A Possible Mechanism of Peptide Bond Formation on Ribosome without Mediation of Peptidyl Transferase

1999 ◽  
Vol 200 (2) ◽  
pp. 193-205 ◽  
Author(s):  
GOURAB KANTI DAS ◽  
DHANANJAY BHATTACHARYYA ◽  
DEBI PROSAD BURMA
Keyword(s):  
Bond Formation ◽  
Peptide Bond ◽  
Peptide Bond Formation ◽  
Peptidyl Transferase

On Ribosome Conservation and Evolution

2006 ◽  
Vol 52 (3-4) ◽  
pp. 359-374 ◽  
Author(s):  
Ilana Agmon ◽  
Anat Bashan ◽  
Ada Yonath
Keyword(s):  
Bond Formation ◽  
Peptide Bond ◽  
Binding Modes ◽  
Peptide Bond Formation ◽  
Peptidyl Transferase ◽  
Peptide Bonds ◽  
Peptidyl Transferase Center ◽  
Enzymatic Function ◽  
Rotatory Motion ◽  
Rna Fold

The ribosome is a ribozyme whose active site, the peptidyl transferase center (PTC), is situated within a highly conserved universal symmetrical region that connects all ribosomal functional centers involved in amino acid polymerization. The linkage between this elaborate architecture and A-site tRNA position revealed that the A-> P-site passage of the tRNA terminus in the peptidyl transferase center is performed by a rotatory motion, synchronized with the overall tRNA/mRNA sideways movement. Guided by the PTC, the rotatory motion leads to stereochemistry suitable for peptide bond formation, as well as for substrate-mediated catalysis, consistent with quantum mechanical calculations elucidating the transition state mechanism for peptide bond formation and indicating that the peptide bond is being formed during the rotatory motion. Analysis of substrate binding modes to inactive and active ribosomes illuminated the significant PTC mobility and supported the hypothesis that the ancient ribosome produced single peptide bonds and non-coded chains, utilizing free amino acids. Genetic control of the reaction evolved after poly-peptides capable of enzymatic function were created, and an ancient stable RNA fold was converted into tRNA molecules. As the symmetry relates only the backbone fold and nucleotide orientations, but not nucleotide sequence, it emphasizes the superiority of functional requirement over sequence conservation, and indicates that the PTC has evolved by gene fusion, presumably by taking advantage of similar RNA fold structures.

scholarly journals Ribosome crystallography: catalysis and evolution of peptide-bond formation, nascent chain elongation and its co-translational folding

2005 ◽  
Vol 33 (3) ◽  
pp. 488-492 ◽  
Author(s):  
A. Bashan ◽  
A. Yonath
Keyword(s):  
Bond Formation ◽  
Peptide Bond ◽  
Trigger Factor ◽  
Chain Elongation ◽  
Peptide Bond Formation ◽  
Peptidyl Transferase ◽  
Chemical Catalysis ◽  
Nascent Chain ◽  
Peptidyl Transferase Centre ◽  
Folding Space

A ribosome is a ribozyme polymerizing amino acids, exploiting positional- and substrate-mediated chemical catalysis. We showed that peptide-bond formation is facilitated by the ribosomal architectural frame, provided by a sizable symmetry-related region in and around the peptidyl transferase centre, suggesting that the ribosomal active site was evolved by gene fusion. Mobility in tunnel components is exploited for elongation arrest as well as for trafficking nascent proteins into the folding space bordered by the bacterial chaperone, namely the trigger factor.

A Competitive Model Reaction for the Ribosomal Peptide Bond Formation Catalyzed by Peptidyl Transferase

2014 ◽  
Vol 496-500 ◽  
pp. 17-20
Author(s):  
Lin Cheng ◽  
Nian Hong ◽  
Xiang Qun Xu ◽  
Jie Yang ◽  
You Quan Zhong
Keyword(s):  
Reaction Pathway ◽  
Bond Formation ◽  
Peptide Bond ◽  
Model Reaction ◽  
Reaction Pathways ◽  
Peptide Bond Formation ◽  
Peptidyl Transferase ◽  
Reaction Field ◽  
Self Consistent ◽  
Competitive Model

In this work, a series of theoretical methods were employed to investigate the reaction mechanisms of ribosomal peptide bond formation catalyzed by peptidyl transferase. For the studies described in this paper, reaction pathways and free energy barriers for the model reaction of the peptide bond synthesis were studied by performing Ab initio calculation. Two self-consistent reaction field (SCRF) methods were used to calculate of the whole reaction pathway. These results show that the present theoretical reaction mechanism is a potential and competitive one for the reaction modeling of the ribosomal peptide synthesis.

scholarly journals Abstract P-29: Cryoem Study of the Inhibition of Bacterial Ribosomes by Madumycin II

2021 ◽  
Vol 11 (Suppl_1) ◽  
pp. S24-S25
Author(s):  
Alena Yakusheva ◽  
Olga Shulenina ◽  
Evgeny Pichkur ◽  
Alena Paleskava ◽  
Alexander Myasnikov ◽  
...  
Keyword(s):  
Amino Acid ◽  
High Resolution ◽  
Bond Formation ◽  
Protein Translation ◽  
Peptide Bond ◽  
Peptide Bond Formation ◽  
Peptidyl Transferase ◽  
Peptidyl Transferase Center ◽  
70S Ribosome ◽  
Madumycin Ii

Background: The efficiency of widely used antibiotics is limited by continuous improvement of resistance mechanisms. Thus, the research of poorly studied drugs that have not received practical use until now becomes relevant again. Protein translation is one of the major targets for antibiotics. Madumycin II (MADU) is an antibiotic of the streptogramin A class that binds to the peptidyl transferase center of the initiated bacterial 70S ribosome inhibiting the first cycle of peptide bond formation (I.A. Osterman et al. Nucleic Acids Res., 2017). The ability of MADU to interfere with translating ribosome is an open question that we address by investigation of high-resolution cryo-EM structures of MADU bound 70S ribosome complexes from Escherichia coli. Methods: Purified initiated and translating ribosome complexes preincubated with MADU were applied onto freshly glow discharged carbon-coated grids (Quantifoil R 1.2/1.3) and flash-frozen in the liquid ethane pre-cooled by liquid nitrogen in the Vitrobot Mark IV. Frozen grids were transferred into an in-house Titan Krios microscope. Data were collected using EPU software. Movie stacks were preprocessed in Warp software. For image processing, we have used several software packages: Relion 3.1, CryoSPARC, and CisTEM. The model was built in Coot. Results: We have obtained high-resolution cryo-EM structures of two ribosomal complexes with MADU before and after the first cycle of peptide bond formation with an average resolution of 2.3 Å. Preliminary analysis of the structures shows no major differences in the MADU binding mode to the ribosomal complexes under study suggesting that the quantity of amino acid residues attached to the P-site tRNA does not impact MADU bonding. Moreover, in both cases, we observed similar destabilization of the CCA-ends of A- and P-site tRNAs underlining the comparable influence of MADU on the ribosomal complexes. Conclusion: Our results suggest that although MADU binding site is located in the peptidyl transferase center, the presence of the second amino acid residue on the P-site tRNA does not preclude antibiotic binding. We assume that further elongation of the polypeptide chain would not have any impact either. High conformational lability of the CCA-ends of tRNA at the A and P sites upon binding of MADU obviously plays an important role in the inhibition mechanism of the bacterial ribosome. The further structural and biochemical analysis will be necessary to shed more light on the detailed mechanism of MADU action.

scholarly journals Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state

2017 ◽  
Vol 45 (12) ◽  
pp. 7507-7514 ◽  
Author(s):  
Ilya A. Osterman ◽  
Nelli F. Khabibullina ◽  
Ekaterina S. Komarova ◽  
Pavel Kasatsky ◽  
Victor G. Kartsev ◽  
...  
Keyword(s):  
Bond Formation ◽  
Peptide Bond ◽  
Peptide Bond Formation ◽  
Peptidyl Transferase ◽  
Peptidyl Transferase Center ◽  
Inactive State ◽  
Madumycin Ii

scholarly journals Essential Mechanisms in the Catalysis of Peptide Bond Formation on the Ribosome

2005 ◽  
Vol 280 (43) ◽  
pp. 36065-36072 ◽  
Author(s):  
Malte Beringer ◽  
Christian Bruell ◽  
Liqun Xiong ◽  
Peter Pfister ◽  
Peter Bieling ◽  
...  
Keyword(s):  
Ph Dependence ◽  
Bond Formation ◽  
Peptide Bond ◽  
Activation Entropy ◽  
Peptide Bond Formation ◽  
Peptidyl Transferase ◽  
Peptidyl Transferase Center ◽  
Chemical Catalysis ◽  
Catalytic Function ◽  
Peptidyl Transfer

Peptide bond formation is the main catalytic function of the ribo-some. 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.

Antibiotic inhibition of the movement of tRNA substrates through a peptidyl transferase cavity

1995 ◽  
Vol 73 (11-12) ◽  
pp. 877-885 ◽  
Author(s):  
Bo T. Porse ◽  
Cristina Rodriguez-Fonseca ◽  
Ilia Leviev ◽  
Roger A. Garrett
Keyword(s):  
Bond Formation ◽  
Ribosomal Subunit ◽  
Peptide Bond ◽  
Inhibitory Mechanism ◽  
Large Ribosomal Subunit ◽  
Peptide Bond Formation ◽  
Peptidyl Transferase ◽  
Subunit Interactions ◽  
Antibiotic Inhibition ◽  
Peptidyl Transferase Centre

The present review attempts to deal with movement of tRNA substrates through the peptidyl transferase centre on the large ribosomal subunit and to explain how this movement is interrupted by antibiotics. It builds on the concept of hybrid tRNA states forming on ribosomes and on the observed movement of the 5′ end of P-site-bound tRNA relative to the ribosome that occurs on peptide bond formation. The 3′ ends of the tRNAs enter, and move through, a catalytic cavity where antibiotics are considered to act by at least three primary mechanisms: (i) they interfere with the entry of the aminoacyl moiety into the catalytic cavity before peptide bond formation; (ii) they inhibit movement of the nascent peptide along the peptide channel, a process that may generally involve destabilization of the peptidyl tRNA, and (iii) they prevent movement of the newly deacylated tRNA between the P/P and hybrid P/E sites on peptide bond formation.Key words: peptidyl transferase cavity, transient tRNA states, antibiotics, inhibitory mechanism, subunit–subunit interactions.

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