Biology
- Amino Acid Activation
Codons of an mRNA molecule contain genetic messages that are carried by the mRNA and they need to be translated to form the corresponding sequence of amino acids that will form the polypeptide chain and subsequently the protein. The tRNA transfers amino...
- Novel Amino Acids Can Be Inserted At Certain Stop Codons
KEY CONCEPTS:Changes in the reading of specific codons can occur in individual genes. The insertion of seleno-Cys-tRNA at certain UGA codons requires several proteins to modify the Cys-tRNA and insert it into the ribosome. Pyrrolysine can be inserted...
- 23s Rrna Has Peptidyl Transferase Activity
KEY CONCEPTS:Peptidyl transferase activity resides exclusively in the 23S rRNA. The sites involved in the functions of 23S rRNA are less well identified than those of 16S rRNA, but the same general pattern is observed: bases at certain positions...
- The Acceptor Stem And Anticodon Are At Ends Of The Tertiary Structure
KEY CONCEPTS:The clover-leaf forms an L-shaped tertiary structure with the acceptor arm at one end and the anticodon arm at the other end. The secondary structure of each tRNA folds into a compact L-shaped tertiary structure in which the 3 end that binds...
- Transfer Rna (trna) Forms A Cloverleaf
KEY TERMS:Transfer RNA (tRNA) is the intermediate in protein synthesis that interprets the genetic code. Each tRNA can be linked to an amino acid. The tRNA has an anticodon sequence that complementary to a triplet codon representing the amino acid....
Biology
Aminoacyl-tRNA synthetases fall into two groups
KEY CONCEPTS:
- Aminoacyl-tRNA synthetases are divided into the class I and class II groups by sequence and structural similarities.
Synthetases have been divided into two general groups, each containing 10 enzymes, on the basis of the structure of the domain that contains the active site. A general type of organization that applies to both groups is represented in Figure 7.14. The catalytic domain includes the binding sites for ATP and amino acid. It can be recognized as a large region that is interrupted by an insertion of the domain that binds the acceptor helix of the tRNA. This places the terminus of the tRNA in proximity to the catalytic site. A separate domain binds the anticodon region of tRNA. Those synthetases that are multimeric also possess an oligomerization domain (for review see Schimmel, 1987).
Class I synthetases have an N-terminal catalytic domain that is identified by the presence of two short, partly conserved sequences of amino acids, sometimes called "signature sequences." The catalytic domain takes the form of a motif called a nucleotide-binding fold (which is also found in other classes of enzymes that bind nucleotides). The nucleotide fold consists of alternating parallel ?-strands and ?-helices; the signature sequence forms part of the ATP-binding site. The insertion that contacts the acceptor helix of tRNA differs widely between different class I enzymes. The C-terminal domains of the class I synthetases, which include the tRNA anticodon-binding domain and any oligomerization domain, also are quite different from one another.
Class II enzymes share three rather general similarities of sequence in their catalytic domains. The active site contains a large antiparallel ?-sheet surrounded by ?-helices. Again, the acceptor helix-binding domain that interrupts the catalytic domain has a structure that depends on the individual enzyme. The anticodon-binding domain tends to be N-terminal. The location of any oligomerization domain is widely variable.
The lack of any apparent relationship between the two groups of synthetases is a puzzle. Perhaps they evolved independently of one another. This makes it seem possible even that an early form of life could have existed with proteins that were made up of just the 10 amino acids coded by one type or the other.
A general model for synthetase·tRNA binding suggests that the protein binds the tRNA along the "side" of the L-shaped molecule. The same general principle applies for all synthetase·tRNA binding: the tRNA is bound principally at its two extremities, and most of the tRNA sequence is not involved in recognition by a synthetase. However, the detailed nature of the interaction is different between class I and class II enzymes, as can be seen from the models of Figure 7.15, which are based on crystal structures. The two types of enzyme approach the tRNA from opposite sides, with the result that the tRNA-protein models look almost like mirror images of one another.
A class I enzyme (Gln-tRNA synthetase) approaches the D-loop side of the tRNA. It recognizes the minor groove of the acceptor stem at one end of the binding site, and interacts with the anticodon loop at the other end. Figure 7.16 is a diagrammatic representation of the crystal structure of the tRNAGln·synthetase complex. A revealing feature of the structure is that contacts with the enzyme change the structure of the tRNA at two important points. These can be seen by comparing the dotted and solid lines in the anticodon loop and acceptor stem:
- Bases U35 and U36 in the anticodon loop are pulled farther out of the tRNA into the protein.
- The end of the acceptor stem is seriously distorted, with the result that base pairing between U1 and A72 is disrupted. The single-stranded end of the stem pokes into a deep pocket in the synthetase protein, which also contains the binding site for ATP.
This structure explains why changes in U35, G73, or the U1-A72 base pair affect the recognition of the tRNA by its synthetase. At all of these positions, hydrogen bonding occurs between the protein and tRNA (Rould et al., 1989).
A class II enzyme (Asp-tRNA synthetase) approaches the tRNA from the other side, and recognizes the variable loop, and the major groove of the acceptor stem, as drawn in Figure 7.17. The acceptor stem remains in its regular helical conformation. ATP is probably bound near to the terminal adenine. At the other end of the binding site, there is a tight contact with the anticodon loop, which has a change in conformation that allows the anticodon to be in close contact with the protein (Ruff et al., 1991).
- Amino Acid Activation
Codons of an mRNA molecule contain genetic messages that are carried by the mRNA and they need to be translated to form the corresponding sequence of amino acids that will form the polypeptide chain and subsequently the protein. The tRNA transfers amino...
- Novel Amino Acids Can Be Inserted At Certain Stop Codons
KEY CONCEPTS:Changes in the reading of specific codons can occur in individual genes. The insertion of seleno-Cys-tRNA at certain UGA codons requires several proteins to modify the Cys-tRNA and insert it into the ribosome. Pyrrolysine can be inserted...
- 23s Rrna Has Peptidyl Transferase Activity
KEY CONCEPTS:Peptidyl transferase activity resides exclusively in the 23S rRNA. The sites involved in the functions of 23S rRNA are less well identified than those of 16S rRNA, but the same general pattern is observed: bases at certain positions...
- The Acceptor Stem And Anticodon Are At Ends Of The Tertiary Structure
KEY CONCEPTS:The clover-leaf forms an L-shaped tertiary structure with the acceptor arm at one end and the anticodon arm at the other end. The secondary structure of each tRNA folds into a compact L-shaped tertiary structure in which the 3 end that binds...
- Transfer Rna (trna) Forms A Cloverleaf
KEY TERMS:Transfer RNA (tRNA) is the intermediate in protein synthesis that interprets the genetic code. Each tRNA can be linked to an amino acid. The tRNA has an anticodon sequence that complementary to a triplet codon representing the amino acid....