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PDBsum entry 1mef
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Transcription regulation PDB id
1mef

 

 

 

 

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Contents
Protein chain
70 a.a.
Superseded by: 3mef 3mef
PDB id:
1mef
Name: Transcription regulation
Title: Cold-shock protein, nmr, 10 structures
Structure: Cold-shock protein a. Chain: null. Synonym: cspa, cs7.4
Source: Escherichia coli
NMR struc: 10 models
Authors: W.Feng,R.Tejero,K.Newkirk,G.T.Montelione
Key ref: K.Newkirk et al. (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. PubMed id: 7515185 DOI: 10.1073/pnas.91.11.5114
Date:
16-Feb-96     Release date:   11-Jul-96    
PROCHECK
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 Headers
 References

Protein chain
P15277  (CSPA_ECOLI) - 
Key:    Secondary structure

 

 
DOI no: 10.1073/pnas.91.11.5114 Proc Natl Acad Sci U S A 91:5114-5118 (1994)
PubMed id: 7515185  
 
 
Solution NMR structure of the major cold shock protein (CspA) from Escherichia coli: identification of a binding epitope for DNA.
K.Newkirk, W.Feng, W.Jiang, R.Tejero, S.D.Emerson, M.Inouye, G.T.Montelione.
 
  ABSTRACT  
 
Sequence-specific 1H and 15N resonance assignments have been determined for the major cold shock protein (CspA) from Escherichia coli with recently developed three-dimensional triple-resonance NMR experiments. By use of these assignments, five antiparallel beta-strands were identified from analysis of NMR data. Strands 1-4 have a classical 3-2-1-4 Greek key beta-sheet topology and there are two beta-bulges, at positions Lys10-Trp11 and Gly65-Asn66. Three-dimensional structures of CspA were generated from NMR data by using simulated annealing with molecular dynamics. The overall chain fold of CspA is a beta-barrel structure, with a tightly packed hydrophobic core. Two-dimensional isotope-edited pulsed-field gradient 15N-1H heteronuclear single-quantum coherence spectroscopy was used to characterize the 15N-1H fingerprint spectrum with and without a 24-base oligodeoxyribonucleotide, 5'-AACGGTTTGACGTACAGACCATTA-3'. Protein-DNA complex formation perturbs a subset of the amide resonances that are located mostly on one face of the CspA molecule. This portion of the CspA molecular surface includes two putative RNA-binding sequence motifs which contribute to an unusual cluster of eight surface aromatic side chains: Trp11, Phe12, Phe18, Phe20, Phe31, His33, Phe34, and Tyr42. These surface aromatic groups, and also residues Lys16, Ser44, and Lys60 located on this same face of CspA, are highly conserved in the family of CspA homologues. These isotope-edited pulsed-field gradient NMR data provide a low-resolution mapping of a DNA-binding epitope on CspA.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20091073 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.
  Extremophiles, 14, 171-183.  
21221937 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.
  J Microbiol, 48, 798-802.  
20734145 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.
  J Struct Funct Genomics, 11, 223-232.
PDB code: 2l15
19145605 A.L.Stewart, and M.L.Waters (2009).
Structural effects on ss- and dsDNA recognition by a beta-hairpin peptide.
  Chembiochem, 10, 539-544.  
19596808 D.A.Rowe-Magnus (2009).
Integrase-directed recovery of functional genes from genomic libraries.
  Nucleic Acids Res, 37, e118.  
19004832 H.A.Vincent, and M.P.Deutscher (2009).
The roles of individual domains of RNase R in substrate binding and exoribonuclease activity. The nuclease domain is sufficient for digestion of structured RNA.
  J Biol Chem, 284, 486-494.  
19242651 H.Ohba, K.Satoh, H.Sghaier, T.Yanagisawa, and I.Narumi (2009).
Identification of PprM: a modulator of the PprI-dependent DNA damage response in Deinococcus radiodurans.
  Extremophiles, 13, 471-479.  
19840122 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.
  Genes Cells, 14, 1227-1239.  
  18391418 J.Ren, J.E.Nettleship, S.Sainsbury, N.J.Saunders, and R.J.Owens (2008).
Structure of the cold-shock domain protein from Neisseria meningitidis reveals a strand-exchanged dimer.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 247-251.
PDB code: 3cam
17981525 R.Russell (2008).
RNA misfolding and the action of chaperones.
  Front Biosci, 13, 1.  
17545280 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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17203395 M.J.Kim, Y.K.Lee, H.K.Lee, and H.Im (2007).
Characterization of cold-shock protein A of Antarctic Streptomyces sp. AA8321.
  Protein J, 26, 51-59.  
17384193 S.Phadtare, T.Kazakov, M.Bubunenko, D.L.Court, T.Pestova, and K.Severinov (2007).
Transcription antitermination by translation initiation factor IF1.
  J Bacteriol, 189, 4087-4093.  
16788067 K.Nakaminami, D.T.Karlson, and R.Imai (2006).
Functional conservation of cold shock domains in bacteria and higher plants.
  Proc Natl Acad Sci U S A, 103, 10122-10127.  
16956971 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.
  Nucleic Acids Res, 34, 4561-4571.
PDB code: 2f52
16997528 X.He, J.Thornton, S.Carmicle-Davis, and L.S.McDaniel (2006).
Tex, a putative transcriptional accessory factor, is involved in pathogen fitness in Streptococcus pneumoniae.
  Microb Pathog, 41, 199-206.  
16214801 S.Phadtare, and K.Severinov (2005).
Nucleic acid melting by Escherichia coli CspE.
  Nucleic Acids Res, 33, 5583-5590.  
15671167 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.
  Proc Natl Acad Sci U S A, 102, 1396-1401.
PDB code: 2bh8
15235764 B.H.Kim, H.G.Kim, G.I.Bae, I.S.Bang, S.H.Bang, J.H.Choi, and Y.K.Park (2004).
Expression of cspH upon nutrient up-shift in Salmonella enterica serovar Typhimurium.
  Arch Microbiol, 182, 37-43.  
15317764 E.A.Lang, and M.V.Marques (2004).
Identification and transcriptional control of Caulobacter crescentus genes encoding proteins containing a cold shock domain.
  J Bacteriol, 186, 5603-5613.  
12859904 E.Skordalakes, and J.M.Berger (2003).
Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading.
  Cell, 114, 135-146.
PDB codes: 1pv4 1pvo
14627742 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.
  Protein Sci, 12, 2823-2830.
PDB code: 1ny4
12493834 M.Zeeb, and J.Balbach (2003).
Single-stranded DNA binding of the cold-shock protein CspB from Bacillus subtilis: NMR mapping and mutational characterization.
  Protein Sci, 12, 112-123.  
12547426 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.
  Curr Opin Chem Biol, 7, 44-54.  
14602587 P.P.Datta, and R.K.Bhadra (2003).
Cold shock response and major cold shock proteins of Vibrio cholerae.
  Appl Environ Microbiol, 69, 6361-6369.  
14553929 P.Serror, R.Dervyn, S.D.Ehrlich, and E.Maguin (2003).
csp-like genes of Lactobacillus delbrueckii ssp. bulgaricus and their response to cold shock.
  FEMS Microbiol Lett, 226, 323-330.  
14531859 S.Phadtare, J.Hwang, K.Severinov, and M.Inouye (2003).
CspB and CspL, thermostable cold-shock proteins from Thermotoga maritima.
  Genes Cells, 8, 801-810.  
11752341 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.
  Nucleic Acids Res, 30, 375-378.  
12171653 M.H.Weber, and M.A.Marahiel (2002).
Coping with the cold: the cold shock response in the Gram-positive soil bacterium Bacillus subtilis.
  Philos Trans R Soc Lond B Biol Sci, 357, 895-907.  
11298285 B.Xia, H.Ke, and M.Inouye (2001).
Acquirement of cold sensitivity by quadruple deletion of the cspA family and its suppression by PNPase S1 domain in Escherichia coli.
  Mol Microbiol, 40, 179-188.  
11567094 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.
  Protein Sci, 10, 2028-2036.  
11260474 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.
  Mol Microbiol, 39, 1572-1584.  
11717297 M.H.Weber, C.L.Beckering, and M.A.Marahiel (2001).
Complementation of cold shock proteins by translation initiation factor IF1 in vivo.
  J Bacteriol, 183, 7381-7386.  
11322871 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.
  Eur J Biochem, 268, 2527-2539.
PDB code: 1g6p
11376140 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.  
10681466 D.T.Leeson, F.Gai, H.M.Rodriguez, L.M.Gregoret, and R.B.Dyer (2000).
Protein folding and unfolding on a complex energy landscape.
  Proc Natl Acad Sci U S A, 97, 2527-2532.  
10960094 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.  
  10048332 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.  
10542339 K.Yamanaka, M.Inouye, and S.Inouye (1999).
Identification and characterization of five cspA homologous genes from Myxococcus xanthus.
  Biochim Biophys Acta, 1447, 357-365.  
  10515916 K.Yamanaka, M.Mitta, and M.Inouye (1999).
Mutation analysis of the 5' untranslated region of the cold shock cspA mRNA of Escherichia coli.
  J Bacteriol, 181, 6284-6291.  
10562563 M.Stoldt, J.Wöhnert, O.Ohlenschläger, M.Görlach, and L.R.Brown (1999).
The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition.
  EMBO J, 18, 6508-6521.
PDB code: 1d6k
  10049393 N.Wang, K.Yamanaka, and M.Inouye (1999).
CspI, the ninth member of the CspA family of Escherichia coli, is induced upon cold shock.
  J Bacteriol, 181, 1603-1609.  
10483731 S.Fujii, K.Nakasone, and K.Horikoshi (1999).
Cloning of two cold shock genes, cspA and cspG, from the deep-sea psychrophilic bacterium Shewanella violacea strain DSS12.
  FEMS Microbiol Lett, 178, 123-128.  
10476034 S.Phadtare, and M.Inouye (1999).
Sequence-selective interactions with RNA by CspB, CspC and CspE, members of the CspA family of Escherichia coli.
  Mol Microbiol, 33, 1004-1014.  
10216949 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.  
10200963 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.
  Mol Microbiol, 31, 1429-1441.  
9565753 B.J.Hillier, H.M.Rodriguez, and L.M.Gregoret (1998).
Coupling protein stability and protein function in Escherichia coli CspA.
  Fold Des, 3, 87-93.  
  9422597 L.Fang, Y.Hou, and M.Inouye (1998).
Role of the cold-box region in the 5' untranslated region of the cspA mRNA in its transient expression at low temperature in Escherichia coli.
  J Bacteriol, 180, 90-95.  
9799245 M.Stoldt, J.Wöhnert, M.Görlach, and L.R.Brown (1998).
The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases.
  EMBO J, 17, 6377-6384.
PDB code: 1b75
9365254 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.  
  9260955 K.Yamanaka, and M.Inouye (1997).
Growth-phase-dependent expression of cspD, encoding a member of the CspA family in Escherichia coli.
  J Bacteriol, 179, 5126-5130.  
9032054 M.A.Kercher, P.Lu, and M.Lewis (1997).
Lac repressor-operator complex.
  Curr Opin Struct Biol, 7, 76-85.  
  9287018 M.P.Chapot-Chartier, C.Schouler, A.S.Lepeuple, J.C.Gripon, and M.C.Chopin (1997).
Characterization of cspB, a cold-shock-inducible gene from Lactococcus lactis, and evidence for a family of genes homologous to the Escherichia coli cspA major cold shock gene.
  J Bacteriol, 179, 5589-5593.  
9135158 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: 1ah9
  9393697 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.  
  9371456 W.Bae, P.G.Jones, and M.Inouye (1997).
CspA, the major cold shock protein of Escherichia coli, negatively regulates its own gene expression.
  J Bacteriol, 179, 7081-7088.  
  8631682 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.  
8946851 B.T.Farmer, K.L.Constantine, V.Goldfarb, M.S.Friedrichs, M.Wittekind, J.Yanchunas, J.G.Robertson, and L.Mueller (1996).
Localizing the NADP+ binding site on the MurB enzyme by NMR.
  Nat Struct Biol, 3, 995-997.  
8987900 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.  
  8845749 D.Bassolino-Klimas, R.Tejero, S.R.Krystek, W.J.Metzler, G.T.Montelione, and R.E.Bruccoleri (1996).
Simulated annealing with restrained molecular dynamics using a flexible restraint potential: theory and evaluation with simulated NMR constraints.
  Protein Sci, 5, 593-603.  
  8655472 F.Berger, N.Morellet, F.Menu, and P.Potier (1996).
Cold shock and cold acclimation proteins in the psychrotrophic bacterium Arthrobacter globiformis SI55.
  J Bacteriol, 178, 2999-3007.  
  8919809 J.A.Vasina, and F.Baneyx (1996).
Recombinant protein expression at low temperatures under the transcriptional control of the major Escherichia coli cold shock promoter cspA.
  Appl Environ Microbiol, 62, 1444-1447.  
  8844142 K.H.Hu, E.Liu, K.Dean, M.Gingras, W.DeGraff, and N.J.Trun (1996).
Overproduction of three genes leads to camphor resistance and chromosome condensation in Escherichia coli.
  Genetics, 143, 1521-1532.  
  8631696 K.Nakashima, K.Kanamaru, T.Mizuno, and K.Horikoshi (1996).
A novel member of the cspA family of genes that is induced by cold shock in Escherichia coli.
  J Bacteriol, 178, 2994-2997.  
8552679 P.G.Jones, M.Mitta, Y.Kim, W.Jiang, and M.Inouye (1996).
Cold shock induces a major ribosomal-associated protein that unwinds double-stranded RNA in Escherichia coli.
  Proc Natl Acad Sci U S A, 93, 76-80.  
  8755892 P.Graumann, K.Schröder, R.Schmid, and M.A.Marahiel (1996).
Cold shock stress-induced proteins in Bacillus subtilis.
  J Bacteriol, 178, 4611-4619.  
8967899 P.Graumann, and M.A.Marahiel (1996).
A case of convergent evolution of nucleic acid binding modules.
  Bioessays, 18, 309-315.  
8608120 T.N.Jaishree, V.Ramakrishnan, and S.W.White (1996).
Solution structure of prokaryotic ribosomal protein S17 by high-resolution NMR spectroscopy.
  Biochemistry, 35, 2845-2853.  
  8759856 W.Jiang, L.Fang, and M.Inouye (1996).
The role of the 5'-end untranslated region of the mRNA for CspA, the major cold-shock protein of Escherichia coli, in cold-shock adaptation.
  J Bacteriol, 178, 4919-4925.  
  7628456 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: 1stu
  7556054 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: 1pfs
7552728 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.  
7565651 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.  
  7703860 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.  
8197194 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: 1mjc
7530842 M.Ladomery, and J.Sommerville (1994).
Binding of Y-box proteins to RNA: involvement of different protein domains.
  Nucleic Acids Res, 22, 5582-5589.  
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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