scholarly journals Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Eike C. Schulz ◽  
Markus Seiler ◽  
Cecilia Zuliani ◽  
Franka Voigt ◽  
Vladimir Rybin ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Base Stacking ◽  
Rna Chaperone ◽  
Rna Interaction

scholarly journals Structure of anEscherichia coliHfq:RNA complex at 0.97 Å resolution

2014 ◽  
Vol 70 (11) ◽  
pp. 1492-1497 ◽  
Author(s):  
Eike C. Schulz ◽  
Orsolya Barabas
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Binding Site ◽  
Small Rnas ◽  
Target Genes ◽  
Rna Binding ◽  
Base Pairing ◽  
Rna Chaperone ◽  
Target Mrnas ◽  
Rna Interaction

In bacteria, small RNAs (sRNAs) silence or activate target genes through base pairing with the mRNA, thereby modulating its translation. A central player in this process is the RNA chaperone Hfq, which facilitates the annealing of sRNAs with their target mRNAs. Hfq has two RNA-binding surfaces that recognize A-rich and U-rich sequences, and is believed to bind an sRNA–mRNA pair simultaneously. However, how Hfq promotes annealing remains unclear. Here, the crystal structure ofEscherichia coliHfq is presented in complex with U6-RNA bound to its proximal binding site at 0.97 Å resolution, revealing the Hfq–RNA interaction in exceptional detail.

scholarly journals Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI

2020 ◽  
Vol 48 (9) ◽  
pp. 5106-5118
Author(s):  
Ken-ichi Miyazono ◽  
Delong Wang ◽  
Tomoko Ito ◽  
Masaru Tanokura
Keyword(s):  
Crystal Structure ◽  
Complex Structure ◽  
Dna Glycosylase ◽  
Protein Surface ◽  
Base Stacking ◽  
Recognition Sequence ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Recognition Sites ◽  
Indirect Readout

Abstract R.PabI is a restriction DNA glycosylase that recognizes the sequence 5′-GTAC-3′ and hydrolyses the N-glycosidic bond of adenine in the recognition sequence. R.PabI drastically bends and unwinds the recognition sequence of double-stranded DNA (dsDNA) and flips the adenine and guanine bases in the recognition sequence into the catalytic and recognition sites on the protein surface. In this study, we determined the crystal structure of the R.PabI-dsDNA complex in which the dsDNA is drastically bent by the binding of R.PabI but the base pairs are not unwound. This structure is predicted to be important for the indirect readout of the recognition sequence by R.PabI. In the complex structure, wedge loops of the R.PabI dimer are inserted into the minor groove of dsDNA to stabilize the deformed dsDNA structure. A base stacking is distorted between the two wedge-inserted regions. R.PabI is predicted to utilize the distorted base stacking for the detection of the recognition sequence.

O6-carboxymethyl-G forms a sequence context dependent wobble base pair with T

2014 ◽  
Vol 70 (a1) ◽  
pp. C215-C215
Author(s):  
Fang Zhang ◽  
Masaru Tsunoda ◽  
Kaoru Suzuki ◽  
Yuji Kikuchi ◽  
Oliver Wilkinson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Base Pair ◽  
Twist Angle ◽  
Pair Formation ◽  
Carboxyl Group ◽  
Major Groove ◽  
Base Stacking ◽  
Sequence Context ◽  
X Ray

Previously, we reported the crystal structure of DNA d(CGCGXATTCGCG), which revealed that X (O6-carboxymethyl-G) at the 5th position forms a Watson-Crick (WC) type pair with T (Fig. 1a) similar to the canonical A:T pair [1]. In order to investigate the versatility of X in the base-pair formation, another DNA d(CGCXAATTTGCG) containing X at the 4th position has been X-ray analyzed using four different crystals. In the four crystals, the T bases are always largely wobbled into the major groove side to form a hydrogen bond between N3 of T and the carboxyl group of X. In addition, a water molecule bridges between the two bases through two hydrogen bonds to stabilize the pair formation (Fig.1b). This high-wobble (hW) pair is quite different from the previously reported one [1]. Now we succeeded to reveal the two types of pairing modes of X:T pair, WC type and hW type. Since the four crystals were obtained in different conditions, the large displacement of T cannot be ascribed to the interactions with solvent cations. Another possibility is Hoechst33258 used for crystallization. But, as the crystals were obtained in both the presence and the absence of Hoechst33258, this is not the case. The remaining possibility would be the location of the modified base, because the sequence of the used DNA contains an AATT tract at the center and two CGCG tracts at the both ends. The AATT tract is well known to be more flexible (ω*≍ -160) than CGCG tract (ω*≍ -8.70). We found that the WC type X:T pairing requires a large ω angle (-180) between the bases. When X is located at the 5th position (in the AATT tract), the WC type is allowed to occur, while at the 4th position (in the CGCG tract) the WC type is difficult to occur. Here it could be concluded that X form a pair with T in the mode of WC if it is in the flexible tract, while in the mode of hW if it is in the rigid tract, because T base is out of the base stacking. * propeller twist angle between the two bases.

scholarly journals Crystal structure of Bacillus subtilis anti-TRAP protein, an antagonist of TRAP/RNA interaction

2005 ◽  
Vol 102 (49) ◽  
pp. 17600-17605 ◽  
Author(s):  
M. B. Shevtsov ◽  
Y. Chen ◽  
P. Gollnick ◽  
A. A. Antson
Keyword(s):  
Crystal Structure ◽  
Bacillus Subtilis ◽  
Rna Interaction

Crystal Structure Determination of Glycerol-Containing Lipids from Electron Diffraction Data. Use of Analog Compounds Based upon Configurational Isomers of Cyclopentane-1, 2, 3-TRIOL

1977 ◽  
Vol 35 ◽  
pp. 24-25
Author(s):  
Douglas L. Dorset ◽  
Anthony J. Hancock
Keyword(s):  
Crystal Structure ◽  
Electron Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Crystal Surface ◽  
Coherent Scattering ◽  
Crystal Structure Determination ◽  
Electron Diffraction Data ◽  
Polar Group ◽  
Axis Orientation

Lipids containing long polymethylene chains were among the first compounds subjected to electron diffraction structure analysis. It was only recently realized, however, that various distortions of thin lipid microcrystal plates, e.g. bends, polar group and methyl end plane disorders, etc. (1-3), restrict coherent scattering to the methylene subcell alone, particularly if undistorted molecular layers have well-defined end planes. Thus, ab initio crystal structure determination on a given single uncharacterized natural lipid using electron diffraction data can only hope to identify the subcell packing and the chain axis orientation with respect to the crystal surface. In lipids based on glycerol, for example, conformations of long chains and polar groups about the C-C bonds of this moiety still would remain unknown.One possible means of surmounting this difficulty is to investigate structural analogs of the material of interest in conjunction with the natural compound itself. Suitable analogs to the glycerol lipids are compounds based on the three configurational isomers of cyclopentane-1,2,3-triol shown in Fig. 1, in which three rotameric forms of the natural glycerol derivatives are fixed by the ring structure (4-7).

Spherulitic crystal growth in the prodissoconch larval of Crassostrea virginica

1983 ◽  
Vol 41 ◽  
pp. 518-519
Author(s):  
George G. Cocks ◽  
Louis Leibovitz ◽  
DoSuk D. Lee
Keyword(s):  
Crystal Structure ◽  
Crassostrea Virginica ◽  
Crystal Orientation ◽  
Developmental Changes ◽  
Gastrula Stage ◽  
Orthorhombic Crystal ◽  
Orthorhombic Crystal Structure ◽  
Stages Of Growth ◽  
Early Stages ◽  
Initial Deposition

Our understanding of the structure and the formation of inorganic minerals in the bivalve shells has been considerably advanced by the use of electron microscope. However, very little is known about the ultrastructure of valves in the larval stage of the oysters. The present study examines the developmental changes which occur between the time of conception to the early stages of Dissoconch in the Crassostrea virginica(Gmelin), focusing on the initial deposition of inorganic crystals by the oysters.The spawning was induced by elevating the temperature of the seawater where the adult oysters were conditioned. The eggs and sperm were collected separately, then immediately mixed for the fertilizations to occur. Fertilized animals were kept in the incubator where various stages of development were stopped and observed. The detailed analysis of the early stages of growth showed that CaCO3 crystals(aragonite), with orthorhombic crystal structure, are deposited as early as gastrula stage(Figuresla-b). The next stage in development, the prodissoconch, revealed that the crystal orientation is in the form of spherulites.

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