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Structure of Staphylococcus aureus threonyl-tRNA synthetase complexed with ATP

Source organism: Staphylococcus aureus
Biochemical function: metal ion binding
Biological process: tRNA aminoacylation
Cellular component: cytoplasm

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EC 6.1.1.3: Threonine--tRNA ligase

Reaction catalysed:
ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr)
Systematic name:
L-threonine:tRNA(Thr) ligase (AMP-forming)
Alternative Name(s):
  • TRS
  • Threonine translase
  • Threonine-transfer ribonucleate synthetase
  • Threonyl ribonucleic synthetase
  • Threonyl-tRNA synthetase
  • Threonyl-transfer RNA synthetase
  • Threonyl-transfer ribonucleate synthetase
  • Threonyl-transfer ribonucleic acid synthetase

GO terms

Sequence families

Pfam Protein families (Pfam)
PF03129
Domain description: Anticodon binding domain
Occurring in:
  1. Threonine--tRNA ligase
The deposited structure of PDB entry 1nyr contains 2 copies of Pfam domain PF03129 (Anticodon binding domain) in Threonine--tRNA ligase. Showing 1 copy in chain A.

PF00587
Domain description: tRNA synthetase class II core domain (G, H, P, S and T)
Occurring in:
  1. Threonine--tRNA ligase
The deposited structure of PDB entry 1nyr contains 2 copies of Pfam domain PF00587 (tRNA synthetase class II core domain (G, H, P, S and T)) in Threonine--tRNA ligase. Showing 1 copy in chain A.

PF07973
Domain description: Threonyl and Alanyl tRNA synthetase second additional domain
Occurring in:
  1. Threonine--tRNA ligase
The deposited structure of PDB entry 1nyr contains 2 copies of Pfam domain PF07973 (Threonyl and Alanyl tRNA synthetase second additional domain) in Threonine--tRNA ligase. Showing 1 copy in chain A.

PF02824
Domain description: TGS domain
Occurring in:
  1. Threonine--tRNA ligase
The deposited structure of PDB entry 1nyr contains 2 copies of Pfam domain PF02824 (TGS domain) in Threonine--tRNA ligase. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR002320
Domain description: Threonine-tRNA ligase, class IIa
Occurring in:
  1. Threonine--tRNA ligase
IPR045864
Domain description: Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Occurring in:
  1. Threonine--tRNA ligase
IPR004095
Domain description: TGS
Occurring in:
  1. Threonine--tRNA ligase
IPR004154
Domain description: Anticodon-binding
Occurring in:
  1. Threonine--tRNA ligase
IPR047246
Domain description: Threonine-tRNA ligase, class IIa, anticodon-binding domain
Occurring in:
  1. Threonine--tRNA ligase
IPR036621
Domain description: Anticodon-binding domain superfamily
Occurring in:
  1. Threonine--tRNA ligase
IPR002314
Domain description: Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)
Occurring in:
  1. Threonine--tRNA ligase
IPR033728
Domain description: Threonine-tRNA ligase catalytic core domain
Occurring in:
  1. Threonine--tRNA ligase
IPR006195
Domain description: Aminoacyl-tRNA synthetase, class II
Occurring in:
  1. Threonine--tRNA ligase
IPR012947
Domain description: Threonyl/alanyl tRNA synthetase, SAD
Occurring in:
  1. Threonine--tRNA ligase
IPR018163
Domain description: Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily
Occurring in:
  1. Threonine--tRNA ligase
IPR012676
Domain description: TGS-like
Occurring in:
  1. Threonine--tRNA ligase
IPR012675
Domain description: Beta-grasp domain superfamily
Occurring in:
  1. Threonine--tRNA ligase

Structure domains

CATH CATH domains
3.30.930.10
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: BirA Bifunctional Protein; domain 2
Homology: Bira Bifunctional Protein; Domain 2
Occurring in:
  1. Threonine--tRNA ligase
The deposited structure of PDB entry 1nyr contains 2 copies of CATH domain 3.30.930.10 (BirA Bifunctional Protein; domain 2) in Threonine--tRNA ligase. Showing 1 copy in chain A.
3.40.50.800
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Rossmann fold
Homology: Anticodon-binding domain
Occurring in:
  1. Threonine--tRNA ligase
The deposited structure of PDB entry 1nyr contains 2 copies of CATH domain 3.40.50.800 (Rossmann fold) in Threonine--tRNA ligase. Showing 1 copy in chain A.
3.30.980.10
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Threonyl-tRNA Synthetase; Chain A, domain 2
Homology: Threonyl-trna Synthetase; Chain A, domain 2
Occurring in:
  1. Threonine--tRNA ligase
The deposited structure of PDB entry 1nyr contains 2 copies of CATH domain 3.30.980.10 (Threonyl-tRNA Synthetase; Chain A, domain 2) in Threonine--tRNA ligase. Showing 1 copy in chain A.
3.10.20.30
Class: Alpha Beta
Architecture: Roll
Topology: Ubiquitin-like (UB roll)
Homology: Ubiquitin-like (UB roll)
Occurring in:
  1. Threonine--tRNA ligase
The deposited structure of PDB entry 1nyr contains 2 copies of CATH domain 3.10.20.30 (Ubiquitin-like (UB roll)) in Threonine--tRNA ligase. Showing 1 copy in chain A.
SCOP SCOP annotations
52955
Class: Alpha and beta proteins (a/b)
Fold: Anticodon-binding domain-like
Superfamily: Class II aaRS ABD-related
Occurring in:
  1. Threonine--tRNA ligase
The deposited structure of PDB entry 1nyr contains 2 copies of SCOP domain 52955 (Anticodon-binding domain of Class II aaRS) in Threonine--tRNA ligase. Showing 1 copy in chain A.
55682
Class: Alpha and beta proteins (a+b)
Fold: Class II aaRS and biotin synthetases
Superfamily: Class II aaRS and biotin synthetases
Occurring in:
  1. Threonine--tRNA ligase
The deposited structure of PDB entry 1nyr contains 2 copies of SCOP domain 55682 (Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain) in Threonine--tRNA ligase. Showing 1 copy in chain A.
55187
Class: Alpha and beta proteins (a+b)
Fold: RRF/tRNA synthetase additional domain-like
Superfamily: ThrRS/AlaRS common domain
Occurring in:
  1. Threonine--tRNA ligase
The deposited structure of PDB entry 1nyr contains 2 copies of SCOP domain 55187 (Threonyl-tRNA synthetase (ThrRS), second 'additional' domain) in Threonine--tRNA ligase. Showing 1 copy in chain A.
81270
Class: Alpha and beta proteins (a+b)
Fold: beta-Grasp (ubiquitin-like)
Superfamily: TGS-like
Occurring in:
  1. Threonine--tRNA ligase
The deposited structure of PDB entry 1nyr contains 2 copies of SCOP domain 81270 (TGS domain) in Threonine--tRNA ligase. Showing 1 copy in chain A.

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