5CK9

E. coli MazF form I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.898 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Substrate Recognition and Activity Regulation of the Escherichia coli mRNA Endonuclease MazF.

Zorzini, V.Mernik, A.Lah, J.Sterckx, Y.G.De Jonge, N.Garcia-Pino, A.De Greve, H.Versees, W.Loris, R.

(2016) J.Biol.Chem. 291: 10950-10960

  • DOI: 10.1074/jbc.M116.715912
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Escherichia coli MazF (EcMazF) is the archetype of a large family of ribonucleases involved in bacterial stress response. The crystal structure of EcMazF in complex with a 7-nucleotide substrate mimic explains the relaxed substrate specificity of the ...

    Escherichia coli MazF (EcMazF) is the archetype of a large family of ribonucleases involved in bacterial stress response. The crystal structure of EcMazF in complex with a 7-nucleotide substrate mimic explains the relaxed substrate specificity of the E. coli enzyme relative to its Bacillus subtilis counterpart and provides a framework for rationalizing specificity in this enzyme family. In contrast to a conserved mode of substrate recognition and a conserved active site, regulation of enzymatic activity by the antitoxin EcMazE diverges from its B. subtilis homolog. Central in this regulation is an EcMazE-induced double conformational change as follows: a rearrangement of a crucial active site loop and a relative rotation of the two monomers in the EcMazF dimer. Both are induced by the C-terminal residues Asp-78-Trp-82 of EcMazE, which are also responsible for strong negative cooperativity in EcMazE-EcMazF binding. This situation shows unexpected parallels to the regulation of the F-plasmid CcdB activity by CcdA and further supports a common ancestor despite the different activities of the MazF and CcdB toxins. In addition, we pinpoint the origin of the lack of activity of the E24A point mutant of EcMazF in its inability to support the substrate binding-competent conformation of EcMazF.


    Organizational Affiliation

    From the Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium, the Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussels, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endoribonuclease MazF
A, B
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: mazF (chpA, chpAK)
EC: 3.1.27.-
Find proteins for P0AE70 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AE70
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download SDF File 
Download CCD File 
A, B
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.898 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.194 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 52.190α = 90.00
b = 52.190β = 90.00
c = 197.840γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-07-15 
  • Released Date: 2016-04-06 
  • Deposition Author(s): Zorzini, V., Loris, R.

Funding OrganizationLocationGrant Number
Fonds Wetenschappelijk Onderzoek Vlaanderen (FWO)Belgium--
Biostruct-X--

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-04-13
    Type: Database references
  • Version 1.2: 2016-06-08
    Type: Database references