7EPI

Crystal structure of E.coli CcdB mutant S60E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.170 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Mechanistic insights into global suppressors of protein folding defects.

Chattopadhyay, G.Bhowmick, J.Manjunath, K.Ahmed, S.Goyal, P.Varadarajan, R.

(2022) PLoS Genet 18: e1010334-e1010334

  • DOI: https://doi.org/10.1371/journal.pgen.1010334
  • Primary Citation of Related Structures:  
    7EPG, 7EPI, 7EPJ

  • PubMed Abstract: 

    Most amino acid substitutions in a protein either lead to partial loss-of-function or are near neutral. Several studies have shown the existence of second-site mutations that can rescue defects caused by diverse loss-of-function mutations. Such global suppressor mutations are key drivers of protein evolution. However, the mechanisms responsible for such suppression remain poorly understood. To address this, we characterized multiple suppressor mutations both in isolation and in combination with inactive mutants. We examined six global suppressors of the bacterial toxin CcdB, the known M182T global suppressor of TEM-1 β-lactamase, the N239Y global suppressor of p53-DBD and three suppressors of the SARS-CoV-2 spike Receptor Binding Domain. When coupled to inactive mutants, they promote increased in-vivo solubilities as well as regain-of-function phenotypes. In the case of CcdB, where novel suppressors were isolated, we determined the crystal structures of three such suppressors to obtain insight into the specific molecular interactions responsible for the observed effects. While most individual suppressors result in small stability enhancements relative to wildtype, which can be combined to yield significant stability increments, thermodynamic stabilisation is neither necessary nor sufficient for suppressor action. Instead, in diverse systems, we observe that individual global suppressors greatly enhance the foldability of buried site mutants, primarily through increase in refolding rate parameters measured in vitro. In the crowded intracellular environment, mutations that slow down folding likely facilitate off-pathway aggregation. We suggest that suppressor mutations that accelerate refolding can counteract this, enhancing the yield of properly folded, functional protein in vivo.


  • Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin CcdB101Escherichia coli K-12Mutation(s): 1 
Gene Names: ccdBGletBletDECOK12F043
UniProt
Find proteins for P62554 (Escherichia coli (strain K12))
Explore P62554 
Go to UniProtKB:  P62554
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62554
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.81α = 90
b = 36.64β = 114.97
c = 35.67γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaBT/COE/34/SP15219/2015
Department of Science & Technology (DST, India)India--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release
  • Version 1.1: 2022-12-21
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description