A photo-cross-linkable tertiary structure motif found in functionally distinct RNA molecules essential for catalytic function of the hairpin ribozyme

Biochemistry ◽  
1994 ◽  
Vol 33 (4) ◽  
pp. 992-999 ◽  
Author(s):  
Samuel E. Butcher ◽  
John M. Burke
Keyword(s):  
Tertiary Structure ◽  
Hairpin Ribozyme ◽  
Rna Molecules ◽  
Catalytic Function

RNA Structure Analysis: A Multifaceted Approach

1999 ◽  
Author(s):  
Bruce A. Shapiro ◽  
Wojciech Kasprzak
Keyword(s):  
Nucleic Acid ◽  
Secondary Structure ◽  
Tertiary Structure ◽  
Hammerhead Ribozyme ◽  
3D Structure ◽  
Computer Prediction ◽  
Rna Molecules ◽  
Tertiary Interactions ◽  
The One ◽  
Secondary And Tertiary Structure

Genomic information (nucleic acid and amino acid sequences) completely determines the characteristics of the nucleic acid and protein molecules that express a living organism’s function. One of the greatest challenges in which computation is playing a role is the prediction of higher order structure from the one-dimensional sequence of genes. Rules for determining macromolecule folding have been continually evolving. Specifically in the case of RNA (ribonucleic acid) there are rules and computer algorithms/systems (see below) that partially predict and can help analyze the secondary and tertiary interactions of distant parts of the polymer chain. These successes are very important for determining the structural and functional characteristics of RNA in disease processes and hi the cell life cycle. It has been shown that molecules with the same function have the potential to fold into similar structures though they might differ in their primary sequences. This fact also illustrates the importance of secondary and tertiary structure in relation to function. Examples of such constancy in secondary structure exist in transfer RNAs (tRNAs), 5s RNAs, 16s RNAs, viroid RNAs, and portions of retroviruses such as HIV. The secondary and tertiary structure of tRNA Phe (Kim et al., 1974), of a hammerhead ribozyme (Pley et al., 1994), and of Tetrahymena (Cate et al., 1996a, 1996b) have been shown by their crystal structure. Currently little is known of tertiary interactions, but studies on tRNA indicate these are weaker than secondary structure interactions (Riesner and Romer, 1973; Crothers and Cole, 1978; Jaeger et al., 1989b). It is very difficult to crystallize and/or get nuclear magnetic resonance spectrum data for large RNA molecules. Therefore, a logical place to start in determining the 3D structure of RNA is computer prediction of the secondary structure. The sequence (primary structure) of an RNA molecule is relatively easy to produce. Because experimental methods for determining RNA secondary and tertiary structure (when the primary sequence folds back on itself and forms base pairs) have not kept pace with the rapid discovery of RNA molecules and their function, use of and methods for computer prediction of secondary and tertiary structures have increasingly been developed.

Hairpin and hammerhead ribozymes: how different are they?

2002 ◽  
Vol 30 (6) ◽  
pp. 1116-1119 ◽  
Author(s):  
J. M. Burke
Keyword(s):  
Metal Ions ◽  
Conformational Changes ◽  
Experimental Work ◽  
Hammerhead Ribozyme ◽  
Active Conformation ◽  
Hairpin Ribozyme ◽  
Hammerhead Ribozymes ◽  
Active Structure ◽  
Catalytic Function ◽  
Recent Experimental Work

Recent experimental work on the hairpin and hammerhead ribozymes suggests that they have more similarities than previously suspected. Notably, each is now known to function as a true RNA catalyst, not requiring metal ions for folding or catalytic function. The active conformation of the hairpin ribozyme has been established by crystallography, and is well supported by biochemical and biophysical evidence that has identified conformational changes and key nucleotides required for catalysis. Analogous work is under way to establish the active structure of the hammerhead ribozyme.

PROTON PROBES OF THE TERTIARY STRUCTURE OF TRANSFER RNA MOLECULES

1978 ◽  
pp. 493-516 ◽  
Author(s):  
David R. Kearns ◽  
Philip H. Bolton
Keyword(s):  
Tertiary Structure ◽  
Transfer Rna ◽  
Rna Molecules

scholarly journals Four ribose 2'-hydroxyl groups essential for catalytic function of the hairpin ribozyme.

1993 ◽  
Vol 268 (26) ◽  
pp. 19458-19462
Author(s):  
B.M. Chowrira ◽  
A Berzal-Herranz ◽  
C.F. Keller ◽  
J.M. Burke
Keyword(s):  
Hydroxyl Groups ◽  
Hairpin Ribozyme ◽  
Catalytic Function

Tertiary Structure Stabilization Promotes Hairpin Ribozyme Ligation†

Biochemistry ◽  
1999 ◽  
Vol 38 (34) ◽  
pp. 11040-11050 ◽  
Author(s):  
Martha J. Fedor
Keyword(s):  
Tertiary Structure ◽  
Hairpin Ribozyme ◽  
Structure Stabilization

scholarly journals Characterization of a Cellulase Containing a Family 30 Carbohydrate-Binding Module (CBM) Derived from Clostridium thermocellum CelJ: Importance of the CBM to Cellulose Hydrolysis

2003 ◽  
Vol 185 (2) ◽  
pp. 504-512 ◽  
Author(s):  
Takamitsu Arai ◽  
Rie Araki ◽  
Akiyoshi Tanaka ◽  
Shuichi Karita ◽  
Tetsuya Kimura ◽  
...  
Keyword(s):  
Clostridium Thermocellum ◽  
Tertiary Structure ◽  
Cellulose Hydrolysis ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Module ◽  
Strong Activity ◽  
Catalytic Function ◽  
Catalytic Module ◽  
Calorimetric Studies

ABSTRACT Clostridium thermocellum CelJ is a modular enzyme containing a family 30 carbohydrate-binding module (CBM) and a family 9 catalytic module at its N-terminal moiety. To investigate the functions of the CBM and the catalytic module, truncated derivatives of CelJ were constructed and characterized. Isothermal titration calorimetric studies showed that the association constants (Ka ) of the CBM polypeptide (CBM30) for the binding of cellopentaose and cellohexaose were 1.2 × 104 and 6.4 × 104 M−1, respectively, and that the binding of CBM30 to these ligands is enthalpically driven. Qualitative analyses showed that CBM30 had strong affinity for cellulose and β-1,3-1,4-mixed glucan such as barley β-glucan and lichenan. Analyses of the hydrolytic action of the enzyme comprising the CBM and the catalytic module showed that the enzyme is a processive endoglucanse with strong activity towards carboxymethylcellulose, barley β-glucan and lichenan. By contrast, the catalytic module polypeptide devoid of the CBM showed negligible activity toward these substrates. These observations suggest that the CBM is extremely important not only because it mediates the binding of the enzyme to the substrates but also because it participates in the catalytic function of the enzyme or contributes to maintaining the correct tertiary structure of the family 9 catalytic module for expressing enzyme activity.

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