Solution NMR Structure and Backbone Dynamics of the Major Cold-Shock Protein (CspA) fromEscherichia coli:  Evidence for Conformational Dynamics in the Single-Stranded RNA-Binding Site†,‡

Biochemistry ◽  
1998 ◽  
Vol 37 (31) ◽  
pp. 10881-10896 ◽  
Author(s):  
Wenqing Feng ◽  
Roberto Tejero ◽  
Diane E. Zimmerman ◽  
Masayori Inouye ◽  
Gaetano T. Montelione
Keyword(s):  
Binding Site ◽  
Cold Shock ◽  
Rna Binding ◽  
Conformational Dynamics ◽  
Nmr Structure ◽  
Backbone Dynamics ◽  
Cold Shock Protein ◽  
Solution Nmr ◽  
Fromescherichia Coli

scholarly journals Solution NMR structure of the cold-shock protein from the hyperthermophilic bacterium Thermotoga maritima

2001 ◽  
Vol 268 (9) ◽  
pp. 2527-2539 ◽  
Author(s):  
Werner Kremer ◽  
Benjamin Schuler ◽  
Stefan Harrieder ◽  
Matthias Geyer ◽  
Wolfram Gronwald ◽  
...  
Keyword(s):  
Cold Shock ◽  
Thermotoga Maritima ◽  
Nmr Structure ◽  
Cold Shock Protein ◽  
Solution Nmr ◽  
Hyperthermophilic Bacterium

scholarly journals NMR structure and dynamics of the RNA-binding site for the histone mRNA stem-loop binding protein

RNA ◽  
2002 ◽  
Vol 8 (1) ◽  
pp. 83-96 ◽  
Author(s):  
ERIC S. DEJONG ◽  
WILLIAM F. MARZLUFF ◽  
EDWARD P. NIKONOWICZ
Keyword(s):  
Binding Site ◽  
Rna Binding ◽  
Binding Protein ◽  
Nmr Structure ◽  
Histone Mrna ◽  
Stem Loop ◽  
Structure And Dynamics

Solution NMR Structure of Ribosome-binding Factor A (RbfA), A Cold-shock Adaptation Protein from Escherichia coli

2003 ◽  
Vol 327 (2) ◽  
pp. 521-536 ◽  
Author(s):  
Yuanpeng Janet Huang ◽  
G.V.T. Swapna ◽  
P.K. Rajan ◽  
Haiping Ke ◽  
Bing Xia ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Cold Shock ◽  
Nmr Structure ◽  
Solution Nmr ◽  
Ribosome Binding ◽  
Binding Factor

scholarly journals Solution NMR Structure and Functional Analysis of the Integral Membrane Protein YgaP fromEscherichia coli

2014 ◽  
Vol 289 (34) ◽  
pp. 23482-23503 ◽  
Author(s):  
Cédric Eichmann ◽  
Christos Tzitzilonis ◽  
Enrica Bordignon ◽  
Innokentiy Maslennikov ◽  
Senyon Choe ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Membrane Protein ◽  
Integral Membrane Protein ◽  
Nmr Structure ◽  
Solution Nmr ◽  
Fromescherichia Coli

scholarly journals Solution NMR Structure of Yeast Succinate Dehydrogenase Flavinylation Factor Sdh5 Reveals a Putative Sdh1 Binding Site

Biochemistry ◽  
2012 ◽  
Vol 51 (43) ◽  
pp. 8475-8477 ◽  
Author(s):  
Alexander Eletsky ◽  
Mi-Young Jeong ◽  
Hyung Kim ◽  
Hsiau-Wei Lee ◽  
Rong Xiao ◽  
...  
Keyword(s):  
Binding Site ◽  
Succinate Dehydrogenase ◽  
Nmr Structure ◽  
Solution Nmr

scholarly journals RNA and DNA Binding Epitopes of the Cold Shock Protein TmCsp from the Hyperthermophile Thermotoga maritima

2020 ◽  
Vol 39 (5) ◽  
pp. 487-500
Author(s):  
Konstanze von König ◽  
Norman Kachel ◽  
Hans Robert Kalbitzer ◽  
Werner Kremer
Keyword(s):  
Nucleic Acids ◽  
Cold Shock ◽  
Rna Binding ◽  
Dissociation Constants ◽  
Thermotoga Maritima ◽  
Cold Shock Protein ◽  
Binding Motif ◽  
Purine Base ◽  
High Affinity ◽  
Binding Epitope

AbstractProkaryotic cold shock proteins (CSPs) are considered to play an important role in the transcriptional and translational regulation of gene expression, possibly by acting as transcription anti-terminators and “RNA chaperones”. They bind with high affinity to single-stranded nucleic acids. Here we report the binding epitope of TmCsp from Thermotoga maritima for both single-stranded DNA and RNA, using heteronuclear 2D NMR spectroscopy. At “physiological” growth temperatures of TmCsp (≥ 343 K), all oligonucleotides studied have dissociation constants between 1.6 ((dT)7) and 25.2 ((dA)7) μM as determined by tryptophan fluorescence quenching. Reduction of the temperature to 303 K leads to a pronounced increase of affinity for thymidylate (dT)7 and uridylate (rU)7 heptamers with dissociation constants of 4.0 and 10.8 nM, respectively, whereas the weak binding of TmCsp to cytidylate, adenylate, and guanylate heptamers (dC)7, (dA)7, and (dT)7 is almost unaffected by temperature. The change of affinities of TmCsp for (dT)7 and (rU)7 by approximately 3 orders of magnitude shows that it represents a cold chock sensor that switches on the cold shock reaction of the cell. A temperature dependent conformational switch of the protein is required for this action. The binding epitope on TmCsp for the ssDNA and RNA heptamers is very similar and comprises β-strands 1 and 2, the loop β1–β2 as well as the loops connecting β3 with β4 and β4 with β5. Besides the loop regions, surprisingly, mainly the RNA-binding motif RNP1 is involved in ssDNA and RNA binding, while only two amino acids, H28 and W29, of the postulated RNA-binding motif RNP2 interact with the uridylate and thymidylate homonucleotides, although a high affinity in the nanomolar range is achieved. This is in contrast to the binding properties of other CSPs or cold shock domains, where RNP1 as well as RNP2 are involved in binding. TmCsp takes up a unique position since it is the only one which possesses a tryptophan residue instead of a usually highly conserved phenylalanine or tyrosine residue at the end of RNP2. NMR titrations suggest that neither (dT)7 nor (rU)7 represent the full binding motif and that non-optimal intercalation of W29 into these oligonucleotides blocks the access of the RNP2 site to the DNA or RNA. NMR-experiments with (dA)7 suggest an interaction of W29 with the adenine ring. Full binding seems to require at least one single purine base well-positioned within a thymine- or uracil-rich stretch of nucleic acids.

scholarly journals Solution NMR Structure, Backbone Dynamics, and Heme-Binding Properties of a Novel CytochromecMaturation Protein CcmE fromDesulfovibrio vulgaris

Biochemistry ◽  
2012 ◽  
Vol 51 (18) ◽  
pp. 3705-3707 ◽  
Author(s):  
James M. Aramini ◽  
Keith Hamilton ◽  
Paolo Rossi ◽  
Asli Ertekin ◽  
Hsiau-Wei Lee ◽  
...  
Keyword(s):  
Nmr Structure ◽  
Backbone Dynamics ◽  
Solution Nmr ◽  
Heme Binding ◽  
Binding Properties

Solution NMR Structure of the NlpC/P60 Domain of Lipoprotein Spr fromEscherichia coli: Structural Evidence for a Novel Cysteine Peptidase Catalytic Triad†

Biochemistry ◽  
2008 ◽  
Vol 47 (37) ◽  
pp. 9715-9717 ◽  
Author(s):  
James M. Aramini ◽  
Paolo Rossi ◽  
Yuanpeng J. Huang ◽  
Li Zhao ◽  
Mei Jiang ◽  
...  
Keyword(s):  
Catalytic Triad ◽  
Nmr Structure ◽  
Solution Nmr ◽  
Fromescherichia Coli ◽  
Cysteine Peptidase

scholarly journals A Temperature-Independent Cold-Shock Protein Homolog Acts as a Virulence Factor in Xylella fastidiosa

2016 ◽  
Vol 29 (5) ◽  
pp. 335-344 ◽  
Author(s):  
Lindsey P. Burbank ◽  
Drake C. Stenger
Keyword(s):  
Deletion Mutant ◽  
Cold Shock ◽  
Rna Binding ◽  
Xylella Fastidiosa ◽  
Cold Shock Protein ◽  
Plant Colonization ◽  
Wild Type ◽  
Cold Temperatures ◽  
Mrna Stabilization

Xylella fastidiosa, causal agent of Pierce’s disease (PD) of grapevine, is a fastidious organism that requires very specific conditions for replication and plant colonization. Cold temperatures reduce growth and survival of X. fastidiosa both in vitro and in planta. However, little is known regarding physiological responses of X. fastidiosa to temperature changes. Cold-shock proteins (CSP), a family of nucleic acid–binding proteins, act as chaperones facilitating translation at low temperatures. Bacterial genomes often encode multiple CSP, some of which are strongly induced following exposure to cold. Additionally, CSP contribute to the general stress response through mRNA stabilization and posttranscriptional regulation. A putative CSP homolog (Csp1) with RNA-binding activity was identified in X. fastidiosa Stag’s Leap. The csp1 gene lacked the long 5′ untranslated region characteristic of cold-inducible genes and was expressed in a temperature-independent manner. As compared with the wild type, a deletion mutant of csp1 (∆csp1) had decreased survival rates following cold exposure and salt stress in vitro. The deletion mutant also was significantly less virulent in grapevine, as compared with the wild type, in the absence of cold stress. These results suggest an important function of X. fastidiosa Csp1 in response to cellular stress and during plant colonization.

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