5NV5 | pdb_00005nv5

Enterococcus faecalis FIC protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.226 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

A Ca2+-regulated deAMPylation switch in human and bacterial FIC proteins.

Veyron, S.Oliva, G.Rolando, M.Buchrieser, C.Peyroche, G.Cherfils, J.

(2019) Nat Commun 10: 1142-1142

  • DOI: https://doi.org/10.1038/s41467-019-09023-1
  • Primary Citation Related Structures: 
    5NV5, 5NWF, 6EP0, 6EP2, 6EP5, 6ER8, 6ERB

  • PubMed Abstract: 

    FIC proteins regulate molecular processes from bacteria to humans by catalyzing post-translational modifications (PTM), the most frequent being the addition of AMP or AMPylation. In many AMPylating FIC proteins, a structurally conserved glutamate represses AMPylation and, in mammalian FICD, also supports deAMPylation of BiP/GRP78, a key chaperone of the unfolded protein response. Currently, a direct signal regulating these FIC proteins has not been identified. Here, we use X-ray crystallography and in vitro PTM assays to address this question. We discover that Enterococcus faecalis FIC (EfFIC) catalyzes both AMPylation and deAMPylation and that the glutamate implements a multi-position metal switch whereby Mg 2+ and Ca 2+ control AMPylation and deAMPylation differentially without a conformational change. Remarkably, Ca 2+ concentration also tunes deAMPylation of BiP by human FICD. Our results suggest that the conserved glutamate is a signature of AMPylation/deAMPylation FIC bifunctionality and identify metal ions as diffusible signals that regulate such FIC proteins directly.


  • Organizational Affiliation
    • CNRS and Ecole normale supérieure Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée, 61 Avenue du Président Wilson, 94235, Cachan CEDEX, France.

Macromolecule Content 

  • Total Structure Weight: 98.54 kDa 
  • Atom Count: 7,315 
  • Modeled Residue Count: 797 
  • Deposited Residue Count: 828 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fic family protein
A, B, C, D
207Enterococcus faecalisMutation(s): 0 
Gene Names: D350_01176

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.226 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.541α = 90
b = 131.001β = 90
c = 136.935γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXphasing
BUSTERrefinement
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2019-03-20
    Changes: Data collection, Database references
  • Version 1.3: 2019-10-16
    Changes: Data collection
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description