Aminoacyl tRNA synthetase
| Anticodon-binding domain of tRNA | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 leucyl-tRNA synthetase from Thermus thermophilus complexed with a post-transfer editing substrate analogue | |||||||||
| Identifiers | |||||||||
| Symbol | Anticodon_2 | ||||||||
| Pfam | PF08264 | ||||||||
| InterPro | IPR013155 | ||||||||
| SCOP | 1ivs | ||||||||
| SUPERFAMILY | 1ivs | ||||||||
| |||||||||
| DALR anticodon binding domain 1 | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 Thermus thermophilus arginyl-trna synthetase | |||||||||
| Identifiers | |||||||||
| Symbol | DALR_1 | ||||||||
| Pfam | PF05746 | ||||||||
| Pfam clan | CL0258 | ||||||||
| InterPro | IPR008909 | ||||||||
| SCOP | 1bs2 | ||||||||
| SUPERFAMILY | 1bs2 | ||||||||
| |||||||||
| DALR anticodon binding domain 2 | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 crystal structure of cysteinyl-tRNA synthetase binary complex with tRNACys | |||||||||
| Identifiers | |||||||||
| Symbol | DALR_2 | ||||||||
| Pfam | PF09190 | ||||||||
| Pfam clan | CL0258 | ||||||||
| InterPro | IPR015273 | ||||||||
| |||||||||
An aminoacyl tRNA synthetase (aaRS) is an enzyme that attaches the appropriate amino acid onto its tRNA. It does so by catalyzing the esterification of a specific cognate amino acid or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA. In humans, the 21 different types of aa-tRNA are made by the 21 different aminoacyl-tRNA synthetases, one for each amino acid of the genetic code.
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. Aminoacyl tRNA therefore plays an important role in DNA translation, the expression of genes to create proteins.
As genetic efficiency evolved in higher organisms, 13 new domains with no obvious association with the catalytic activity of aaRSs genes have been added.
Mechanism
The synthetase first binds ATP and the corresponding amino acid (or its precursor) to form an aminoacyl-adenylate, releasing inorganic pyrophosphate (PPi). The adenylate-aaRS complex then binds the appropriate tRNA molecule's D arm, 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.
The mechanism can be summarized in the following reaction series:
- Amino Acid + ATP → Aminoacyl-AMP + PPi
- Aminoacyl-AMP + tRNA → Aminoacyl-tRNA + AMP
Summing the reactions, the highly exergonic overall reaction is as follows:
- Amino Acid + tRNA + ATP → Aminoacyl-tRNA + AMP + PPi
Some synthetases also mediate a editing reaction to ensure high fidelity of tRNA charging. If the incorrect tRNA is added (aka. the tRNA is found to be improperly charged), the aminoacyl-tRNA bond is hydrolyzed. This can happen when two amino acids have different properties even if they have similar shapes—as is the case with Valine and Threonine.
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 a terminal adenosine nucleotide on tRNA, and it 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 a terminal adenosine on tRNA, 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. 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[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, 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.
The alpha helical anticodon binding domain of Arginyl, Glycyl and Cysteinyl-tRNA synthetases is known as the DALR domain after characteristic conserved amino acids.[3]
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.
The molecular phylogenies of aaRSs are often not consistent with accepted organismal phylogenies. That is, 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. In addition, aaRS paralogs within the same species show a high degree of divergence between them. These are clear indications that horizontal transfer has occurred several times during the evolutionary history of aaRSs.[4][5]
A widespread belief in the evolutionary stability of this superfamily, meaning that every organism has all the aaRSs for their corresponding aminoacids is misconceived. A large-scale genomic analysis on ~2500 prokaryotic genomes showed that many of them miss one or more aaRS genes whereas many genomes have 1 or more paralogs.[5] AlaRS, GlyRS, LeuRS, IleRS and ValRS are the most evolutionarily stable members of the family. GluRS, LysRS and CysRS often have paralogs, whereas AsnRS, GlnRS, PylRS and SepRS are often absent from many genomes.
Application in biotechnology
In some of the aminoacyl tRNA synthetases, the cavity that holds the amino acid can be mutated and modified to carry unnatural amino acids synthesized in the lab, and to attach them to specific tRNAs. This expands the genetic code, beyond the twenty canonical amino acids found in nature, to include an unnatural amino acid as well. The unnatural amino acid is coded by a nonsense (TAG, TGA, TAA), quadruplet, or in some cases a redundant rare 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, spin-resonant, fluorescent, biotinylated, and redox-active amino acids.[6] Another use is introducing amino acids bearing reactive functional groups for chemically modifying the target protein.
Noncatalytic domains
The novel domain additions to aaRS genes are accretive and progressive up the Tree of Life. [7][8][9]The strong evolutionary pressure for these small non-catalytic protein domains suggested their importance.[10]Findings beginning in 1999 and later revealed a previously unrecognized layer of biology: these proteins control gene expression within the cell of origin, and when released exert homeostatic and developmental control in specific human cell types, tissues and organs during adult or fetal development or both, including pathways associated with angiogenesis, inflammation, the immune response, the mechanistic target of rapamycin (mTOR) signalling, apoptosis, tumorigenesis, and interferon gamma (IFN-γ) and p53 signalling.[11][12][13][14][15][16][17][18][19]The extracellular regions and splice variants of aaRSs responsible for these non-canonical functions are referred to as Physiocrines.
Prediction Servers
- ICAARS: B. Pawar, and GPS Raghava (2010) Prediction and classification of aminoacyl tRNA synthetases using PROSITE domains. BMC Genomics 2010, 11:507
- MARSpred: Pawar, B.; Raghava, GPS (2011). "Predicting sub-cellular localization of tRNA synthetases from their primary structures". Amino Acids. 42 (5): 1703–13. PMID 21400228. doi:10.1007/s00726-011-0872-8.
- Prokaryotic AARS database: Chaliotis et al., (2017). The complex evolutionary history of aminoacyl-tRNA synthetases. Nucleic Acids Res. 2017 Feb 17;45(3):1059-1068. doi:10.1093/nar/gkw1182.
See also
References
- ↑ "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. PMID 10447505. doi:10.1101/gr.9.8.689.
- ↑ Woese, CR; Olsen, GJ; Ibba, M; Söll, D (March 2000). "Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process.". Microbiology and molecular biology reviews : MMBR. 64 (1): 202–36. PMC 98992
. PMID 10704480. doi:10.1128/MMBR.64.1.202-236.2000. - 1 2 Chaliotis, Anargyros; Vlastaridis, Panayotis; Mossialos, Dimitris; Ibba, Michael; Becker, Hubert D.; Stathopoulos, Constantinos; Amoutzias, Grigorios D. (2017-02-17). "The complex evolutionary history of aminoacyl-tRNA synthetases". Nucleic Acids Research. 45 (3): 1059–1068. ISSN 0305-1048. PMC 5388404 . PMID 28180287. doi:10.1093/nar/gkw1182.
- ↑ Peter G. Schultz, Expanding the genetic code
- ↑ Ludmerer, SW; Schimmel, P (August 5, 1987). "Construction and analysis of deletions in the amino-terminal extension of glutamine tRNA synthetase of Saccharomyces cerevisiae.". Journal of Biological Chemistry : JBC. 262 (22): 10807–10813. PMID 3301842.
- ↑ Eriani, Gilbert; Delarue, M (Sep 13, 1990). "Partition of tNRA Synthetases into Two Classes Based on Mutually Exclusive Sets of Sequence Motifs". Nature. 347 (6289): 203–206. PMID 2203971. doi:10.1038/347203a0.
- ↑ Cusack, S (Dec 1, 1997). "Aminoacyl-tRNA synthetases.". Curr opin Struct Biol. 7 (6): 881–889. PMID 9434910.
- ↑ Lo, Wing-Sze; Gardiner, E (July 18, 2014). "Human tRNA Synthetase Catalytic Nulls with Diverse Functions". Nature. 345 (6194): 328–332. doi:10.1126/science.1252943.
- ↑ Wakasugi; Schimmel, P (April 2, 1999). "Two Distinct Cytokines Released from a Human Aminoacyl-tRNA Synthetase". Science. 284 (5411): 147–151. doi:10.1126/science.284.5411.147.
- ↑ Lareau, LF; Green, RE (June 1, 2004). "The evolving roles of alternative splicing". Current Opinion in Structural Biology. 14 (3): 273–282. doi:10.1016/j.sbi.2004.05.002.
- ↑ Wakasugi, K; Slike, BM (Jan 8, 2002). "A human aminoacyl-tRNA synthetase as a regulator of angiogenesis". 99 (1): 173–177. doi:10.1073/pnas.012602099.
- ↑ Tzima, E; Reader, JS (Dec 3, 2004). "VE-cadherin Links tRNA Synthetase Cytokine to Anti-angiogenic Function". 280: 2405–2408. doi:10.1074/jbc.C400431200.
- ↑ Kawahara, A; Didier, YR (August 2009). "Noncanonical Activity of Seryl-Transfer RNA Synthetase and Vascular Development". Trends in Cardiovascular Medicine. 19 (6): 179–182. doi:10.1016/j.tcm.2009.11.001.
- ↑ Zhou, Q; Kapoor, M (Jan 2010). "Orthogonal use of a human tRNA synthetase active site to achieve multifunctionality". Nature Structural & Molecular Biology. 17 (1): 57–61. doi:10.1038/nsmb.1706.
- ↑ Park, SG; Hye, JK (May 3, 2005). "Human lysyl-tRNA synthetase is secreted to trigger proinflammatory response". PNAS. 102 (18): 6356–6361. doi:10.1073/pnas.0500226102.
- ↑ Arif, A; Jai, J (Jan 25, 2011). "Phosphorylation of glutamyl-prolyl tRNA synthetase by cyclin-dependent kinase 5 dictates transcript-selective translational control". PNAS. 108 (4): 1415–1420. doi:10.1073/pnas.1011275108.
- ↑ Guo, M; Schimmel , P (March 2013). "Essential nontranslational functions of tRNA synthetases.". Nat Chem Biol. 9 (3): 145–153. doi:10.1038/nchembio.1158.
External links
- 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.
This article incorporates text from the public domain Pfam and InterPro IPR015273
This article incorporates text from the public domain Pfam and InterPro IPR008909