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 
  • R-Value Observed: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Structures With Same Primary Citation

  • 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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Plasmid stabilization systemB, D117Mesorhizobium opportunistum WSM2075Mutation(s): 0 
Gene Names: Mesop_5598
Find proteins for F7YBW7 (Mesorhizobium opportunistum (strain LMG 24607 / HAMBI 3007 / WSM2075))
Explore F7YBW7 
Go to UniProtKB:  F7YBW7
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Addiction module antidote protein, CopG/Arc/MetJ familyA, C93Mesorhizobium opportunistum WSM2075Mutation(s): 0 
Gene Names: Mesop_5599
Find proteins for F7YBW8 (Mesorhizobium opportunistum (strain LMG 24607 / HAMBI 3007 / WSM2075))
Explore F7YBW8 
Go to UniProtKB:  F7YBW8
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

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

Download CCD File 
A, B, C, D
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-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 
  • R-Value Observed: 0.169 
  • Space Group: I 2 2 2
  • Diffraction Data DOI: 10.15785/SBGRID/198 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.18α = 90
b = 118.84β = 90
c = 211.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History 

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence