Serine-tRNA ligase (archaeal)

 

Serine-tRNA ligase (EC:6.1.1.11) exists as monomer and belongs to class IIa [PMID: 7540217]. The serine-tRNA ligases from a few of the archaea that belong to this group are different from the set of mutually more closely related serine-tRNA ligases from eubacteria, eukaryotes, and other archaea (IPR002317).

 

Reference Protein and Structure

Sequence
Q46AN5 UniProt (6.1.1.11) IPR004503 (Sequence Homologues) (PDB Homologues)
Biological species
Methanosarcina barkeri str. Fusaro (Archaea) Uniprot
PDB
2cja - Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with ATP (2.2 Å) PDBe PDBsum 2cja
Catalytic CATH Domains
3.30.930.10 CATHdb (see all for 2cja)
Cofactors
Zinc(2+) (1), Magnesium(2+) (2)
Click To Show Structure

Enzyme Reaction (EC:6.1.1.11)

L-serine zwitterion
CHEBI:33384ChEBI
+
ATP(4-)
CHEBI:30616ChEBI
+
AMP 3'-end(1-) residue
CHEBI:78442ChEBI
→
3'-(L-seryl)adenylyl(1-) group
CHEBI:78533ChEBI
+
adenosine 5'-monophosphate(2-)
CHEBI:456215ChEBI
+
diphosphate(3-)
CHEBI:33019ChEBI
+
hydron
CHEBI:15378ChEBI
Alternative enzyme names: SerRS, Serine translase, Seryl-tRNA synthetase, Seryl-transfer RNA synthetase, Seryl-transfer ribonucleate synthetase, Seryl-transfer ribonucleic acid synthetase,

Enzyme Mechanism

Introduction

The reaction mechanism of aSerRS would follow an in-line displacement mechanism as observed in other class II proteins. The active site binds ATP in a U-shaped conformation with the α-phosphate in proximity to the carboxylate group of the serine, which leads to the in-line nucleophilic attack by the carboxylate group of serine and the inversion of configuration at the α -phosphate group. The second substrates then attacks the intermediate to form the amino acyl-tRNA and phosphate products.

Catalytic Residues Roles

UniProt PDB* (2cja)
Glu338 Glu338(358)A Forms part of the magnesium 1 binding site (along with ATP) metal ligand
Asp416, Glu432, Asn435 Asp416(436)A, Glu432(452)A, Asn435(455)A Forms part of the magnesium 2 binding site (along with ATP). metal ligand
Arg336, Arg347, Arg468 Arg336(356)A, Arg347(367)A, Arg468(488)A The approaching negative charges of the serine carboxylate and of the phosphate is offset by the positively charged side chain of the conserved argenine residues and the metal ions. electrostatic stabiliser
Glu355, Cys461, Cys306 Glu355(375)A, Cys461(481)A, Cys306(326)A Forms part of the catalytic zinc binding site. metal ligand
*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

References

  1. Bilokapic S et al. (2006), EMBO J, 25, 2498-2509. Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition. DOI:10.1038/sj.emboj.7601129. PMID:16675947.

Step 1.

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Catalytic Residues Roles

Residue Roles
Cys306(326)A metal ligand
Glu338(358)A metal ligand
Glu355(375)A metal ligand
Asp416(436)A metal ligand
Glu432(452)A metal ligand
Asn435(455)A metal ligand
Cys461(481)A metal ligand
Arg336(356)A electrostatic stabiliser
Arg347(367)A electrostatic stabiliser
Arg468(488)A electrostatic stabiliser

Chemical Components

Step 1.

Contributors

Gemma L. Holliday