Related ArticlesExtending the family of UNCG-like tetraloop motifs: NMR structure of a CACG tetraloop from coxsackievirus B3.
Biochemistry. 2003 Apr 22;42(15):4373-83
Authors: Du Z, Yu J, Andino R, James TL
Stable RNA tetraloop motifs are found frequently in biologically active RNAs. These motifs carry out a wide variety of functions in RNA folding, in RNA-RNA and RNA-protein interactions. A great deal of knowledge about the structures and functions of tetraloop motifs has accumulated largely due to intensive theoretical, biochemical, and biophysical studies on three most frequently occurring families of tetraloop sequences, namely, the cUNCGg, the cGNRAg, and the gCUUGc sequences. Our knowledge surely is not exhaustive, and efforts are still being made to gain a better understanding. Here we report the NMR structure of a uCACGg tetraloop that occurs naturally within the cloverleaf RNA structure of the 5'-UTR of coxsackievirus B3. This tetraloop is the major determinant for interaction between the cloverleaf RNA and viral 3C protease, which is an essential part of a ribonucleoprotein complex that plays a critical role in the regulation of viral translation and replication. Our structure shows that the CACG tetraloop is closed by a wobble U.G base pair. The structure of the CACG tetraloop is stabilized by extensive base stacking and hydrogen bonding interactions strikingly similar to those previously reported for the cUUCGg tetraloop. Identification of these hallmark structural features strongly supports the existence of an extended YNCG tetraloop family. The U.G base pair closing the stem and the A residue in the loop introduce some small structural and themodynamic distinctions from the canonical cUUCGg tetraloop that may be important for recognition by the viral 3C protease.
Identification of helix capping and beta-turn motifs from NMR chemical shifts
Identification of helix capping and beta-turn motifs from NMR chemical shifts
Abstract We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and 13Cβ chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of beta-turns: I, II, I', II' and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and β-turn motifs are used as input data for...
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02-11-2012 10:31 AM
Solution NMR structure of Dsy0195 homodimer from Desulfitobacterium hafniense: first structure representative of the YabP domain family of proteins involved in spore coat assembly.
Solution NMR structure of Dsy0195 homodimer from Desulfitobacterium hafniense: first structure representative of the YabP domain family of proteins involved in spore coat assembly.
Solution NMR structure of Dsy0195 homodimer from Desulfitobacterium hafniense: first structure representative of the YabP domain family of proteins involved in spore coat assembly.
J Struct Funct Genomics. 2011 Sep 9;
Authors: Yang Y, Ramelot TA, Cort JR, Wang H, Ciccosanti C, Jiang M, Janjua H, Acton TB, Xiao R, Everett JK, Montelione GT, Kennedy MA
Abstract
...
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09-10-2011 06:51 PM
NMR structure of the Bordetella bronchiseptica protein NP_888769.1 establishes a new phage-related protein family PF13554.
NMR structure of the Bordetella bronchiseptica protein NP_888769.1 establishes a new phage-related protein family PF13554.
NMR structure of the Bordetella bronchiseptica protein NP_888769.1 establishes a new phage-related protein family PF13554.
Protein Sci. 2011 Apr 21;
Authors: Atia-Tul-Wahab , Serrano P, Geralt M, Wüthrich K
The solution structure of the hypothetical phage-related protein NP_888769.1 from the gram-negative bacterium Bordetella bronchoseptica contains a well-structured core comprising a five-stranded, antiparallel ?-sheet packed...
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04-27-2011 04:03 PM
[NMR paper] NMR application probes a novel and ubiquitous family of enzymes that alter monosaccha
NMR application probes a novel and ubiquitous family of enzymes that alter monosaccharide configuration.
Related Articles NMR application probes a novel and ubiquitous family of enzymes that alter monosaccharide configuration.
J Biol Chem. 2004 Jun 11;279(24):25544-8
Authors: Ryu KS, Kim C, Kim I, Yoo S, Choi BS, Park C
By exploiting nuclear magnetic resonance (NMR) techniques along with novel applications of saturation difference analysis, we deciphered the functions of the previously uncharacterized products of three bacterial genes, rbsD,...
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11-24-2010 09:51 PM
[NMR paper] Molecular interactions of the Gbeta binding domain of the Ste20p/PAK family of protei
Molecular interactions of the Gbeta binding domain of the Ste20p/PAK family of protein kinases. An isolated but fully functional Gbeta binding domain from Ste20p is only partially folded as shown by heteronuclear NMR spectroscopy.
Related Articles Molecular interactions of the Gbeta binding domain of the Ste20p/PAK family of protein kinases. An isolated but fully functional Gbeta binding domain from Ste20p is only partially folded as shown by heteronuclear NMR spectroscopy.
J Biol Chem. 2001 Nov 2;276(44):41205-12
Authors: Song J, Chen Z, Xu P, Gingras R,...
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11-19-2010 08:44 PM
[NMR paper] Design and NMR analyses of compact, independently folded BBA motifs.
Design and NMR analyses of compact, independently folded BBA motifs.
Related Articles Design and NMR analyses of compact, independently folded BBA motifs.
Fold Des. 1998;3(2):95-103
Authors: Struthers M, Ottesen JJ, Imperiali B
BACKGROUND: Small folded polypeptide motifs represented highly simplified systems for theoretical and experimental studies on protein structure and folding. We have recently reported the design and characterization of a metal-ion-independent 23-residue peptide with a beta beta alpha structure (BBA1), based on the zinc...
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11-17-2010 11:06 PM
[NMR paper] The dimerization stability of the HLH-LZ transcription protein family is modulated by
The dimerization stability of the HLH-LZ transcription protein family is modulated by the leucine zippers: a CD and NMR study of TFEB and c-Myc.
Related Articles The dimerization stability of the HLH-LZ transcription protein family is modulated by the leucine zippers: a CD and NMR study of TFEB and c-Myc.
Biochemistry. 1994 Sep 20;33(37):11296-306
Authors: Muhle-Goll C, Gibson T, Schuck P, Schubert D, Nalis D, Nilges M, Pastore A
In the HLH-LZ protein family, the helix-loop-helix DNA-binding dimerization domain is followed in the sequence by a...
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08-22-2010 03:29 AM
[KPWU blog] [IDP] RTX calcium-binding motifs
RTX calcium-binding motifs
Title:RTX calcium-binding motifs are intrinsically disordered in the absence of calcium: Implication for protein secretion Authors: Alexandre Chenal, J. Iñaki Guijarro, Bertrand Raynal, Muriel Delepierre, and Daniel Ladant Journal: J. Biol. Chem, 10.1074/jbc.M807312200 (online publish first) Note: Not an NMR-based study.http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=194&subd=kpwu&ref=&feed=1
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Extending the family of UNCG-like tetraloop motifs: NMR structure of a CACG tetraloop
Linear Mode
