2K7V | pdb_00002k7v

Deletions in a surface loop divert the folding of a protein domain into a metastable dimeric form


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

A surface loop directs conformational switching of a lipoyl domain between a folded and a novel misfolded structure.

Stott, K.M.Yusof, A.M.Perham, R.N.Jones, D.D.

(2009) Structure 17: 1117-1127

  • DOI: https://doi.org/10.1016/j.str.2009.07.001
  • Primary Citation Related Structures: 
    2K7V

  • PubMed Abstract: 

    A prominent surface loop links the first two beta strands of the lipoyl domain (E2plip) from the pyruvate dehydrogenase multienzyme complex of Escherichia coli. We show here that shortening this loop by two residues generates a protein that populates two structurally distinct stable conformers: an active, native-like monomer (HM) and a functionally compromised misfolded dimer (LM). Conversion of LM to HM was observed after exposure to temperatures above 50 degrees C. Removal of two additional residues from the loop caused the protein to adopt exclusively the misfolded conformation. Detailed NMR structural studies of the misfolded dimer reveal that the N-terminal half of the domain was unfolded and dynamic, whereas the C-terminal halves of two monomers had associated to form a structure with two-fold symmetry and a topology mimicking that of the folded monomer. The surface loop is therefore a hitherto unsuspected determinant in the folding process that leads to a functional protein.


  • Organizational Affiliation
    • Department of Biochemistry, University of Cambridge, Cambridge, UK.

Macromolecule Content 

  • Total Structure Weight: 17.77 kDa 
  • Atom Count: 1,240 
  • Modeled Residue Count: 170 
  • Deposited Residue Count: 170 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
A, B
85Escherichia coli K-12Mutation(s): 0 
Gene Names: aceF
EC: 2.3.1.12
UniProt
Find proteins for P06959 (Escherichia coli (strain K12))
Explore P06959 
Go to UniProtKB:  P06959
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06959
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-02-19
    Changes: Database references, Derived calculations, Other
  • Version 1.3: 2023-06-14
    Changes: Database references, Other
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references