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PDBsum entry 3mef
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Gene regulation
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PDB id
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3mef
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Contents |
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* Residue conservation analysis
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DOI no:
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Biochemistry
37:10881-10896
(1998)
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PubMed id:
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Solution NMR structure and backbone dynamics of the major cold-shock protein (CspA) from Escherichia coli: evidence for conformational dynamics in the single-stranded RNA-binding site.
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W.Feng,
R.Tejero,
D.E.Zimmerman,
M.Inouye,
G.T.Montelione.
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ABSTRACT
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The major cold-shock protein (CspA) from Escherichia coli is a single-stranded
nucleic acid-binding protein that is produced in response to cold stress. We
have previously reported its overall chain fold as determined by NMR
spectroscopy [Newkirk, K., Feng, W., Jiang, W., Tejero, R., Emerson, S. D.,
Inouye, M., and Montelione, G. T. (1994) Proc. Natl. Acad. Sci. U.S.A. 91,
5114-5118]. Here we describe the complete analysis of 1H, 13C, and 15N resonance
assignments for CspA, together with a refined solution NMR structure based on
699 conformational constraints and an analysis of backbone dynamics based on 15N
relaxation rate measurements. An extensive set of triple-resonance NMR
experiments for obtaining the backbone and side chain resonance assignments were
carried out on uniformly 13C- and 15N-enriched CspA. Using a subset of these
triple-resonance experiments, the computer program AUTOASSIGN provided automatic
analysis of sequence-specific backbone N, Calpha, C', HN, Halpha, and side chain
Cbeta resonance assignments. The remaining 1H, 13C, and 15N resonance
assignments for CspA were then obtained by manual analysis of additional NMR
spectra. Dihedral angle constraints and stereospecific methylene Hbeta resonance
assignments were determined using a new conformational grid search program,
HYPER, and used together with longer-range constraints as input for
three-dimensional structure calculations. The resulting solution NMR structure
of CspA is a well-defined five-stranded beta-barrel with surface-exposed
aromatic groups that form a single-stranded nucleic acid-binding site. Backbone
dynamics of CspA have also been characterized by 15N T1, T2, and heteronuclear
15N-1H NOE measurements and analyzed using the extended Lipari-Szabo formalism.
These dynamic measurements indicate a molecular rotational correlation time taum
of 4.88 +/- 0.04 ns and provide evidence for fast time scale (taue < 500 ps)
dynamics in surface loops and motions on the microsecond to millisecond time
scale within the proposed nucleic acid-binding epitope.
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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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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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J.H.Uh,
Y.H.Jung,
Y.K.Lee,
H.K.Lee,
and
H.Im
(2010).
Rescue of a cold-sensitive mutant at low temperatures by cold shock proteins from Polaribacter irgensii KOPRI 22228.
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J Microbiol,
48,
798-802.
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S.T.Vaiphei,
L.Mao,
T.Shimazu,
J.H.Park,
and
M.Inouye
(2010).
Use of amino acids as inducers for high-level protein expression in the single-protein production system.
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Appl Environ Microbiol,
76,
6063-6068.
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Y.Tang,
W.M.Schneider,
Y.Shen,
S.Raman,
M.Inouye,
D.Baker,
M.J.Roth,
and
G.T.Montelione
(2010).
Fully automated high-quality NMR structure determination of small (2)H-enriched proteins.
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J Struct Funct Genomics,
11,
223-232.
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PDB code:
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D.A.Rowe-Magnus
(2009).
Integrase-directed recovery of functional genes from genomic libraries.
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Nucleic Acids Res,
37,
e118.
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K.M.Guardino,
S.R.Sheftic,
R.E.Slattery,
and
A.T.Alexandrescu
(2009).
Relative Stabilities of Conserved and Non-Conserved Structures in the OB-Fold Superfamily.
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Int J Mol Sci,
10,
2412-2430.
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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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E.Watson,
W.M.Matousek,
E.L.Irimies,
and
A.T.Alexandrescu
(2007).
Partially folded states of staphylococcal nuclease highlight the conserved structural hierarchy of OB-fold proteins.
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Biochemistry,
46,
9484-9494.
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L.Giaquinto,
P.M.Curmi,
K.S.Siddiqui,
A.Poljak,
E.DeLong,
S.DasSarma,
and
R.Cavicchioli
(2007).
Structure and function of cold shock proteins in archaea.
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J Bacteriol,
189,
5738-5748.
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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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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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S.Phadtare,
and
K.Severinov
(2005).
Nucleic acid melting by Escherichia coli CspE.
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Nucleic Acids Res,
33,
5583-5590.
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S.de Bono,
L.Riechmann,
E.Girard,
R.L.Williams,
and
G.Winter
(2005).
A segment of cold shock protein directs the folding of a combinatorial protein.
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Proc Natl Acad Sci U S A,
102,
1396-1401.
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PDB code:
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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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A.T.Alexandrescu
(2004).
Strategy for supplementing structure calculations using limited data with hydrophobic distance restraints.
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Proteins,
56,
117-129.
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J.M.Aramini,
Y.J.Huang,
J.R.Cort,
S.Goldsmith-Fischman,
R.Xiao,
L.Y.Shih,
C.K.Ho,
J.Liu,
B.Rost,
B.Honig,
M.A.Kennedy,
T.B.Acton,
and
G.T.Montelione
(2003).
Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii.
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Protein Sci,
12,
2823-2830.
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PDB code:
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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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N.Lan,
G.T.Montelione,
and
M.Gerstein
(2003).
Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level.
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Curr Opin Chem Biol,
7,
44-54.
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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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M.P.Joachimiak,
and
F.E.Cohen
(2002).
JEvTrace: refinement and variations of the evolutionary trace in JAVA.
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Genome Biol,
3,
RESEARCH0077.
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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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S.Phadtare,
M.Inouye,
and
K.Severinov
(2002).
The nucleic acid melting activity of Escherichia coli CspE is critical for transcription antitermination and cold acclimation of cells.
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J Biol Chem,
277,
7239-7245.
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S.Phadtare,
S.Tyagi,
M.Inouye,
and
K.Severinov
(2002).
Three amino acids in Escherichia coli CspE surface-exposed aromatic patch are critical for nucleic acid melting activity leading to transcription antitermination and cold acclimation of cells.
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J Biol Chem,
277,
46706-46711.
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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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D.M.Vu,
K.L.Reid,
H.M.Rodriguez,
and
L.M.Gregoret
(2001).
Examination of the folding of E. coli CspA through tryptophan substitutions.
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Protein Sci,
10,
2028-2036.
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J.E.Shea,
and
C.L.Brooks
(2001).
From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding.
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Annu Rev Phys Chem,
52,
499-535.
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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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S.Dellerue,
A.J.Petrescu,
J.C.Smith,
and
M.C.Bellissent-Funel
(2001).
Radially softening diffusive motions in a globular protein.
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Biophys J,
81,
1666-1676.
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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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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.
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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.
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J Bacteriol,
182,
5105-5113.
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V.A.Jaravine,
K.Rathgeb-Szabo,
and
A.T.Alexandrescu
(2000).
Microscopic stability of cold shock protein A examined by NMR native state hydrogen exchange as a function of urea and trimethylamine N-oxide.
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Protein Sci,
9,
290-301.
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K.Yamanaka,
M.Inouye,
and
S.Inouye
(1999).
Identification and characterization of five cspA homologous genes from Myxococcus xanthus.
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Biochim Biophys Acta,
1447,
357-365.
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K.Yamanaka,
M.Mitta,
and
M.Inouye
(1999).
Mutation analysis of the 5' untranslated region of the cold shock cspA mRNA of Escherichia coli.
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J Bacteriol,
181,
6284-6291.
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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.
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J Biol Chem,
274,
33601-33608.
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N.Wang,
K.Yamanaka,
and
M.Inouye
(1999).
CspI, the ninth member of the CspA family of Escherichia coli, is induced upon cold shock.
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J Bacteriol,
181,
1603-1609.
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S.Phadtare,
J.Alsina,
and
M.Inouye
(1999).
Cold-shock response and cold-shock proteins.
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Curr Opin Microbiol,
2,
175-180.
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S.Phadtare,
and
M.Inouye
(1999).
Sequence-selective interactions with RNA by CspB, CspC and CspE, members of the CspA family of Escherichia coli.
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Mol Microbiol,
33,
1004-1014.
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W.Bae,
S.Phadtare,
K.Severinov,
and
M.Inouye
(1999).
Characterization of Escherichia coli cspE, whose product negatively regulates transcription of cspA, the gene for the major cold shock protein.
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Mol Microbiol,
31,
1429-1441.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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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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Links
