I. Structure and Mechanism: Protein Synthesis “Mechanism of the peptidyl-transfer reaction of the prokaryotic ribosome” By: Trang Bui

Overview Introduction-Ribosome Structure of Peptidyl Transferase Center Mechanism of Peptide Bond Formation Acid-base catalysis (enthalpic) Proper substrate positioning (entropic) Future Prospects

Ribosome Prokaryote –50S subunit: 23S rRNA and 5S rRNA 31 proteins –30S subunit: 26S rRNA 21 proteins Eukaryote –60S subunit: 28S rRNA, 5.8S rRNA, & 5S rRNA 49 proteins –40S subunit: 18S rRNA 33 proteins

The acceptor ends of A-site and P-site tRNAs are located in the 50S subunit facing the 30S subunit

Review: peptide bond formation

Peptidyl -transferase Peptidyl transferase (PT) center is the site for peptide bond formation Located on 50S Composed of RNA only and no protein is found within 15 Ǻ What can you conclude from this? Ribosome  Ribozyme L27 protein might be involved - deletion of 3 a.a. leads to impaired activity - only exits in some organisms - suggesting that L27 facilitates the proper placement of the tRNA at the PTC

Structure of the PT center Conserved & are located at the core of the PT center tRNA analog (A site) tRNA analog (P site) 23S rRNA bases

Knowing that ribosome is a ribozyme, what mechanism(s) do you think might be used to form peptide bonds between 20 different a.a.?

Chemistry of peptide-bond formation 1: Deprotonation of the amino group 2: Nucleophilic attack and formation of the zwitterionic tetrahedral intermediate 3: Deprotonation and formation of the negatively charged intermediate 4: Product formation and protonation of the leaving oxygen

Mechanism of Peptide Bond Formation 1. Contribution of general acid-base catalysis 2. Contribution of substrate positioning

Acid-base Catalysis In general, this means either proton transfer or abstraction Transition state: chemicals bonds are in the process of being made and broken Unstable + and – charges are being developed Stabilizing charges catalyzes the reaction by lowering the energy of the transition state

Acid-base Catalysis Facilitates the activation of weak nucleophiles Stabilization of poor leaving groups

Role of active site residue A2451 as general acid-base catalyst Crystallized ribosomes with a transition analog CCdA- pPuro N3 A2451 is in close contact (3 Ǻ) with a transition state analog of peptide bond formation, CCdA-pPuro A2451U mutation led to significantly reduced activity Thought to be involved in acid-base catalysis

N3 of A2451 X-ray structures of the ribosome with a P-site tRNA A76 2’OH instead of 2’- deoxyadenosine Within hydrogen bond distance of the  -amino group only in the pre- reaction state Intermediate’s oxyanion points away from the A2451-N3 A site P site 23S rRNA bases WRONG

Experimental Procedure Acid-base Catalysis

A site Aminoacyl-tRNA binds to the A site in the range of 10 s-1 The intrinsic rate of peptide-bond formation was estimated to be > 300 s-1 Thus, the mechanism of peptide-bond formation cannot be studied with the native aa-tRNA under current experimental capabilities. Adio et al. (2006) examined the contribution of acid-base catalysis to peptide bond formation using ribosomes from E.coli with native aa-tRNA

Experimental Procedure The  -amino group of aa-tRNA has a pKa of 8. Assuming that an ionization group (pKa = 7) on the ribosome is involved in the reaction, the rate of the peptide bond formation should be pH dependent. Since the accommodation step is pH independent, the reaction rate may become lower than the accommodation rate at a certain pH. Measured rates of aa-tRNA accommodation and peptide bond formation in the pH range between 6 and 9. pH<6 = EF-Tu precipitation pH>9 = tRNA cleavage

A-site Accommodation Measuring the rate of A-site accommodation using FRET –fMet-tRNA was labeled with a fluorescence donor, fluorescein –Phe-tRNA was labeled with a fluorescence quencher, QSY35 –Time course of accommodation was measured using the stopped-flow method Conclusion: the rates of accommodation were identical at pH values of 6,7, and 8 Curve 1: Phe-tRNA (QSY) Curve 2: Phe-tRNA

Peptide Bond Formation Time course of accommodation was measured using the quench flow method –f[3H]Met-tRNA –[14C]Phe-tRNA Conclusion: The rate of peptide bond formation was independent of pH and indistinguishable from the rate of accommodation

Conclusion from pH reactions This can be explained in 2 ways: 1) The ionization group has no affect on the rate of the PT reaction 2) The chemical step was so fast that the contribution from the protonation step was insignificant If you can’t study the chemistry step using native aa-tRNA, what can you do?

Uncoupling the Chemistry Step from the Accommodation Step Phelac-tRNA -OH is the nucleophile instead of -NH2 Does not change the catalytic mechanism Formation of ester bond  rate limiting step Measuring the reaction rate at pH 6-9 reveals that the reaction rate is independent of pH This indicates that acid-base catalysis is not used to a great extent

Peptide Bond Formation 1. Contribution of general acid-base catalysis 2. Contribution of substrate positioning

2’OH of A76 CCdA-p-Puro inhibits peptidyl transferase activity Substituting 2’-OH of A76 by either 2’-deoxy or 2’- fluoro reduce the activity ~10^6 fold 2’-OH receives a proton from the a-amino group while simultaneously protonates the leaving 3’OH—proton shuttle 2’-OH of A76 orients the nucleophile A site tRNA substrate P site tRNA substrate Ribosome residues HOH* might be used for a proton shuttle

Other Groups Involvement?? 2’-OH of A2451 -Substitution of 2’OH of A2451 by hydrogen impairs peptidyl-transferase activity -Interacts directly with the 2’OH group of the P-site tRNA A site tRNA susbtrates P site tRNA substrates Ribosome residues

The ribosome brings ~10^7 fold enhancement in the rate of PT reaction compared with the second-order reaction in solution Entropy of activation is lowered Enthalpy of activation is the same for both reactions In acid-base and covalent catalysis, enzymes act by lowering the activation enthalpy

Mechanism of Peptide-bond Formation Conclusion: entropic catalysis is the major catalytic mechanism of peptide bond formation  Intra-reactant proton shuttling via the 2’OH of A76 of the P-site tRNA

Future Prospects Obtain structural and mechanistic information for eukaryotic ribosomes Examine the second important function of the PT center: termination of protein synthesis