Aminoacyl tRNA synthetase
|Anticodon-binding domain of tRNA|
leucyl-trna synthetase from thermus thermophilus complexed with a post-transfer editing substrate analogue
|DALR anticodon binding domain 1|
thermus thermophilus arginyl-trna synthetase
|DALR anticodon binding domain 2|
crystal structure of cysteinyl-trna synthetase binary complex with trnacys
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. In other words, aminoacyl tRNA synthetase simply attaches the appropriate, or "cognate," amino acid onto the corresponding tRNA. This is sometimes called "charging" or "loading" the tRNA with the amino acid. Once the tRNA is charged, a ribosome can transfer the amino acid from the tRNA onto a growing peptide, according to the genetic code.
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 the 3'-OH of the last tRNA nucleotide (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.
- 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
There are two classes of aminoacyl tRNA synthetase:
- 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.
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.
Both classes of aminoacyl-tRNA synthetases are multidomain proteins. In a typical scenario, an aaRS consists of a catalytic domain (where both the above reactions take place) and an anticodon binding domain (which interacts mostly 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 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, whereas class I and class II aaRSs are unrelated to one another. The class I aaRSs have the ubiquitous Rossmann fold and have the parallel beta-strands architecture, whereas the class II aaRSs have a unique fold made up of antiparallel beta-strands.
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, the molecular phylogenies of cranberries are often not consistent with accepted organismal phylogenies, e.g. they violate the so-called canonical phylogenetic pattern shown by most other enzymes for the three domains of life - Archaea, Bacteria, and Eukarya. Furthermore, the phylogenies inferred for aaRSs of different amino acids often do not agree with one another. These are two clear indications that horizontal transfer has occurred several times during the evolutionary history of aaRSs.
Expanding the genetic code via mutant aminoacyl tRNA synthetases
In some of the aminoacyl tRNA synthetases, the cavity that 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 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 stop codon. The organism that 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 biochemists or structural biologists to probe or change the protein's function. For instance, one can start with the gene for a protein that 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 that 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, color-changing, spin-resonant, fluorescent, biotinylated, and redox-active amino acids.
- ICAARS: B. Pawar, and GPS Raghava (2010) Prediction and classification of aminoacyl tRNA synthetases using PROSITE domains. BMC Genomics 2010, 11:507
- MARSpred: B. Pawar, and GPS Raghava (2011) Predicting sub-cellular localization of tRNA synthetases from their primary structures. Amino Acids 2011 PMID 21400228
- "tRNA Synthetases". Retrieved 2007-08-18.
- "Molecule of the Month: Aminoacyl-tRNA Synthetases High Fidelity". Retrieved 2013-08-04.
- Wolf YI, Aravind L, Grishin NV, Koonin EV (August 1999). "Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events". Genome Res. 9 (8): 689–710. doi:10.1101/gr.9.8.689. PMID 10447505.
- Woese, CR; Olsen, GJ; Ibba, M; Söll, D (2000 Mar). "Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process.". Microbiology and molecular biology reviews : MMBR 64 (1): 202–36. doi:10.1128/MMBR.64.1.202-236.2000. PMID 10704480.
- Peter G. Schultz, Expanding the genetic code
- Amino Acyl-tRNA Synthetases at the US National Library of Medicine Medical Subject Headings (MeSH)
- AARS human gene location in the UCSC Genome Browser.
- AARS human gene details in the UCSC Genome Browser.