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-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 ...

    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

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-discriminating and archaeal-type aspartyl-tRNA synthetase A, B, C, D422Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1452, aspS2
EC: 6.1.1.23
Find proteins for Q5SIC2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SIC2 
Go to UniProtKB:  Q5SIC2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamyl-tRNA(Gln) amidotransferase subunit A E, H471Thermus thermophilus HB8Mutation(s): 0 
Gene Names: gatA, TTHA0573
EC: 6.3.5 (PDB Primary Data), 6.3.5.7 (UniProt)
Find proteins for Q9LCX3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q9LCX3 
Go to UniProtKB:  Q9LCX3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B F, I466Thermus thermophilus HB8Mutation(s): 0 
Gene Names: gatB, TTHA0366
EC: 6.3.5
Find proteins for Q9LCX2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q9LCX2 
Go to UniProtKB:  Q9LCX2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamyl-tRNA(Gln) amidotransferase subunit C G, J92Thermus thermophilus HB8Mutation(s): 0 
Gene Names: gatC, TTHA0876
EC: 6.3.5
Find proteins for Q9LCX4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q9LCX4 
Go to UniProtKB:  Q9LCX4
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
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 Ideal Coordinates CCD File 
F, I
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
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

View Full Validation Report


View more in-depth experimental data

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