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 1.3 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: https://doi.org/10.1016/j.cell.2015.09.055
  • Primary Citation of Related Structures:  
    5CEG

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Addiction module antidote protein, CopG/Arc/MetJ family
A, C
93Mesorhizobium opportunistum WSM2075Mutation(s): 0 
Gene Names: Mesop_5599
UniProt
Find proteins for F7YBW8 (Mesorhizobium opportunistum (strain LMG 24607 / HAMBI 3007 / WSM2075))
Explore F7YBW8 
Go to UniProtKB:  F7YBW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF7YBW8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Plasmid stabilization system
B, D
117Mesorhizobium opportunistum WSM2075Mutation(s): 0 
Gene Names: Mesop_5598
UniProt
Find proteins for F7YBW7 (Mesorhizobium opportunistum (strain LMG 24607 / HAMBI 3007 / WSM2075))
Explore F7YBW7 
Go to UniProtKB:  F7YBW7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF7YBW7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
K [auth B]
M [auth C]
Q [auth D]
F [auth A],
G [auth A],
K [auth B],
M [auth C],
Q [auth D],
R [auth D],
S [auth D],
T [auth D]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
H [auth B]
I [auth B]
L [auth C]
N [auth D]
E [auth A],
H [auth B],
I [auth B],
L [auth C],
N [auth D],
O [auth D],
P [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

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  (Full details and data files)

  • 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
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Derived calculations