Aminoacyl tRNA synthetase
From Wikipedia, the free encyclopedia
An aminoacyl tRNA synthetase (aaRS) is an enzyme that catalyzes the esterification of a specific amino acid or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA.
Contents |
Mechanism
The synthetase first binds ATP and the corresponding amino acid or its precursor to form an aminoacyl-adenylate and release inorganic pyrophosphate (PPi). The adenylate-aaRS complex then binds the appropriate tRNA molecule, and the amino acid is transferred from the aa-AMP to either the 2'- or 3'-OH of the last tRNA base (A76) at the 3'-end. Some synthetases also mediate a proofreading reaction to ensure high fidelity of tRNA charging; if the tRNA is found to be improperly charged, the aminoacyl-tRNA bond is hydrolyzed.
Reaction
Reaction:
- amino acid + ATP → aminoacyl-AMP + PPi
- aminoacyl-AMP + tRNA → aminoacyl-tRNA + AMP
Sum of 1 and 2: amino acid + tRNA + ATP → aminoacyl-tRNA + AMP + PPi
Classes
There are two classes of aminoacyl tRNA synthetase:[1]
- Class I has two highly conserved sequence motifs. It aminoacylates at the 2'-OH of an adenosine nucleotide, and is usually monomeric or dimeric (one or two subunits, respectively).
- Class II has three highly conserved sequence motifs. It aminoacylates at the 3'-OH of the same adenosine, and is usually dimeric or tetrameric (two or four subunits, respectively). Although phenylalanine-tRNA synthetase is class II, it aminoacylates at the 2'-OH.
The amino acids are attached to the hydroxyl (-OH) group of the adenosine via the carboxyl (-COOH) group.
Regardless of where the aminoacyl is initially attached to the nucleotide, the 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
Structures
Both classes of aminoacyl-tRNA synthetases are multidomain proteins. Typically, an aaRS consists of a catalytic domain (where both the above reactions take place) and an anticodon binding domain (which mostly interacts with the anticodon region of the tRNA and ensures binding of the correct tRNA to the amino acid). In addition, some aaRSs have additional RNA binding domains and editing domains[2] that cleave incorrectly paired aminoacyl-tRNA molecules.
The catalytic domains of all the aaRSs of a given class are found to be homologous to one another, while class I and class II aaRSs are unrelated to one another. The class I aaRSs have the ubiquitous Rossmann fold and have the antiparallel beta-strands architecture while the class II aaRSs have a unique fold made up of antiparallel beta-strands.
Evolution
Most of the aaRSs of a given specificity are evolutionarily closer to one another than to aaRSs of another specificity. However, AsnRS and GlnRS group within AspRS and GluRS respectively. Most of the aaRSs of a given specificity also belong to a single class. However, there are two distinct versions of the LysRS - one belonging to the class I family and the other belonging to the class II family.
In addition, most of the aaRSs of a given specificity display the so-called canonical phylogenetic pattern in which the enzymes are grouped by the three domains of life - Archaea, Bacteria, and Eukarya, and the root of the phylogenetic tree is present in between the Bacterial branch and the Archaeal/Eukaryal branch.
Expanding the genetic code by means of mutant aminoacyl tRNA synthetases
In some of the aminoacyl tRNA synthetases, the cavity which holds the amino acid can be mutated and modified to carry artificial, unnatural amino acids synthesized in the lab, and to attach them to specific tRNAs. This expands the genetic code, beyond the twenty amino acids which are universal in nature, to include an unnatural amino acid as well. The unnatural amino acid is coded by an otherwise non-coding base triplet such as the "amber codon". The organism which expresses the mutant synthetase can then be genetically programmed to incorporate the unnatural amino acid into any desired position in any protein of interest, allowing chemists to probe, or change, the protein's function. For instance, one can start with the gene for a protein which binds a certain sequence of DNA, and, by directing an unnatural amino acid with a reactive side-chain into the binding site, create a new protein which cuts the DNA at the target-sequence, rather than binding it.
By mutating aminoacyl tRNA synthetases, chemists have expanded the genetic codes of various organisms to include lab-synthesized amino acids with all kinds of useful properties: photoreactive, metal-chelating, xenon-chelating, crosslinking, sugar-bearing, color-changing, spin-resonant, fluorescent, biotinylated, and redox-active amino acids. [3]
References
- ^ "tRNA Synthetases". http://www.biochem.ucl.ac.uk/bsm/xtal/teach/trna/trna.html. Retrieved 2007-08-18.
- ^ "High Fidelity". http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb16_3.html. Retrieved 2007-08-18.
- ^ Peter G. Schultz, http://www3.interscience.wiley.com/journal/109858221/abstract
See also
External links
|