4OU1

Crystal structure of a computationally designed retro-aldolase covalently bound to folding probe 1 [(6-methoxynaphthalen-2-yl)(oxiran-2-yl)methanol]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts.

Liu, Y.Tan, Y.L.Zhang, X.Bhabha, G.Ekiert, D.C.Genereux, J.C.Cho, Y.Kipnis, Y.Bjelic, S.Baker, D.Kelly, J.W.

(2014) Proc.Natl.Acad.Sci.USA 111: 4449-4454

  • DOI: 10.1073/pnas.1323268111

  • PubMed Abstract: 
  • Although much is known about protein folding in buffers, it remains unclear how the cellular protein homeostasis network functions as a system to partition client proteins between folded and functional, soluble and misfolded, and aggregated conformat ...

    Although much is known about protein folding in buffers, it remains unclear how the cellular protein homeostasis network functions as a system to partition client proteins between folded and functional, soluble and misfolded, and aggregated conformations. Herein, we develop small molecule folding probes that specifically react with the folded and functional fraction of the protein of interest, enabling fluorescence-based quantification of this fraction in cell lysate at a time point of interest. Importantly, these probes minimally perturb a protein's folding equilibria within cells during and after cell lysis, because sufficient cellular chaperone/chaperonin holdase activity is created by rapid ATP depletion during cell lysis. The folding probe strategy and the faithful quantification of a particular protein's functional fraction are exemplified with retroaldolase, a de novo designed enzyme, and transthyretin, a nonenzyme protein. Our findings challenge the often invoked assumption that the soluble fraction of a client protein is fully folded in the cell. Moreover, our results reveal that the partitioning of destabilized retroaldolase and transthyretin mutants between the aforementioned conformational states is strongly influenced by cytosolic proteostasis network perturbations. Overall, our results suggest that applying a chemical folding probe strategy to other client proteins offers opportunities to reveal how the proteostasis network functions as a system to regulate the folding and function of individual client proteins in vivo.


    Organizational Affiliation

    Departments of Molecular and Experimental Medicine and Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retro-aldolase, design RA114
A
258Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: trpC
EC: 4.1.1.48
Find proteins for Q06121 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q06121
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
BEZ
Query on BEZ

Download SDF File 
Download CCD File 
A
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
 Ligand Interaction
2V7
Query on 2V7

Download SDF File 
Download CCD File 
A
(1S,2S)-1-(6-methoxynaphthalen-2-yl)propane-1,2-diol
(6-methoxynaphthalen-2-yl)(oxiran-2-yl)methanol, bound form
C14 H16 O3
CWZNIRHUMZESFD-LKFCYVNXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.175 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 61.730α = 90.00
b = 61.730β = 90.00
c = 121.820γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
Blu-Icedata collection
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-04-02
    Type: Database references
  • Version 1.2: 2014-04-23
    Type: Database references