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 
  • R-Value Observed: 0.205 

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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:  
    4WQ4, 4WQ5, 4YDU

  • 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-anticodon interaction ...

    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 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA N6-adenosine threonylcarbamoyltransferaseA, B343Escherichia coliMutation(s): 0 
Gene Names: tsaD, gcp, ygjD, b3064, JW3036
EC: 2.6.99.4 (PDB Primary Data), 2.3.1.234 (UniProt)
UniProt
Find proteins for P05852 (Escherichia coli (strain K12))
Explore P05852 
Go to UniProtKB:  P05852
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05852
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA threonylcarbamoyladenosine biosynthesis protein TsaBC, D237Escherichia coliMutation(s): 0 
Gene Names: tsaB, yeaZ, b1807, JW1796
UniProt
Find proteins for P76256 (Escherichia coli (strain K12))
Explore P76256 
Go to UniProtKB:  P76256
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76256
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
Q [auth C],
T [auth D]		ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
ACT
Query on ACT
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H [auth A],
I [auth A],
J [auth A],
K [auth A],
O [auth B],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
O [auth B],
P [auth B],
R [auth C],
S [auth C],
U [auth D],
V [auth D],
W [auth D],
X [auth D],
Y [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
FE
Query on FE
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G [auth A],
N [auth B]		FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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F [auth A],
M [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-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 
  • R-Value Observed: 0.205 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.62α = 109.38
b = 68.48β = 92.66
c = 87.07γ = 117.66
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Cootmodel building
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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