| Anticodon-binding domain of tRNA |
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leucyl-tRNA synthetase from Thermus thermophilus complexed with a post-transfer editing substrate analogue
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| Identifiers |
| Symbol |
Anticodon_1 |
| Pfam |
PF08264 |
| InterPro |
IPR013155 |
| SCOP |
1ivs |
| SUPERFAMILY |
1ivs |
| Available protein structures: |
| Pfam |
structures |
| PDB |
RCSB PDB; PDBe; PDBj |
| PDBsum |
structure summary |
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| DALR anticodon binding domain 1 |
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Thermus thermophilus arginyl-trna synthetase
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| Identifiers |
| Symbol |
DALR_1 |
| Pfam |
PF05746 |
| Pfam clan |
CL0258 |
| InterPro |
IPR008909 |
| SCOP |
1bs2 |
| SUPERFAMILY |
1bs2 |
| Available protein structures: |
| Pfam |
structures |
| PDB |
RCSB PDB; PDBe; PDBj |
| PDBsum |
structure summary |
|
| DALR anticodon binding domain 2 |
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crystal structure of cysteinyl-tRNA synthetase binary complex with tRNACys
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| Identifiers |
| Symbol |
DALR_2 |
| Pfam |
PF09190 |
| Pfam clan |
CL0258 |
| InterPro |
IPR015273 |
| Available protein structures: |
| Pfam |
structures |
| PDB |
RCSB PDB; PDBe; PDBj |
| PDBsum |
structure summary |
|
An aminoacyl tRNA synthetase (aaRS) is an enzyme that catalyzes 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 other words, aminoacyl tRNA synthetase attaches the appropriate amino acid onto its 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. Aminoacyl tRNA therefore plays an important role in DNA translation, the expression of genes to create proteins.
Contents
- 1 Mechanism
- 2 Classes
- 3 Structures
- 4 Evolution
- 5 Application in biotechnology
- 6 Prediction Servers
- 7 See also
- 8 References
- 9 External links
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, 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 two reactions, the overall reaction is as following:
amino acid + tRNA + ATP → aminoacyl-tRNA + AMP + PPi
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.
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.
In addition, 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. These are two clear indications that horizontal transfer has occurred several times during the evolutionary history of aaRSs.[4]
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.[5] They are also to introduce amino acids bearing reactive functional groups for chemically modifying the target protein.
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: B. Pawar, and GPS Raghava (2011) Predicting sub-cellular localization of tRNA synthetases from their primary structures. Amino Acids 2011 PMID 21400228
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. doi:10.1101/gr.9.8.689. PMID 10447505.
- ^ 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. doi:10.1128/MMBR.64.1.202-236.2000. PMC 98992. PMID 10704480.
- ^ Peter G. Schultz, Expanding the genetic code
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
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Enzymes: CO CS and CN ligases (EC 6.1-6.3)
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| 6.1: Carbon-Oxygen |
- Aminoacyl tRNA synthetase
- Alanine
- Arginine
- Asparagine
- Aspartate
- Cysteine
- D-alanine—poly(phosphoribitol) ligase
- Glutamate
- Glutamine
- Glycine
- Histidine
- Isoleucine
- Leucine
- Lysine
- Methionine
- Phenylalanine
- Proline
- Serine
- Threonine
- Tryptophan
- Tyrosine
- Valine
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| 6.2: Carbon-Sulfur |
- Succinyl coenzyme A synthetase
- Acetyl—CoA synthetase
- Long-chain-fatty-acid—CoA ligase
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| 6.3: Carbon-Nitrogen |
- Glutamine synthetase
- Ubiquitin ligase
- Cullin
- Von Hippel–Lindau tumor suppressor
- UBE3A
- Mdm2
- Anaphase-promoting complex
- UBR1
- Glutathione synthetase
- CTP synthetase
- Adenylosuccinate synthase
- Argininosuccinate synthase
- Holocarboxylase synthetase
- GMP synthase
- Asparagine synthetase
- Carbamoyl phosphate synthetase
- Glutamate–cysteine ligase
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- Biochemistry overview
- Enzymes overview
- By EC number: 1.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
- 10
- 11
- 13
- 14
- 15-18
- 2.1
- 3.1
- 4.1
- 5.1
- 6.1-3
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Ligases: carbon-carbon ligases (EC 6.4)
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| Biotin dependent carboxylation |
- Pyruvate carboxylase
- Acetyl-CoA carboxylase
- Propionyl-CoA carboxylase
- Methylcrotonyl-CoA carboxylase
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| Other |
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- Biochemistry overview
- Enzymes overview
- By EC number: 1.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
- 10
- 11
- 13
- 14
- 15-18
- 2.1
- 3.1
- 4.1
- 5.1
- 6.1-3
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Enzymes: Phosphoric ester and nitrogen-metal ligases (EC 6.5-6.6)
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| 6.5: Phosphoric Ester |
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| 6.6: Nitrogen-Metal |
- Magnesium chelatase
- Cobalt chelatase
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- Biochemistry overview
- Enzymes overview
- By EC number: 1.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
- 10
- 11
- 13
- 14
- 15-18
- 2.1
- 3.1
- 4.1
- 5.1
- 6.1-3
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