3KFU

Crystal structure of the transamidosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

Starting Models: experimental
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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of a transfer-ribonucleoprotein particle that promotes asparagine formation.

Blaise, M.Bailly, M.Frechin, M.Behrens, M.A.Fischer, F.Oliveira, C.L.Becker, H.D.Pedersen, J.S.Thirup, S.Kern, D.

(2010) EMBO J 29: 3118-3129

  • DOI: https://doi.org/10.1038/emboj.2010.192
  • Primary Citation of Related Structures:  
    3KFU

  • PubMed Abstract: 

    Four out of the 22 aminoacyl-tRNAs (aa-tRNAs) are systematically or alternatively synthesized by an indirect, two-step route requiring an initial mischarging of the tRNA followed by tRNA-dependent conversion of the non-cognate amino acid. During tRNA-dependent asparagine formation, tRNA(Asn) promotes assembly of a ribonucleoprotein particle called transamidosome that allows channelling of the aa-tRNA from non-discriminating aspartyl-tRNA synthetase active site to the GatCAB amidotransferase site. The crystal structure of the Thermus thermophilus transamidosome determined at 3 A resolution reveals a particle formed by two GatCABs, two dimeric ND-AspRSs and four tRNAs(Asn) molecules. In the complex, only two tRNAs are bound in a functional state, whereas the two other ones act as an RNA scaffold enabling release of the asparaginyl-tRNA(Asn) without dissociation of the complex. We propose that the crystal structure represents a transient state of the transamidation reaction. The transamidosome constitutes a transfer-ribonucleoprotein particle in which tRNAs serve the function of both substrate and structural foundation for a large molecular machine.


  • Organizational Affiliation

    Department of Molecular Biology, CARB Centre, University of Aarhus, Arhus C, Denmark. mickael.blaise@gmail.com


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-discriminating and archaeal-type aspartyl-tRNA synthetase
A, B, C, D
422Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1452
UniProt
Find proteins for Q5SIC2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Go to UniProtKB:  Q5SIC2
Entity Groups  
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UniProt GroupQ5SIC2
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamyl-tRNA(Gln) amidotransferase subunit A
E, H
471Thermus thermophilus HB8Mutation(s): 0 
Gene Names: gatATTHA0573
EC: 6.3.5
UniProt
Find proteins for Q9LCX3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Go to UniProtKB:  Q9LCX3
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UniProt GroupQ9LCX3
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
F, I
466Thermus thermophilus HB8Mutation(s): 0 
Gene Names: gatBTTHA0366
EC: 6.3.5
UniProt
Find proteins for Q9LCX2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Go to UniProtKB:  Q9LCX2
Entity Groups  
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UniProt GroupQ9LCX2
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamyl-tRNA(Gln) amidotransferase subunit C
G, J
92Thermus thermophilus HB8Mutation(s): 0 
Gene Names: gatCTTHA0876
EC: 6.3.5
UniProt
Find proteins for Q9LCX4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ9LCX4
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  • Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
tRNA-Asn
K, L, M, N
76Thermus thermophilus HB8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.92α = 90
b = 214β = 93.36
c = 127.84γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description