6EP2 | pdb_00006ep2

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

PDB DOI: https://doi.org/10.2210/pdb6EP2/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: 2.15 Å
R-Value Free:
0.218 (Depositor), 0.218 (DCC)
R-Value Work:
0.187 (Depositor), 0.188 (DCC)
R-Value Observed:
0.188 (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: 301.72 kDa
Atom Count: 22,137
Modeled Residue Count: 2,430
Deposited Residue Count: 2,484
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, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	207	Enterococcus faecalis	Mutation(s): 0 Gene Names: D350_01176

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain V [auth D] SDF format, chain TA [auth L] SDF format, chain S [auth C] SDF format, chain RA [auth K] SDF format, chain P [auth B] SDF format, chain OA [auth J] SDF format, chain MA [auth I] SDF format, chain M [auth A] SDF format, chain IA [auth H] SDF format, chain EA [auth G] SDF format, chain BA [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain V [auth D] MOL2 format, chain TA [auth L] MOL2 format, chain S [auth C] MOL2 format, chain RA [auth K] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth J] MOL2 format, chain MA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain IA [auth H] MOL2 format, chain EA [auth G] MOL2 format, chain BA [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain V [auth D] mmCIF format, chain TA [auth L] mmCIF format, chain S [auth C] mmCIF format, chain RA [auth K] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth J] mmCIF format, chain MA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain IA [auth H] mmCIF format, chain EA [auth G] mmCIF format, chain BA [auth F]	BA [auth F] EA [auth G] IA [auth H] M [auth A] MA [auth I] BA [auth F], EA [auth G], IA [auth H], M [auth A], MA [auth I], OA [auth J], P [auth B], RA [auth K], S [auth C], TA [auth L], V [auth D], Y [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth F] Focus chain EA [auth G] Focus chain IA [auth H] Focus chain M [auth A] Focus chain MA [auth I] Focus chain OA [auth J] Focus chain P [auth B] Focus chain RA [auth K] Focus chain S [auth C] Focus chain TA [auth L] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain EA [auth G] Focus chain IA [auth H] Focus chain M [auth A] Focus chain MA [auth I] Focus chain OA [auth J] Focus chain P [auth B] Focus chain RA [auth K] Focus chain S [auth C] Focus chain TA [auth L] Focus chain V [auth D] Focus chain Y [auth E]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain VA [auth L] SDF format, chain UA [auth L] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain SA [auth K] SDF format, chain R [auth B] SDF format, chain QA [auth J] SDF format, chain Q [auth B] SDF format, chain PA [auth J] SDF format, chain O [auth A] SDF format, chain NA [auth I] SDF format, chain N [auth A] SDF format, chain LA [auth H] SDF format, chain KA [auth H] SDF format, chain JA [auth H] SDF format, chain HA [auth G] SDF format, chain GA [auth G] SDF format, chain FA [auth G] SDF format, chain DA [auth F] SDF format, chain CA [auth F] SDF format, chain AA [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain VA [auth L] MOL2 format, chain UA [auth L] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain SA [auth K] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth J] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth J] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth I] MOL2 format, chain N [auth A] MOL2 format, chain LA [auth H] MOL2 format, chain KA [auth H] MOL2 format, chain JA [auth H] MOL2 format, chain HA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain DA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain VA [auth L] mmCIF format, chain UA [auth L] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain SA [auth K] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth J] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth J] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth I] mmCIF format, chain N [auth A] mmCIF format, chain LA [auth H] mmCIF format, chain KA [auth H] mmCIF format, chain JA [auth H] mmCIF format, chain HA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain FA [auth G] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] CA [auth F] DA [auth F] FA [auth G] GA [auth G] AA [auth E], CA [auth F], DA [auth F], FA [auth G], GA [auth G], HA [auth G], JA [auth H], KA [auth H], LA [auth H], N [auth A], NA [auth I], O [auth A], PA [auth J], Q [auth B], QA [auth J], R [auth B], SA [auth K], T [auth C], U [auth C], UA [auth L], VA [auth L], W [auth D], X [auth D], Z [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain N [auth A] Focus chain NA [auth I] Focus chain O [auth A] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain QA [auth J] Focus chain R [auth B] Focus chain SA [auth K] Focus chain T [auth C] Focus chain U [auth C] Focus chain UA [auth L] Focus chain VA [auth L] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain N [auth A] Focus chain NA [auth I] Focus chain O [auth A] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain QA [auth J] Focus chain R [auth B] Focus chain SA [auth K] Focus chain T [auth C] Focus chain U [auth C] Focus chain UA [auth L] Focus chain VA [auth L] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.218 (Depositor), 0.218 (DCC)
R-Value Work: 0.187 (Depositor), 0.188 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.311	α = 90
b = 125.311	β = 90
c = 362.879	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

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