5CQX

E. coli MazF mutant E24A in complex with MazE residues 68-82 form I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.178 

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:  
    5CK9, 5CKF, 5CKE, 5CKH, 5CKB, 5CKD, 5CO7, 5CQX, 5CQY, 5CR2

  • 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, reloris@vub.ac.be.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endoribonuclease MazFAB119Escherichia coli K-12Mutation(s): 1 
Gene Names: mazFchpAchpAKb2782JW2753
EC: 3.1.27
Find proteins for P0AE70 (Escherichia coli (strain K12))
Explore P0AE70 
Go to UniProtKB:  P0AE70
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Antitoxin MazEC15Escherichia coli K-12Mutation(s): 0 
Gene Names: mazEchpAIchpRb2783JW2754
Find proteins for P0AE72 (Escherichia coli (strain K12))
Explore P0AE72 
Go to UniProtKB:  P0AE72
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.76α = 90
b = 32.25β = 97.66
c = 86.26γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-07-22 
  • Released Date: 2016-04-06 
  • Deposition Author(s): Zorzini, V., Loris, R.

Funding OrganizationLocationGrant Number
Fonds Wetenschappelijk Onderzoek-VlaanderenBelgium--
Biostruct-XBelgium--

Revision History 

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