› 4wj3

X-ray diffraction
3.7Å resolution

Crystal structure of the asparagine transamidosome from Pseudomonas aeruginosa

Released:
DOI: 10.2210/pdb4wj3/pdb
PDB entry 4wj3 coloured by chain, front view.
PDB entry 4wj3 coloured by chain, side view.
PDB entry 4wj3 coloured by chain, top view.
Source organism: Pseudomonas aeruginosa PAO1
Primary publication:
Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis.
Suzuki T, Nakamura A, Kato K, Söll D, Tanaka I, Sheppard K, Yao M
Proc Natl Acad Sci U S A 112 382-7 (2015)
PMID: 25548166

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
PDBe Complex ID:
PDB-CPX-175934 (preferred)
Entry contents:
4 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (5 distinct):
Glutamyl-tRNA(Gln) amidotransferase subunit A Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
Length: 484 amino acids
Theoretical weight: 51.91 KDa
Source organism: Pseudomonas aeruginosa PAO1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9HVT8 (Residues: 1-484; Coverage: 100%)
Gene names: PA4483, gatA
Sequence domains: Amidase
Structure domains: Amidase signature (AS) domain
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
Length: 481 amino acids
Theoretical weight: 51.24 KDa
Source organism: Pseudomonas aeruginosa PAO1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9HVT7 (Residues: 1-403; Coverage: 84%)
Gene names: PA4484, gatB
Sequence domains:
Glutamyl-tRNA(Gln) amidotransferase subunit C Chains: C, F, I, L
Molecule details ›
Chains: C, F, I, L
Length: 104 amino acids
Theoretical weight: 11.56 KDa
Source organism: Pseudomonas aeruginosa PAO1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9HVT9 (Residues: 1-96; Coverage: 100%)
Gene names: PA4482, gatC
Sequence domains: Glu-tRNAGln amidotransferase C subunit
Structure domains: Glu-tRNAGln amidotransferase C subunit, N-terminal domain
Aspartate--tRNA(Asp/Asn) ligase Chains: M, N, O, P
Molecule details ›
Chains: M, N, O, P
Length: 599 amino acids
Theoretical weight: 67.31 KDa
Source organism: Pseudomonas aeruginosa PAO1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q51422 (Residues: 1-591; Coverage: 100%)
Gene names: PA0963, aspS
Sequence domains:
Structure domains:
76mer-tRNA Chains: Q, R, S, T
Molecule details ›
Chains: Q, R, S, T
Length: 76 nucleotides
Theoretical weight: 24.47 KDa
Sequence domains: tRNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21
Unit cell:
a: 93.14Å b: 185.675Å c: 290.359Å
α: 90° β: 92.98° γ: 90°
R-values:
R R work R free
0.294 0.292 0.329
Expression system: Escherichia coli

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Citations

1 review citation

Unconventional genetic code systems in archaea.
Meng et al. (2022)
7 other articles

13 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)
12 more