Escherichia coli, whose members show a high sequence similarity with the eukaryotic Y-box binding proteins.
|
| |
Mol Microbiol,
11,
833-839.
|
|
|
|
|
|
|
E.Birney,
S.Kumar,
and
A.R.Krainer
(1993).
Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors.
|
| |
Nucleic Acids Res,
21,
5803-5816.
|
|
|
|
|
|
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
