The hairpin ribozyme substrate binding-domain: A highly constrained D-shaped conformation

Pinard, R., Lambert, D., Heckman, J. E., Esteban, J. A., Gundlach, C. W., Hampel, K. J., Glick, G. D., Walter, N. G., Major, F., Burke, J. M. (March 2001) The hairpin ribozyme substrate binding-domain: A highly constrained D-shaped conformation. Journal of Molecular Biology, 307 (1). pp. 51-65. ISSN 0022-2836

URL: http://www.ncbi.nlm.nih.gov/pubmed/11243803
DOI: 10.1006/jmbi.2000.4472

Abstract

The two domains of the hairpin ribozyme-substrate complex, usually depicted as straight structural elements, must interact with one another in order to form an active conformation. Little is known about the internal geometry of the individual domains in an active docked complex. Using various crosslinking and structural approaches in conjunction with molecular modeling (constraint-satisfaction program MC-SYM), we have investigated the conformation of the substrate-binding domain in the context of the active docked ribozyme-substrate complex. The model generated by MC-SYM showed that the domain is not straight but adopts a bent conformation (D-shaped) in the docked state of the ribozyme, indicating that the two helices bounding the internal loop are closer than was previously assumed. This arrangement rationalizes the observed ability of hairpin ribozymes with a circularized substrate-binding strand to cleave a circular substrate, and provides essential information concerning the organization of the substrate in the active conformation. The internal geometry of the substrate-binding strand places G8 of the substrate-binding strand near the cleavage site, which has allowed us to predict the crucial role played by this nucleotide in the reaction chemistry.

Item Type: Paper
Uncontrolled Keywords: hairpin ribozyme modeling crosslinking domain A RNA TERTIARY STRUCTURE DISULFIDE CROSS-LINKS HAMMERHEAD RIBOZYME CATALYTIC CLEAVAGE CRYSTAL-STRUCTURE LOOP-B COMPLEX MOLECULES KINETICS RESIDUES
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification
CSHL Authors:
Communities: CSHL labs > Malinow lab
Depositing User: Matt Covey
Date: March 2001
Date Deposited: 16 Jan 2014 17:37
Last Modified: 16 Jan 2014 17:37
Related URLs:
URI: http://repository.cshl.edu/id/eprint/29286

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