Glutamyl-tRNA reductase

 

Glutamyl-tRNA Reductase catalyses the reduction of the activated alpha-carboxyl group of glutamate from glutamyl-tRNA using NADPH to form glutamate-1-semialdehyde(GSA). GSA is then converted to 5-aminolevulenic acid, a precursor molecule for the biosynthesis of tetrapyrroles like chlorophylls, hemes and coenzyme B12.

 

Reference Protein and Structure

Sequence
Q9UXR8 UniProt (1.2.1.70) IPR000343 (Sequence Homologues) (PDB Homologues)
Biological species
Methanopyrus kandleri AV19 (Archaea) Uniprot
PDB
1gpj - Glutamyl-tRNA Reductase from Methanopyrus kandleri (1.95 Å) PDBe PDBsum 1gpj
Catalytic CATH Domains
3.30.460.30 CATHdb (see all for 1gpj)
Click To Show Structure

Enzyme Reaction (EC:1.2.1.70)

hydron
CHEBI:15378ChEBI
+
NADPH(4-)
CHEBI:57783ChEBI
+
3'-(L-glutamate)adenylyl(1-) group
CHEBI:78520ChEBI
→
AMP 3'-end(1-) residue
CHEBI:78442ChEBI
+
(S)-4-amino-5-oxopentanoic acid zwitterion
CHEBI:57501ChEBI
+
NADP(3-)
CHEBI:58349ChEBI

Enzyme Mechanism

Introduction

Cys48 acts as a nucleophile to attack the alpha-carboxyl group of glutamate, which is activated by an ester linkage to tRNA, forming a highly reactive enzyme-localised thioester and tRNA is released. Direct hydride transfer from NADPH, facilitated by His84, which acts as a base catalyst to stabilise the protonated tetrahedral intermediate, leads to the formation of the product GSA.

Catalytic Residues Roles

UniProt PDB* (1gpj)
Cys48 Ser48A It acts as a nucleophile to attack the alpha-carboxyl group of glutamate activated by an ester linkage to tRNA, forming a highly reactive enzyme-localised thioester. covalently attached, nucleofuge, nucleophile
His84 His84A It acts as a base catalyst to stabilise the protonated tetrahedral intermediate formed during the hydride transfer from NADPH to the enzyme-substrate complex, hence facilitating the hydride transfer. electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

bimolecular nucleophilic substitution, intermediate formation, overall reactant used, enzyme-substrate complex formation, aromatic unimolecular elimination by the conjugate base, bimolecular nucleophilic addition, hydride transfer, unimolecular elimination by the conjugate base, overall product formed, native state of enzyme regenerated, enzyme-substrate complex cleavage

References

  1. Moser J et al. (1999), J Biol Chem, 274, 30679-30685. Methanopyrus kandleri Glutamyl-tRNA Reductase. DOI:10.1074/jbc.274.43.30679. PMID:10521455.
  2. Moser J et al. (2001), EMBO J, 20, 6583-6590. V-shaped structure of glutamyl-tRNA reductase, the first enzyme of tRNA-dependent tetrapyrrole biosynthesis. DOI:10.1093/emboj/20.23.6583. PMID:11726494.

Step 1. The sulfryl group of Cys48 acts as a nucleophile to attack glutamate and the tRNA residue is eliminated. An enzyme thioester intermediate is formed.

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Catalytic Residues Roles

Residue Roles
His84A electrostatic stabiliser
Ser48A covalently attached, nucleophile

Chemical Components

ingold: bimolecular nucleophilic substitution, intermediate formation, overall reactant used, enzyme-substrate complex formation

Step 2. A hydride is transferred from NADPH to the thioester intermediate. This is promoted by His84.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His84A electrostatic stabiliser
Ser48A covalently attached

Chemical Components

ingold: aromatic unimolecular elimination by the conjugate base, ingold: bimolecular nucleophilic addition, hydride transfer, intermediate formation

Step 3. The tetrahedral intermediate collapses, releasing Cys48 and forming the product.

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Catalytic Residues Roles

Residue Roles
Ser48A nucleofuge

Chemical Components

ingold: unimolecular elimination by the conjugate base, overall product formed, native state of enzyme regenerated, enzyme-substrate complex cleavage
Download: Image, Marvin File

Step 1. The sulfryl group of Cys48 acts as a nucleophile to attack glutamate and the tRNA residue is eliminated. An enzyme thioester intermediate is formed.

Step 2. A hydride is transferred from NADPH to the thioester intermediate. This is promoted by His84.

Step 3. The tetrahedral intermediate collapses, releasing Cys48 and forming the product.

Products.

Contributors

Mei Leung, Gemma L. Holliday, Amelia Brasnett