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Fig. 18.10
The Elongation Cycle (inprokaryotes)
Footprinting drug binding sites on rRNA (Moazed & Noller)
• Analogous to footprinting a protein binding site on DNA or RNA
• Can map where antibiotics bind to rRNA in the ribosome
• Bound drug prevents chemical modification of the bases (use DMS for purines and CMCT for U)
• Modified bases cause reverse transcriptase to stop during primer extension; doesn’t stop at unmodified (protected) residues
PT loop
PT loop
PT loop
Antibiotic footprints(circled bases)
Antibiotic resistance mutations(circled bases)
Antibiotics that inhibit PT bind to a loop in Domain V of 23S rRNA
PT loop – peptidyl transferase loop
Locating the peptidyl transferase on the large ribosomal subunit
2 analogues (b and c) that should bind to the active site of PT on the large ribosomal subunit
(b) resembles the transition state formed during the real reaction (a)
(c) resembles a substrate and docks into the A site
“Yarus analogue” Fig. 19.21 3rd ed.
From Nissen et al., Science 289:920, 2000
50S subunit from Haloarcula
X-ray crystal structure
Yarus analogue
Fig. 19.16
RNA - greyproteins - gold
Nissen et al., Science 289: 920-930 (2000)
From Nissen et al., Science 289:920, 2000Also Fig. 19.25 in Weaver
Active site: RNA + proteins
Active site: only proteins, closest protein is at least 18 angstroms from the phosphate of the Yarus analogue.
Fig. 19.17
Evidence for rRNA as the PT
1. No ribosomal proteins have been identified that have peptidyl transferase (PT) activity.
2. Drugs (e.g., Chloramphenicol) that inhibit PT bind to the 23S rRNA, in the PT loop of Domain V.
3. Mutations that provide resistance to the drugs that inhibit PT map to the same loop.
4. Nearly all (99%) of the protein can be stripped from the 50S subunit, and still have PT activity.
5. The X-ray crystal structure of the 50S subunit shows that only RNA chains (PT loop, etc.) are
close enough to catalyze a reaction.
• Are there any potential deficiencies with this model or the data that support it?
• How could it be made stronger?
Fig. 19.28
tRNA Charging: The Second Genetic Code
1. tRNA structure
2. the charging reaction
3. aminoacyl tRNA synthetases and tRNA recognition
4. proofreading mechanism
General 3D structure of tRNA
Fig. 19.26
Variable loop
Fig. 19.25
Amino acids are attached to the 3’ terminal nt of tRNAs (adenosine), via the 3’ or 2’ OH group.
Amino acid portion
3’ term. A
tRNA Charging
• Occurs in two steps:
1. AA + ATP Aminoacyl-AMP + PP
2. Aminoacyl-AMP + tRNA Aminoacyl-tRNA + AMP
• Catalyzed by Aminoacyl-tRNA synthetases• Cells must have at least 20 aminoacyl-tRNA
synthetases, one for each amino acid
Recognition of tRNAs by Aminoacyl-tRNA
synthetases: the Second Genetic Code
Aminoacyl-tRNA synthetases recognize mainly the acceptor stem and the anticodon.
From Voet and Voet, Biochemistry
Aminoacyl-tRNA synthetases (cont.)
• Diverse group of enzymes despite recognizing fairly similar substrates
• Not well conserved, however there are 2 main classes– Class I (aminoacylate the 2’ OH) – Class II (aminoacylate the 3’ OH)
• Each class has the same 10 members in all organisms
• The classes bind tRNA somewhat differently, but both bind to the acceptor stem and the anticodon loop
Fig. 19.30
GlnRS – tRNAGln
(Class I)
AspRS-tRNAAsp
(Class II)
Class I - binds from the D loop side
Class II – binds from the Variable loop side
How is charging accuracy achieved, given the structure of amino acids?
• Isoleucine tRNA synthetase (IleRS is Class I) discriminates > 50,000-fold for Ile over
valine • Ile and Val differ by only one methylene
group (Isoleucine has 1 more)• Accuracy achieved by the IleRS having 2
active sites: 1st one activates most small amino acids (to aa-AMP) and the 2nd one hydrolyzes the aa-AMPs smaller than Isoleucine (the editing site)
The double-sieve model for IleRS
Fig. 19.31