6EP5 | pdb_00006ep5

Enterococcus faecalis FIC protein in complex with ADP.

• PDB DOI: https://doi.org/10.2210/pdb6EP5/pdb

• Classification: TOXIN
• Organism(s): Enterococcus faecalis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-10-10 Released: 2019-02-06 
• Deposition Author(s): Veyron, S., Cherfils, J.
• Funding Organization(s): DIM Malinf

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.240 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

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

• PubMed: 30850593 
• 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.

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Organizational Affiliation: 
• CNRS and Ecole normale supérieure Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée, 61 Avenue du Président Wilson, 94235, Cachan CEDEX, France.
Institut Pasteur and CNRS UMR 3525, Biologie des Bactéries Intracellulaires, 25-28 Rue du Dr Roux, 75015, Paris, France.
Sorbonne Université, Collège doctoral, 75005, Paris, France.
CNRS and Ecole normale supérieure Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée, 61 Avenue du Président Wilson, 94235, Cachan CEDEX, France. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 150.38 kDa 
• Atom Count: 11,142 
• Modeled Residue Count: 1,200 
• Deposited Residue Count: 1,242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fic family protein	A, B, C, D, E, F	207	Enterococcus faecalis	Mutation(s): 0  Gene Names: D350_01176

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.240 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.836	α = 90
b = 87.836	β = 90
c = 364.936	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Veyron, S., Cherfils, J.

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Funding Organization	Location	Grant Number
DIM Malinf	France	--

Revision History  

• Version 1.0: 2019-02-06
  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: 2024-01-17
  Changes: Data collection, Database references, Refinement description