Biomaterial Database

Evidence for RNA in the peptidyl transferase center of Escherichia coli ribosomes as indicated by fluorescence. 1992

W D Picking, and O W Odom, and B Hardesty

Department of Chemistry, University of Texas, Austin 78712.

A coumarin derivative was covalently attached to either the amino acid or the 5' end of phenylalanine-specific transfer RNA (tRNA(phe)). Its fluorescence was quenched by methyl viologen when the tRNA was free in solution or bound to Escherichia coli ribosomes. Methyl viologen as a cation in solution has a strong affinity for the ionized phosphates of a nucleic acid and so can be used to qualitatively measure the presence of RNA in the immediate vicinity of the tRNA-linked coumarins upon binding to ribosomes. Fluorescence lifetime measurements indicate that the increase in fluorescence quenching observed when the tRNAs are bound into the peptidyl site of ribosomes is due to static quenching by methyl viologen bound to RNA in the immediate vicinity of the fluorophore. The data lead to the conclusion that the ribosome peptidyl transferase center is rich in ribosomal RNA. Movement of the fluorophore at the N-terminus of the nascent peptide as it is extended or movement of the tRNA acceptor stem away from the peptidyl transferase center during peptide bond formation appears to result in movement of the probe into a region containing less rRNA.

UI	MeSH Term	Description	Entries
D010269	Paraquat	A poisonous dipyridilium compound used as contact herbicide. Contact with concentrated solutions causes irritation of the skin, cracking and shedding of the nails, and delayed healing of cuts and wounds.	Methyl Viologen,Gramoxone,Paragreen A,Viologen, Methyl
D010458	Peptidyl Transferases	Acyltransferases that use AMINO ACYL TRNA as the amino acid donor in formation of a peptide bond. There are ribosomal and non-ribosomal peptidyltransferases.	Peptidyl Transferase,Peptidyl Translocase,Peptidyl Translocases,Peptidyltransferase,Transpeptidase,Transpeptidases,Peptidyltransferases,Transferase, Peptidyl,Transferases, Peptidyl,Translocase, Peptidyl,Translocases, Peptidyl
D004926	Escherichia coli	A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.	Alkalescens-Dispar Group,Bacillus coli,Bacterium coli,Bacterium coli commune,Diffusely Adherent Escherichia coli,E coli,EAggEC,Enteroaggregative Escherichia coli,Enterococcus coli,Diffusely Adherent E. coli,Enteroaggregative E. coli,Enteroinvasive E. coli,Enteroinvasive Escherichia coli
D012270	Ribosomes	Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.	Ribosome
D012329	RNA, Bacterial	Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.	Bacterial RNA
D012360	RNA, Transfer, Phe	A transfer RNA which is specific for carrying phenylalanine to sites on the ribosomes in preparation for protein synthesis.	Phenylalanine-Specific tRNA,Transfer RNA, Phe,tRNAPhe,tRNA(Phe),Phe Transfer RNA,Phenylalanine Specific tRNA,RNA, Phe Transfer,tRNA, Phenylalanine-Specific