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Nucleic Acids Research 2004 32(18):5512-5518; doi:10.1093/nar/gkh888
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Published online 12 October 2004

Nucleic Acids Research, Vol. 32 No. 18 © Oxford University Press 2004; all rights reserved

The A2453-C2499 wobble base pair in Escherichia coli 23S ribosomal RNA is responsible for pH sensitivity of the peptidyltransferase active site conformation

Mark A. Bayfield, Jill Thompson and Albert E. Dahlberg*

Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI 02912, USA

* To whom correspondence should be addressed. Tel: +1 401 863 2223; Fax: +1 401 863 1182; Email: Albert_Dahlberg{at}Brown.edu
Present address: Mark A. Bayfield, NICHD, NIH, Bethesda, MD 02892, USA

Received August 11, 2004; Revised and Accepted September 26, 2004

Peptide bond formation, catalyzed by the ribosomal peptidyltransferase, has long been known to be sensitive to monovalent cation concentrations and pH. More recently, we and others have shown that residue A2451 in the peptidyltransferase center of the Escherichia coli 50S ribosomal subunit changes conformation in response to alterations in pH, depending on ionic conditions and temperature. Two wobble pairs, A2453-C2499 and A2450-C2063, have been proposed as potential candidates to convey pH-dependent flexibility to the peptidyltransferase center. Each is presumed to possess a near-neutral pKa, and both lie in proximity to A2451. We show through mutagenesis and chemical probing that the identity of the A2453-C2499 base pair, but not the A2450-C2063 base pair, is critical for the pH-dependent structural rearrangement of A2451. We conclude that, while the A2453-C2499 base pair may be important for maintaining the structure of the active site in the E.coli peptidyltransferase center, its lack of conservation makes it, and consequently its near-neutral pKa, unlikely to contribute to function during peptide bond formation.


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