6EP0 | pdb_00006ep0

Enterococcus faecalis FIC protein in complex with AMP and calcium ion.

PDB DOI: https://doi.org/10.2210/pdb6EP0/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.264 (Depositor), 0.253 (DCC)
R-Value Work:
0.218 (Depositor), 0.212 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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

PubMed: 30850593 Search on PubMed Search on PubMed Central
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: 50.28 kDa
Atom Count: 3,528
Modeled Residue Count: 400
Deposited Residue Count: 414
Unique protein chains: 1

Macromolecules

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| 3D Structure

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B]	I [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.264 (Depositor), 0.253 (DCC)
R-Value Work: 0.218 (Depositor), 0.212 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.975	α = 90
b = 64.975	β = 90
c = 246.239	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-02-06

Deposition Author(s):

Veyron, S.

Cherfils, J.

Funding Organization	Location	Grant Number
DIM Malinf	France	--

Revision History (Full details and data files)

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, Derived calculations, Refinement description