4YDU

Crystal structure of E. coli YgjD-YeaZ heterodimer in complex with ADP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

The ATP-mediated formation of the YgjD-YeaZ-YjeE complex is required for the biosynthesis of tRNA t6A in Escherichia coli.

Zhang, W., Collinet, B., Perrochia, L., Durand, D., Van Tilbeurgh, H.

(2015) Nucleic Acids Res. 43: 1804-1817

  • DOI: 10.1093/nar/gku1397
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The essential and universal N(6)-threonylcarbamoyladenosine (t(6)A) modification at position 37 of ANN-decoding tRNAs plays a pivotal role in translational fidelity through enhancement of the cognate codon recognition and stabilization of the codon-a ...

    The essential and universal N(6)-threonylcarbamoyladenosine (t(6)A) modification at position 37 of ANN-decoding tRNAs plays a pivotal role in translational fidelity through enhancement of the cognate codon recognition and stabilization of the codon-anticodon interaction. In Escherichia coli, the YgjD (TsaD), YeaZ (TsaB), YjeE (TsaE) and YrdC (TsaC) proteins are necessary and sufficient for the in vitro biosynthesis of t(6)A, using tRNA, ATP, L-threonine and bicarbonate as substrates. YrdC synthesizes the short-lived L-threonylcarbamoyladenylate (TCA), and YgjD, YeaZ and YjeE cooperate to transfer the L-threonylcarbamoyl-moiety from TCA onto adenosine at position 37 of substrate tRNA. We determined the crystal structure of the heterodimer YgjD-YeaZ at 2.3 Å, revealing the presence of an unexpected molecule of ADP bound at an atypical site situated at the YgjD-YeaZ interface. We further showed that the ATPase activity of YjeE is strongly activated by the YgjD-YeaZ heterodimer. We established by binding experiments and SAXS data analysis that YgjD-YeaZ and YjeE form a compact ternary complex only in presence of ATP. The formation of the ternary YgjD-YeaZ-YjeE complex is required for the in vitro biosynthesis of t(6)A but not its ATPase activity.

    Organizational Affiliation: 

    Institut de Génétique et de Microbiologie, Université Paris-Sud, UMR8621-CNRS, 91405 Orsay, France.,Institut de Biochimie et Biophysique Moléculaire et Cellulaire, UMR 8619, CNRS, Bâtiment 430, Université de Paris-Sud, 91405 Orsay Cedex, France.,Institut de Biochimie et Biophysique Moléculaire et Cellulaire, UMR 8619, CNRS, Bâtiment 430, Université de Paris-Sud, 91405 Orsay Cedex, France Sorbonne Universités, UPMC Univ Paris 06, UFR 927, Sciences de la vie, F-75005 Paris, France herman.van-tilbeurgh@u-psud.fr.,Institut de Biochimie et Biophysique Moléculaire et Cellulaire, UMR 8619, CNRS, Bâtiment 430, Université de Paris-Sud, 91405 Orsay Cedex, France herman.van-tilbeurgh@u-psud.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA N6-adenosine threonylcarbamoyltransferase
A, B
343Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: tsaD (gcp, ygjD)
EC: 2.3.1.234
Find proteins for P05852 (Escherichia coli (strain K12))
Go to UniProtKB:  P05852
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
C, D
237Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: tsaB (yeaZ)
Find proteins for P76256 (Escherichia coli (strain K12))
Go to UniProtKB:  P76256
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT
Download SDF File 
Download CCD File 
A, B, C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
ADP
Query on ADP
Download SDF File 
Download CCD File 
A, B, C, D
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE
Download SDF File 
Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.202 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 63.620α = 109.38
b = 68.480β = 92.66
c = 87.070γ = 117.66
Software Package:
Software NamePurpose
Cootmodel building
XDSdata reduction
MOLREPphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-04
    Type: Initial release