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Aminoacyl tRNA synthetase

 

 
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Aminoacyl tRNA synthetase
 
 
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An aminoacyl tRNA synthetase (aaRS) is an enzyme
Enzyme

Enzymes are biomolecules that catalysis chemical reactions. Almost all enzymes are proteins. In enzymatic reactions, the molecules at the beginning of the process are called Substrate , and the enzyme converts them into different molecules, the products....
 that catalyzes the esterification
Esterification

Esterification is the general name for a chemical reaction in which two reactants form an ester as the product . Esters are common in organic chemistry and biological materials, and often have a characteristic pleasant, fruity odor....
 of a specific amino acid
Amino acid

In chemistry, an amino acid is a molecule containing both amine and carboxyl functional groups. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent....
 or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA
Aminoacyl-tRNA

Aminoacyl-tRNA is tRNA to which its cognated amino acid is adhered. Its role is to deliver the amino acid to the ribosome where it will be incorporated into the polypeptide chain that is being produced....
.

synthetase first binds ATP
Adenosine triphosphate

This article is about the chemical used by cells as an energy carrier. For other uses, see ATP .Adenosine-5'-triphosphate is a multifunctional nucleotide, and plays an important role in cell biology as a coenzyme that is the "molecule unit of currency" of intracellular energy transfer....
 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.






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An aminoacyl tRNA synthetase (aaRS) is an enzyme
Enzyme

Enzymes are biomolecules that catalysis chemical reactions. Almost all enzymes are proteins. In enzymatic reactions, the molecules at the beginning of the process are called Substrate , and the enzyme converts them into different molecules, the products....
 that catalyzes the esterification
Esterification

Esterification is the general name for a chemical reaction in which two reactants form an ester as the product . Esters are common in organic chemistry and biological materials, and often have a characteristic pleasant, fruity odor....
 of a specific amino acid
Amino acid

In chemistry, an amino acid is a molecule containing both amine and carboxyl functional groups. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent....
 or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA
Aminoacyl-tRNA

Aminoacyl-tRNA is tRNA to which its cognated amino acid is adhered. Its role is to deliver the amino acid to the ribosome where it will be incorporated into the polypeptide chain that is being produced....
.

Mechanism

The synthetase first binds ATP
Adenosine triphosphate

This article is about the chemical used by cells as an energy carrier. For other uses, see ATP .Adenosine-5'-triphosphate is a multifunctional nucleotide, and plays an important role in cell biology as a coenzyme that is the "molecule unit of currency" of intracellular energy transfer....
 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:
  1. amino acid + ATP ? aminoacyl-AMP + PPi
  2. 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:
  • Class I has two highly conserved sequence motifs. It aminoacylates
    Aminoacylation

    Aminoacylation is the process of adding an aminoacyl group to a compound.See also*Acylation*Transfer RNA#Aminoacylation...
     at the 2'-OH of an adenosine
    Adenosine

    Adenosine is a nucleoside composed of a molecule of adenine attached to a ribose sugar molecule moiety via a ?-N9-glycosidic bond....
     nucleotide
    Nucleotide

    Nucleotides are molecules that comprise the structural units of RNA and DNA. Additionally, nucleotides play central roles in metabolism. In that capacity, they serve as sources of chemical energy , participate in cell signaling , and are incorporated into important cofactors of enzymatic reactions ....
    , and is usually monomeric or dimeric (one or two subunits, respectively).
  • Class II has three highly conserved sequence motifs. It aminoacylates
    Aminoacylation

    Aminoacylation is the process of adding an aminoacyl group to a compound.See also*Acylation*Transfer RNA#Aminoacylation...
     at the 3'-OH of the same adenosine, and is usually dimeric or tetramer
    Tetramer

    A tetramer is a protein with four subunits . There are homo-tetramers such as glutathione S-transferase or single-strand binding protein, dimers of hetero-dimers such as haemoglobin , and hetero-tetramers, where each subunit is different....
    ic (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
Hydroxyl

Hydroxyl in chemistry stands for a molecule consisting of an oxygen atom and a hydrogen atom connected by a covalent bond. The neutral form is a hydroxyl Radical and the hydroxyl anion is called a hydroxide....
 (-OH) group of the adenosine via their carboxyl (-COOH) groups.

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
Transesterification

In organic chemistry, transesterification is the process of exchanging the alcohol group of an ester compound with another alcohol. These reactions are often catalyst by the addition of an acid or base ....
.

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 protein). 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, while class I and class II aaRSs are unrelated to one another. The class I aaRSs have the ubiquitous Rossmann fold
Rossmann fold

The Rossmann fold is a protein structural motif found in proteins that bind nucleotides, especially the cofactor Nicotinamide adenine dinucleotide....
 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
Archaea

The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon . Archaea, like bacteria, are prokaryotic....
, Bacteria
Bacteria

The Bacteria are a large group of unicellular microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals....
, and Eukarya, and the root of the phylogenetic tree is present in between the Bacterial branch and the Archaeal/Eukaryal branch.

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