title: Essential mechanisms in the catalysis of peptide bond formation on the ribosome.
abstract: Peptide bond formation is the main catalytic function of the ribosome. The mechanism of catalysis is presumed to be highly conserved in all organisms. We tested the conservation by comparing mechanistic features of the peptidyl transfer reaction on ribosomes from Escherichia coli and the Gram-positive bacterium Mycobacterium smegmatis. In both cases, the major contribution to catalysis was the lowering of the activation entropy. The rate of peptide bond formation was pH independent with the natural substrate, amino-acyl-tRNA, but was slowed down 200-fold with decreasing pH when puromycin was used as a substrate analog. Mutation of the conserved base A2451 of 23 S rRNA to U did not abolish the pH dependence of the reaction with puromycin in M. smegmatis, suggesting that A2451 did not confer the pH dependence. However, the A2451U mutation alters the structure of the peptidyl transferase center and changes the pattern of pH-dependent rearrangements, as probed by chemical modification of 23 S rRNA. A2451 seems to function as a pivot point in ordering the structure of the peptidyl transferase center rather than taking part in chemical catalysis.
authors.affiliation: Institute of Physical Biochemistry, University of Witten/Herdecke, Stockumer Strasse 10, 58448 Witten, Germany.
authors.forename: Malte
authors.initials: M
authors.lastname: Beringer
authors.forename: Christian
authors.initials: C
authors.lastname: Bruell
authors.forename: Liqun
authors.initials: L
authors.lastname: Xiong
authors.forename: Peter
authors.initials: P
authors.lastname: Pfister
authors.forename: Peter
authors.initials: P
authors.lastname: Bieling
authors.forename: Vladimir I
authors.initials: VI
authors.lastname: Katunin
authors.forename: Alexander S
authors.initials: AS
authors.lastname: Mankin
authors.forename: Erik C
authors.initials: EC
authors.lastname: Böttger
authors.forename: Marina V
authors.initials: MV
authors.lastname: Rodnina
mesh_terms: D000483:Alleles; D001665:Binding Sites; D002384:Catalysis; D017124:Conserved Sequence; D019277:Entropy; D004926:Escherichia coli / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D016296:Mutagenesis; D009154:Mutation; D020102:Mycobacterium smegmatis / Q000378:metabolism; D010455:Peptides / Q000737:chemistry*; D010957:Plasmids / Q000378:metabolism; D017354:Point Mutation; D011487:Protein Conformation; D011691:Puromycin / Q000737:chemistry / Q000494:pharmacology; D012313:RNA / Q000737:chemistry; D012338:RNA, Ribosomal, 23S / Q000737:chemistry*; D012343:RNA, Transfer / Q000737:chemistry; D012270:Ribosomes / Q000737:chemistry / Q000378:metabolism*; D013379:Substrate Specificity; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D010455:Peptides; D012338:RNA, Ribosomal, 23S; D011691:Puromycin; D012313:RNA; D012343:RNA, Transfer