6X84

Sn-glycerol-3-phosphate binding periplasmic protein UgpB from Escherichia coli - W169S, W172S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A metabolite binding protein moonlights as a bile-responsive chaperone.

Lee, C.Betschinger, P.Wu, K.Zyla, D.S.Glockshuber, R.Bardwell, J.C.

(2020) EMBO J 39: e104231-e104231

  • DOI: https://doi.org/10.15252/embj.2019104231
  • Primary Citation of Related Structures:  
    6X84

  • PubMed Abstract: 

    Bile salts are secreted into the gastrointestinal tract to aid in the absorption of lipids. In addition, bile salts show potent antimicrobial activity in part by mediating bacterial protein unfolding and aggregation. Here, using a protein folding sensor, we made the surprising discovery that the Escherichia coli periplasmic glycerol-3-phosphate (G3P)-binding protein UgpB can serve, in the absence of its substrate, as a potent molecular chaperone that exhibits anti-aggregation activity against bile salt-induced protein aggregation. The substrate G3P, which is known to accumulate in the later compartments of the digestive system, triggers a functional switch between UgpB's activity as a molecular chaperone and its activity as a G3P transporter. A UgpB mutant unable to bind G3P is constitutively active as a chaperone, and its crystal structure shows that it contains a deep surface groove absent in the G3P-bound wild-type UgpB. Our work illustrates how evolution may be able to convert threats into signals that first activate and then inactivate a chaperone at the protein level in a manner that bypasses the need for ATP.


  • Organizational Affiliation

    Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
sn-glycerol-3-phosphate-binding periplasmic protein UgpB
A, B
416Escherichia coli K-12Mutation(s): 2 
Gene Names: ugpBb3453JW3418
UniProt
Find proteins for P0AG80 (Escherichia coli (strain K12))
Explore P0AG80 
Go to UniProtKB:  P0AG80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG80
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.936α = 90.89
b = 46.724β = 98.53
c = 94.792γ = 105.13
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
Swiss National Science FoundationSwitzerland310030B_176403/1
Swiss National Science FoundationSwitzerland31003A_156304

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references
  • Version 1.2: 2020-09-23
    Changes: Database references
  • Version 1.3: 2020-10-28
    Changes: Database references
  • Version 1.4: 2023-10-18
    Changes: Data collection, Database references, Refinement description