› 3kfu

X-ray diffraction
3Å resolution

Crystal structure of the transamidosome

Released:
DOI: 10.2210/pdb3kfu/pdb
PDB entry 3kfu coloured by chain, front view.
PDB entry 3kfu coloured by chain, side view.
PDB entry 3kfu coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Crystal structure of a transfer-ribonucleoprotein particle that promotes asparagine formation.
Blaise M, Bailly M, Frechin M, Behrens MA, Fischer F, Oliveira CL, Becker HD, Pedersen JS, Thirup S, Kern D
EMBO J 29 3118-29 (2010)
PMID: 20717102

Function and Biology Details

Reactions catalysed: 
ATP + L-aspartate + tRNA(Asx) = AMP + diphosphate + L-aspartyl-tRNA(Asx)
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetradecamer (preferred)
PDBe Complex ID:
PDB-CPX-177950 (preferred)
Entry contents:
4 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (5 distinct):
Aspartate--tRNA(Asp/Asn) ligase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 422 amino acids
Theoretical weight: 48.4 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5SIC2 (Residues: 1-422; Coverage: 100%)
Gene names: TTHA1452, aspS2
Sequence domains:
Structure domains:
Glutamyl-tRNA(Gln) amidotransferase subunit A Chains: E, H
Molecule details ›
Chains: E, H
Length: 471 amino acids
Theoretical weight: 50.28 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9LCX3 (Residues: 1-471; Coverage: 100%)
Gene names: TTHA0573, gatA
Sequence domains: Amidase
Structure domains: Amidase signature (AS) domain
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B Chains: F, I
Molecule details ›
Chains: F, I
Length: 466 amino acids
Theoretical weight: 50.55 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9LCX2 (Residues: 1-396; Coverage: 84%)
Gene names: TTHA0366, gatB
Sequence domains:
Glutamyl-tRNA(Gln) amidotransferase subunit C Chains: G, J
Molecule details ›
Chains: G, J
Length: 92 amino acids
Theoretical weight: 10.25 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9LCX4 (Residues: 1-89; Coverage: 100%)
Gene names: TTHA0876, gatC
Sequence domains: Glu-tRNAGln amidotransferase C subunit
Structure domains:
tRNA-Asn Chains: K, L, M, N
Molecule details ›
Chains: K, L, M, N
Length: 76 nucleotides
Theoretical weight: 24.57 KDa
Sequence domains: tRNA

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand MG 2 x MG
3 modified residues:
Ligand H2U 4 x H2U
Ligand 5MU 4 x 5MU
Ligand PSU 4 x PSU

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P21
Unit cell:
a: 115.92Å b: 214Å c: 127.84Å
α: 90° β: 93.36° γ: 90°
R-values:
R R work R free
0.2 0.199 0.252
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Transfer RNA: a dancer between charging and mis-charging for protein biosynthesis.
Zhou et al. (2013)
3 more

10 mentions without citation

Personalized Medicine in Mitochondrial Health and Disease: Molecular Basis of Therapeutic Approaches Based on Nutritional Supplements and Their Analogs.
Tragni et al. (2022)
9 more