Function and Biology

THE CRYSTAL STRUCTURE OF PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH COGNATE TRNAPHE

Source organism: Thermus thermophilus HB8
Biochemical function: metal ion binding
Biological process: phenylalanyl-tRNA aminoacylation
Cellular component: cytoplasm

EC 6.1.1.20: Phenylalanine--tRNA ligase

Reaction catalysed:
ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl-tRNA(Phe)
Systematic name:
L-phenylalanine:tRNA(Phe) ligase (AMP-forming)
Alternative Name(s):
  • L-phenylalanyl-tRNA synthetase
  • Phenylalanine translase
  • Phenylalanine-tRNA synthetase
  • Phenylalanyl-tRNA ligase
  • Phenylalanyl-tRNA synthetase
  • Phenylalanyl-transfer RNA ligase
  • Phenylalanyl-transfer RNA synthetase
  • Phenylalanyl-transfer ribonucleate synthetase

Sequence families

Pfam Protein families (Pfam)
PF03147
Domain description: Ferredoxin-fold anticodon binding domain
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
The deposited structure of PDB entry 1eiy contains 1 copy of Pfam domain PF03147 (Ferredoxin-fold anticodon binding domain) in Phenylalanine--tRNA ligase beta subunit. Showing 1 copy in chain C [auth B].

PF17759
Domain description: Phenylalanyl tRNA synthetase beta chain CLM domain
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
The deposited structure of PDB entry 1eiy contains 1 copy of Pfam domain PF17759 (Phenylalanyl tRNA synthetase beta chain CLM domain) in Phenylalanine--tRNA ligase beta subunit. Showing 1 copy in chain C [auth B].

PF03484
Domain description: tRNA synthetase B5 domain
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
The deposited structure of PDB entry 1eiy contains 1 copy of Pfam domain PF03484 (tRNA synthetase B5 domain) in Phenylalanine--tRNA ligase beta subunit. Showing 1 copy in chain C [auth B].

PF03483
Domain description: B3/4 domain
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
The deposited structure of PDB entry 1eiy contains 1 copy of Pfam domain PF03483 (B3/4 domain) in Phenylalanine--tRNA ligase beta subunit. Showing 1 copy in chain C [auth B].

PF01409
Domain description: tRNA synthetases class II core domain (F)
Occurring in:
  1. Phenylalanine--tRNA ligase alpha subunit
The deposited structure of PDB entry 1eiy contains 1 copy of Pfam domain PF01409 (tRNA synthetases class II core domain (F)) in Phenylalanine--tRNA ligase alpha subunit. Showing 1 copy in chain B [auth A].

PF02912
Domain description: Aminoacyl tRNA synthetase class II, N-terminal domain
Occurring in:
  1. Phenylalanine--tRNA ligase alpha subunit
The deposited structure of PDB entry 1eiy contains 1 copy of Pfam domain PF02912 (Aminoacyl tRNA synthetase class II, N-terminal domain) in Phenylalanine--tRNA ligase alpha subunit. Showing 1 copy in chain B [auth A].

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

InterPro InterPro annotations
IPR045864
Domain description: Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Occurring in:
  1. Phenylalanine--tRNA ligase alpha subunit
  2. Phenylalanine--tRNA ligase beta subunit
IPR005147
Domain description: tRNA synthetase, B5-domain
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
IPR005121
Domain description: Ferrodoxin-fold anticodon-binding domain
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
IPR036690
Domain description: Ferrodoxin-fold anticodon-binding domain superfamily
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
IPR041616
Domain description: Phenylalanyl tRNA synthetase beta chain, core domain
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
IPR005146
Domain description: B3/B4 tRNA-binding domain
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
IPR002547
Domain description: tRNA-binding domain
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
IPR012340
Domain description: Nucleic acid-binding, OB-fold
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
IPR009061
Domain description: Putative DNA-binding domain superfamily
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
IPR004532
Domain description: Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
IPR020825
Domain description: Phenylalanyl-tRNA synthetase-like, B3/B4
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
IPR033714
Domain description: Phenylalanly tRNA synthetase, tRNA-binding-domain
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
IPR045060
Domain description: Phenylalanine-tRNA ligase, class IIc, beta subunit
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
IPR002319
Domain description: Phenylalanyl-tRNA synthetase
Occurring in:
  1. Phenylalanine--tRNA ligase alpha subunit
IPR006195
Domain description: Aminoacyl-tRNA synthetase, class II
Occurring in:
  1. Phenylalanine--tRNA ligase alpha subunit
IPR004529
Domain description: Phenylalanyl-tRNA synthetase, class IIc, alpha subunit
Occurring in:
  1. Phenylalanine--tRNA ligase alpha subunit
IPR004188
Domain description: Phenylalanine-tRNA ligase, class II, N-terminal
Occurring in:
  1. Phenylalanine--tRNA ligase alpha subunit
IPR010978
Domain description: Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm
Occurring in:
  1. Phenylalanine--tRNA ligase alpha subunit
IPR022911
Domain description: Phenylalanine-tRNA ligase alpha chain 1, bacterial
Occurring in:
  1. Phenylalanine--tRNA ligase alpha subunit

Structure domains

CATH CATH domains
3.30.56.10
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homology: Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
The deposited structure of PDB entry 1eiy contains 2 copies of CATH domain 3.30.56.10 (Phenylalanyl-tRNA Synthetase; Chain B, domain 1) in Phenylalanine--tRNA ligase beta subunit. Showing 2 copies in chain C [auth B].
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. Phenylalanine--tRNA ligase alpha subunit
  2. Phenylalanine--tRNA ligase beta subunit
The deposited structure of PDB entry 1eiy contains 1 copy of CATH domain 3.30.930.10 (BirA Bifunctional Protein; domain 2) in Phenylalanine--tRNA ligase alpha subunit. Showing 1 copy in chain B [auth A].
The deposited structure of PDB entry 1eiy contains 1 copy of CATH domain 3.30.930.10 (BirA Bifunctional Protein; domain 2) in Phenylalanine--tRNA ligase beta subunit. Showing 1 copy in chain C [auth B].
3.30.70.380
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Alpha-Beta Plaits
Homology: Ferrodoxin-fold anticodon-binding domain
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
The deposited structure of PDB entry 1eiy contains 1 copy of CATH domain 3.30.70.380 (Alpha-Beta Plaits) in Phenylalanine--tRNA ligase beta subunit. Showing 1 copy in chain C [auth B].
3.50.40.10
Class: Alpha Beta
Architecture: 3-Layer(bba) Sandwich
Topology: Phenylalanyl-tRNA Synthetase; Chain B, domain 3
Homology: Phenylalanyl-trna Synthetase, Chain B, domain 3
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
The deposited structure of PDB entry 1eiy contains 1 copy of CATH domain 3.50.40.10 (Phenylalanyl-tRNA Synthetase; Chain B, domain 3) in Phenylalanine--tRNA ligase beta subunit. Showing 1 copy in chain C [auth B].
2.40.50.140
Class: Mainly Beta
Architecture: Beta Barrel
Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homology: Nucleic acid-binding proteins
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
The deposited structure of PDB entry 1eiy contains 1 copy of CATH domain 2.40.50.140 (OB fold (Dihydrolipoamide Acetyltransferase, E2P)) in Phenylalanine--tRNA ligase beta subunit. Showing 1 copy in chain C [auth B].
SCOP SCOP annotations
46956
Class: All alpha proteins
Fold: Putative DNA-binding domain
Superfamily: Putative DNA-binding domain
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
The deposited structure of PDB entry 1eiy contains 2 copies of SCOP domain 46956 (Domains B1 and B5 of PheRS-beta, PheT) in Phenylalanine--tRNA ligase beta subunit. Showing 2 copies in chain C [auth B].
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. Phenylalanine--tRNA ligase alpha subunit
  2. Phenylalanine--tRNA ligase beta subunit
The deposited structure of PDB entry 1eiy contains 1 copy of SCOP domain 55682 (Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain) in Phenylalanine--tRNA ligase alpha subunit. Showing 1 copy in chain B [auth A].
The deposited structure of PDB entry 1eiy contains 1 copy of SCOP domain 55682 (Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain) in Phenylalanine--tRNA ligase beta subunit. Showing 1 copy in chain C [auth B].
54992
Class: Alpha and beta proteins (a+b)
Fold: Ferredoxin-like
Superfamily: Anticodon-binding domain of PheRS
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
The deposited structure of PDB entry 1eiy contains 1 copy of SCOP domain 54992 (Anticodon-binding domain of PheRS) in Phenylalanine--tRNA ligase beta subunit. Showing 1 copy in chain C [auth B].
56038
Class: All beta proteins
Fold: PheT/TilS domain
Superfamily: PheT/TilS domain
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
The deposited structure of PDB entry 1eiy contains 1 copy of SCOP domain 56038 (B3/B4 domain of PheRS, PheT) in Phenylalanine--tRNA ligase beta subunit. Showing 1 copy in chain C [auth B].
50277
Class: All beta proteins
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Occurring in:
  1. Phenylalanine--tRNA ligase beta subunit
The deposited structure of PDB entry 1eiy contains 1 copy of SCOP domain 50277 (Myf domain) in Phenylalanine--tRNA ligase beta subunit. Showing 1 copy in chain C [auth B].
46593
Class: All alpha proteins
Fold: Long alpha-hairpin
Superfamily: tRNA-binding arm
Occurring in:
  1. Phenylalanine--tRNA ligase alpha subunit
The deposited structure of PDB entry 1eiy contains 1 copy of SCOP domain 46593 (Phenylalanyl-tRNA synthetase (PheRS)) in Phenylalanine--tRNA ligase alpha subunit. Showing 1 copy in chain B [auth A].