5CEG

X-ray structure of toxin/anti-toxin complex from Mesorhizobium opportunistum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Evolving New Protein-Protein Interaction Specificity through Promiscuous Intermediates.

Aakre, C.D.Herrou, J.Phung, T.N.Perchuk, B.S.Crosson, S.Laub, M.T.

(2015) Cell 163: 594-606

  • DOI: 10.1016/j.cell.2015.09.055

  • PubMed Abstract: 
  • Interacting proteins typically coevolve, and the identification of coevolving amino acids can pinpoint residues required for interaction specificity. This approach often assumes that an interface-disrupting mutation in one protein drives selection of ...

    Interacting proteins typically coevolve, and the identification of coevolving amino acids can pinpoint residues required for interaction specificity. This approach often assumes that an interface-disrupting mutation in one protein drives selection of a compensatory mutation in its partner during evolution. However, this model requires a non-functional intermediate state prior to the compensatory change. Alternatively, a mutation in one protein could first broaden its specificity, allowing changes in its partner, followed by a specificity-restricting mutation. Using bacterial toxin-antitoxin systems, we demonstrate the plausibility of this second, promiscuity-based model. By screening large libraries of interface mutants, we show that toxins and antitoxins with high specificity are frequently connected in sequence space to more promiscuous variants that can serve as intermediates during a reprogramming of interaction specificity. We propose that the abundance of promiscuous variants promotes the expansion and diversification of toxin-antitoxin systems and other paralogous protein families during evolution.


    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: laub@mit.edu.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Addiction module antidote protein, CopG/Arc/MetJ family
A, C
93Mesorhizobium opportunistum (strain LMG 24607 / HAMBI 3007 / WSM2075)Mutation(s): 0 
Find proteins for F7YBW8 (Mesorhizobium opportunistum (strain LMG 24607 / HAMBI 3007 / WSM2075))
Go to UniProtKB:  F7YBW8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Plasmid stabilization system
B, D
117Mesorhizobium opportunistum (strain LMG 24607 / HAMBI 3007 / WSM2075)Mutation(s): 0 
Find proteins for F7YBW7 (Mesorhizobium opportunistum (strain LMG 24607 / HAMBI 3007 / WSM2075))
Go to UniProtKB:  F7YBW7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

Download SDF File 
Download CCD File 
A, B, C, D
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.169 
  • Space Group: I 2 2 2
  • Diffraction Data DOI: 
    10.15785/SBGRID/198 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 43.180α = 90.00
b = 118.840β = 90.00
c = 211.420γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence, Derived calculations