Bacteria (70S) — RF1/RF2 terminate; RF3 turns over the factor
50S LARGE SUBUNIT (catalysis; 23S rRNA PTC)
┌──────────────────────────────────────────────────┐
Exit tunnel ───► │ Peptidyl Transferase │
│ Center (PTC) │
│ (rRNA active site pocket) │
│ │
│ RF1/RF2 GGQ loop │
│ (↓ inserts into PTC) │
│ GGQ │
│ │ │
│ │ H₂O (activated) │
│ │ │ │
│ └───────┼─────────► nucleophilic │
│ │ attack on │
│ peptide──C(=O)–O–A76 (P-site tRNA) │
│ ^ │
│ │ ester bond (to be cut) │
└──────────────────────────────────────────────────┘
▲ ▲
│ │
A site │ P site │ E site
30S SMALL SUBUNIT (decoding) ┌──┴──┐ ┌────┴───┐ ┌───┴───┐
(16S rRNA decoding center) │ A │ │ P │ │ E │
│U A A│ STOP CODON │ (peptidyl- │
mRNA 5'→3' ────────────────► │ │◄─ recognized by │ tRNA) │ (exit) │
└──┬──┘ RF1(RFx=PxT) └──────────┘ └──────┘
│ or RF2(SPF) │
│ │
16S rRNA DC: A1492/A1493/G530 flip to │
validate stop + position RF codon-reader│
│ │
RF1 / RF2 body in A site │
(codon-reading motifs) │
PxT (RF1) / SPF (RF2) │
│ │
RF3–GTP docks after hydrolysis, promotes RF1/2 release
│
Recycling (post-release):
RRF + EF-G–GTP split 70S; IF3 resets 30S with mRNA/tRNAs off
Flow: stop enters A → RF1/2 recognize via PxT/SPF at the decoding center → GGQ loop reaches the PTC → positions H₂O to hydrolyze the peptidyl-tRNA ester → peptide released → RF3–GTP ejects RF → RRF/EF-G/IF3 recycle the ribosome.
Eukaryotes (80S) — eRF1 reads all stops; eRF3 gates timing
60S LARGE SUBUNIT (catalysis; 28S rRNA PTC)
┌──────────────────────────────────────────────────┐
│ Peptidyl Transferase │
│ Center (PTC) │
│ │
│ eRF1 GGQ loop (inserted) │
│ GGQ │
│ │ │
│ │ H₂O (activated) │
│ │ │ │
│ └───────┼────────► hydrolysis of │
│ │ peptidyl-tRNA │
│ peptide──C(=O)–O–A76 (P-site tRNA) │
└──────────────────────────────────────────────────┘
▲ ▲
│ │
A site │ P site │ E site
40S SMALL SUBUNIT (decoding) ┌──┴──┐ ┌────┴───┐ ┌───┴───┐
(18S rRNA decoding center) │ A │ │ P │ │ E │
│U A G│ STOP CODON │ (peptidyl-│ (exit)│
mRNA 5'→3' ────────────────► │ │◄─ read by eRF1 │ tRNA) │ └──────┘
└──┬──┘ └──────────┘
│
eRF1 recognition motifs at DC:
NIKS (stop triplet sensor)
YxCxxxF (specificity/fit)
│
eRF3–GTP escorts eRF1, hydrolyzes GTP to time release
│
Recycling: ABCE1 (Rli1) splits 80S → 60S + 40S; factors clear mRNA/tRNA
Flow: stop in A → eRF1 recognizes via NIKS / YxCxxxF (with 18S rRNA DC support) → eRF1-GGQ into PTC → H₂O hydrolysis → peptide release → eRF3-GTP turnover → ABCE1 splits subunits for recycling.
Legend & micro-chemistry
- A/P/E sitesAminoacyl / Peptidyl / Exit tRNA slots on the small+large subunit composite.
- STOPUAA/UAG/UGA in A site; no cognate tRNA exists.
- RF codon readers
- Bacteria: RF1 (PxT) reads UAA/UAG; RF2 (SPF) reads UAA/UGA.
- EukaryoteseRF1 reads all three; motifs NIKS & YxCxxxF engage the stop triplet.
How “stop override” fits (Sec & Pyl)
- UGA→Sec: SECIS RNA + dedicated tRNA^Sec/SelB/eEFSec deliver Sec-tRNA to the A site, out-competing RFs, so GGQ-mediated hydrolysis does not occur.
- UAG→Pyl: tRNA^Pyl + PylRS charge and deliver Pyl-tRNA to A site in organisms with the pyl system; again, RF access is blocked, translation continues.
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