4ML0

Crystal structure of E.coli DinJ-YafQ complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and Functional Characterization of Escherichia coli Toxin-Antitoxin Complex DinJ-YafQ

Liang, Y.Gao, Z.Wang, F.Zhang, Y.Dong, Y.Liu, Q.

(2014) J Biol Chem 289: 21191-21202

  • DOI: https://doi.org/10.1074/jbc.M114.559773
  • Primary Citation of Related Structures:  
    4ML0, 4ML2, 4MMG, 4MMJ

  • PubMed Abstract: 

    Toxin YafQ functions as a ribonuclease in the dinJ-yafQ toxin-antitoxin system of Escherichia coli. Antitoxin DinJ neutralizes YafQ-mediated toxicity by forming a stable protein complex. Here, crystal structures of the (DinJ)2-(YafQ)2 complex and the isolated YafQ toxin have been determined. The structure of the heterotetrameric complex (DinJ)2-(YafQ)2 revealed that the N-terminal region of DinJ folds into a ribbon-helix-helix motif and dimerizes for DNA recognition, and the C-terminal portion of each DinJ exclusively wraps around a YafQ molecule. Upon incorporation into the heterotetrameric complex, a conformational change of YafQ in close proximity to the catalytic site of the typical microbial ribonuclease fold was observed and validated. Mutagenesis experiments revealed that a DinJ mutant restored YafQ RNase activity in a tetramer complex in vitro but not in vivo. An electrophoretic mobility shift assay showed that one of the palindromic sequences present in the upstream intergenic region of DinJ served as a binding sequences for both the DinJ-YafQ complex and the antitoxin DinJ alone. Based on structure-guided and site-directed mutagenesis of DinJ-YafQ, we showed that two pairs of amino acids in DinJ were important for DNA binding; the R8A and K16A substitutions and the S31A and R35A substitutions in DinJ abolished the DNA binding ability of the DinJ-YafQ complex.


  • Organizational Affiliation

    From the School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China, the Multidiscipline Research Center, Institute of High Energy Physics of the Chinese Academy of Sciences, 19B Yuequan Road, Beijing 100049, China, and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Predicted antitoxin of YafQ-DinJ toxin-antitoxin system
A, C, E, G, I
A, C, E, G, I, K, M, O
89Escherichia coli B str. REL606Mutation(s): 0 
Gene Names: dinJECB_00221
UniProt
Find proteins for A0A140ND86 (Escherichia coli (strain B / BL21-DE3))
Explore A0A140ND86 
Go to UniProtKB:  A0A140ND86
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140ND86
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Predicted toxin of the YafQ-DinJ toxin-antitoxin system
B, D, F, H, J
B, D, F, H, J, L, N, P
95Escherichia coli B str. REL606Mutation(s): 0 
Gene Names: yafQECB_00220
UniProt
Find proteins for A0A140NAP5 (Escherichia coli (strain B / BL21-DE3))
Explore A0A140NAP5 
Go to UniProtKB:  A0A140NAP5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140NAP5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth E]
AB [auth N]
BA [auth E]
BB [auth N]
CA [auth E]
AA [auth E],
AB [auth N],
BA [auth E],
BB [auth N],
CA [auth E],
CB [auth N],
DA [auth F],
DB [auth N],
EA [auth F],
EB [auth O],
FA [auth F],
FB [auth P],
GA [auth G],
HA [auth G],
IA [auth H],
JA [auth H],
KA [auth I],
LA [auth J],
MA [auth J],
NA [auth K],
OA [auth K],
PA [auth K],
Q [auth A],
QA [auth K],
R [auth A],
RA [auth L],
S [auth A],
SA [auth L],
T [auth A],
TA [auth L],
U [auth B],
UA [auth L],
V [auth B],
VA [auth M],
W [auth B],
WA [auth M],
X [auth B],
XA [auth M],
Y [auth C],
YA [auth M],
Z [auth D],
ZA [auth N]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.901α = 90
b = 120.25β = 130.4
c = 120.201γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2014-08-20
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations