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 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Non-discriminating and archaeal-type aspartyl-tRNA synthetaseABCD422Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1452aspS2
EC: 6.1.1.23
Find proteins for Q5SIC2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q5SIC2
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamyl-tRNA(Gln) amidotransferase subunit AEH471Thermus thermophilus HB8Mutation(s): 0 
Gene Names: gatATTHA0573
EC: 6.3.5 (PDB Primary Data), 6.3.5.7 (UniProt)
Find proteins for Q9LCX3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q9LCX3
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit BFI466Thermus thermophilus HB8Mutation(s): 0 
Gene Names: gatBTTHA0366
EC: 6.3.5
Find proteins for Q9LCX2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q9LCX2
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamyl-tRNA(Gln) amidotransferase subunit CGJ92Thermus thermophilus HB8Mutation(s): 0 
Gene Names: gatCTTHA0876
EC: 6.3.5
Find proteins for Q9LCX4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
tRNA-AsnK, L, M, N76Thermus thermophilus HB8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
F, I
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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F, I
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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 

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance