Amino-acyl tRNA Synthases:

 

 

http://oregonstate.edu/

 

 

 

The figure shows the 3-D view of the amino acyl-tRNA synthetase; http://www.rcsb.org/pdb

 

 

 

 

 

Important Features of Aminoacyl tRNA Synthases:

 

http://oregonstate.edu/

 

 

Class-I, add a.a to 2’OH group of ribose

Subunits

Class-II, add a.a to 3’OH group of ribose

 

Subunits

Tryptophan

a 2?

---

---

Glutamate

a 1

Glycine

a2 b2

Glutamine

a 1

Alanine

a 4

Arginine

a 1

Proline

a 2

Valine

a 1

Serine

a 2

Isoleucine

a 1

Aspartate

a 2?

Leucine

a 1

Asparagine

a 2

Methionine

a 2

Histidine

a 2

Tyrosine

a 2?

Lysine

a 2

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Basically, all tRNAs have distinct 3D structure; amino acids are covalently linked at 5’ end to 3’OH of ribose of Adenine, 1-2 nucleotides behind CCA and the last nucleotide at 3’ end is A to which amino acids are covalently linked.  All tRNAs have the same ends i.e CCA, but the structure of the tRNA and the aminoacyl-transferase differentiate and determine which amino acid to added to which tRNA.

 

 

 

The above diagram shows two types of a.a-tRNA synthetases. BiochemVII edition; http://oregonstate.edu/

 

Mechanism of Amino-Acylation:

 

The tRNA-aminoacyl synthetase performs admittance, scrutiny and proof reading at post binding stage (kinetic proof reading). 

 

Binding of amino acid to a.a acyl synthetase is determined by their specific complementary sites. Binding of a specific tRNA to a.a acyl tRNA is also based on their complementary surfaces. While selecting an amino acid hardly it makes mistakes, probably one in ten thousand to hundred thousand, while selecting tRNA, if a mistake has occurred it is corrected by cognate tRNA binding, it also performs what is called chemical proof reading i.e. after charging; if found wrong, it is hydrolysed and removed.

http://web.uconn.edu/

a.aacylsynthetase-Threonyl-tRNAsynthetase(editing/activation sites); http://oregonstate.edu.

 

 The aminoacylation reaction is shown here as a two-step process, both parts of which occur on the synthetase. All tRNAs have the same sequence CCA at their 3' ends, and this is where the amino acid is added. The amino acid must be 'activated' and ATP provides the activation energy. A complex of AMP-aa forms as an intermediate and the released PPi (pyrophosphate) is hydrolyzed by the enzyme pyrophosphatase with the release of energy to help make the overall reaction pathway more thermodynamically favorable. The aa is then transferred from its AMP carrier to the 3' terminal adenosine. Synthetases are divided into two classes depending on whether they add the amino acid to the 2' hydroxyl group (Class I) or the 3' hydroxyl group (Class II) of the ribose moiety of adenosine.

 

Three steps in amino acylation of tRNA

http://www.slideshare.net/ and ; http://web.uconn.edu/

 

 

 

 

The binding of amino acid directs its COO- group towards the tRNA site in such a way the COO^- group of the amino acid is positioned close to the 3’  or 2’ end of ‘Adenine’ of tRNA.  Binding of both substrates induces the enzyme to perform catalytic activity, where carboxyl group of amino acid is covalently added to 2’ or 3’ OH group of ribose moiety of the terminal Adenine nucleotide, as carbonyl bond which is a high energy bond.

 

 

The sites or the domains of tRNA that bind to enzymes sites are not yet fully understood.  Based on cross linking studies it is discerned that either acceptor end or the anti-codon region with its geometric dispositions of their nucleotides or both regions can bind to enzyme’s active site.  The DHU loop with species variation in sequence may have an important role in recognition and binding to enzyme surface.

 

 

From a variety of sources 100 or more of these enzymes have been studied.  The over all size of enzymes is very large in comparison to that of substrates. The enzyme endowed with second genetic code for it has to distinguish which amino acid to pick and to which tRNA it has to add.   The tRNA are distinguished for specific amino acids and specific anti codons.