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CRYSTAL STRUCTURE OF THE ARGINYL-TRNA SYNTHETASE COMPLEXED WITH THE TRNA(ARG) AND L-ARG

Source organism: Saccharomyces cerevisiae
Biochemical function: sequence-specific mRNA binding
Biological process: mitochondrial translation
Cellular component: cytosol

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EC 6.1.1.19: Arginine--tRNA ligase

Reaction catalysed:
ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg)
Systematic name:
L-arginine:tRNA(Arg) ligase (AMP-forming)
Alternative Name(s):
  • Arginine translase
  • Arginine-tRNA synthetase
  • Arginyl transfer ribonucleic acid synthetase
  • Arginyl-tRNA synthetase
  • Arginyl-transfer RNA synthetase
  • Arginyl-transfer ribonucleate synthetase

GO terms

Sequence families

Pfam Protein families (Pfam)
PF05746
Domain description: DALR anticodon binding domain
Occurring in:
  1. Arginine--tRNA ligase, cytoplasmic
The deposited structure of PDB entry 1f7u contains 1 copy of Pfam domain PF05746 (DALR anticodon binding domain) in Arginine--tRNA ligase, cytoplasmic. Showing 1 copy in chain B [auth A].

PF00750
Domain description: tRNA synthetases class I (R)
Occurring in:
  1. Arginine--tRNA ligase, cytoplasmic
The deposited structure of PDB entry 1f7u contains 1 copy of Pfam domain PF00750 (tRNA synthetases class I (R)) in Arginine--tRNA ligase, cytoplasmic. Showing 1 copy in chain B [auth A].

PF03485
Domain description: Arginyl tRNA synthetase N terminal domain
Occurring in:
  1. Arginine--tRNA ligase, cytoplasmic
The deposited structure of PDB entry 1f7u contains 1 copy of Pfam domain PF03485 (Arginyl tRNA synthetase N terminal domain) in Arginine--tRNA ligase, cytoplasmic. Showing 1 copy in chain B [auth A].

Rfam RNA family (Rfam)
RF00005
Domain description: tRNA
Occurring in:
  1. TRNA(ARG)
The deposited structure of PDB entry 1f7u contains 1 copy of Rfam domain RF00005 (tRNA) in TRNA(ARG). Showing 1 copy in chain A [auth B].

InterPro InterPro annotations
IPR001278
Domain description: Arginine-tRNA ligase
Occurring in:
  1. Arginine--tRNA ligase, cytoplasmic
IPR035684
Domain description: Arginyl-tRNA synthetase, catalytic core domain
Occurring in:
  1. Arginine--tRNA ligase, cytoplasmic
IPR005148
Domain description: Arginyl tRNA synthetase N-terminal domain
Occurring in:
  1. Arginine--tRNA ligase, cytoplasmic
IPR036695
Domain description: Arginyl tRNA synthetase N-terminal domain superfamily
Occurring in:
  1. Arginine--tRNA ligase, cytoplasmic
IPR008909
Domain description: DALR anticodon binding
Occurring in:
  1. Arginine--tRNA ligase, cytoplasmic
IPR009080
Domain description: Aminoacyl-tRNA synthetase, class Ia, anticodon-binding
Occurring in:
  1. Arginine--tRNA ligase, cytoplasmic
IPR001412
Domain description: Aminoacyl-tRNA synthetase, class I, conserved site
Occurring in:
  1. Arginine--tRNA ligase, cytoplasmic
IPR014729
Domain description: Rossmann-like alpha/beta/alpha sandwich fold
Occurring in:
  1. Arginine--tRNA ligase, cytoplasmic

Structure domains

CATH CATH domains
1.10.730.10
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Isoleucyl-tRNA Synthetase; Domain 1
Homology: Isoleucyl-tRNA Synthetase; Domain 1
Occurring in:
  1. Arginine--tRNA ligase, cytoplasmic
The deposited structure of PDB entry 1f7u contains 1 copy of CATH domain 1.10.730.10 (Isoleucyl-tRNA Synthetase; Domain 1) in Arginine--tRNA ligase, cytoplasmic. Showing 1 copy in chain B [auth A].
3.40.50.620
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Rossmann fold
Homology: HUPs
Occurring in:
  1. Arginine--tRNA ligase, cytoplasmic
The deposited structure of PDB entry 1f7u contains 1 copy of CATH domain 3.40.50.620 (Rossmann fold) in Arginine--tRNA ligase, cytoplasmic. Showing 1 copy in chain B [auth A].
3.30.1360.70
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Gyrase A; domain 2
Homology: Arginyl tRNA synthetase N-terminal domain
Occurring in:
  1. Arginine--tRNA ligase, cytoplasmic
The deposited structure of PDB entry 1f7u contains 1 copy of CATH domain 3.30.1360.70 (Gyrase A; domain 2) in Arginine--tRNA ligase, cytoplasmic. Showing 1 copy in chain B [auth A].
SCOP SCOP annotations
47324
Class: All alpha proteins
Fold: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Superfamily: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Occurring in:
  1. Arginine--tRNA ligase, cytoplasmic
The deposited structure of PDB entry 1f7u contains 1 copy of SCOP domain 47324 (Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases) in Arginine--tRNA ligase, cytoplasmic. Showing 1 copy in chain B [auth A].
52375
Class: Alpha and beta proteins (a/b)
Fold: Adenine nucleotide alpha hydrolase-like
Superfamily: Nucleotidylyl transferase
Occurring in:
  1. Arginine--tRNA ligase, cytoplasmic
The deposited structure of PDB entry 1f7u contains 1 copy of SCOP domain 52375 (Class I aminoacyl-tRNA synthetases (RS), catalytic domain) in Arginine--tRNA ligase, cytoplasmic. Showing 1 copy in chain B [auth A].
55191
Class: Alpha and beta proteins (a+b)
Fold: RRF/tRNA synthetase additional domain-like
Superfamily: Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain
Occurring in:
  1. Arginine--tRNA ligase, cytoplasmic
The deposited structure of PDB entry 1f7u contains 1 copy of SCOP domain 55191 (Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain) in Arginine--tRNA ligase, cytoplasmic. Showing 1 copy in chain B [auth A].

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