6G7O | pdb_00006g7o

Crystal structure of human alkaline ceramidase 3 (ACER3) at 2.7 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6G7O/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Escherichia coli
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2018-04-06 Released: 2019-01-02 
• Deposition Author(s): Leyrat, C., Vasiliauskaite-Brooks, I., Healey, R.D., Sounier, R., Grison, C., Hoh, F., Basu, S., Granier, S.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.270 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.259 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: experimental

Literature

Structure of a human intramembrane ceramidase explains enzymatic dysfunction found in leukodystrophy.

Vasiliauskaite-Brooks, I., Healey, R.D., Rochaix, P., Saint-Paul, J., Sounier, R., Grison, C., Waltrich-Augusto, T., Fortier, M., Hoh, F., Saied, E.M., Arenz, C., Basu, S., Leyrat, C., Granier, S.

(2018) Nat Commun 9: 5437-5437

• PubMed: 30575723 
• DOI: https://doi.org/10.1038/s41467-018-07864-w
• Primary Citation Related Structures: 
  6G7O


• PubMed Abstract: 
  

  Alkaline ceramidases (ACERs) are a class of poorly understood transmembrane enzymes controlling the homeostasis of ceramides. They are implicated in human pathophysiology, including progressive leukodystrophy, colon cancer as well as acute myeloid leukemia. We report here the crystal structure of the human ACER type 3 (ACER3). Together with computational studies, the structure reveals that ACER3 is an intramembrane enzyme with a seven transmembrane domain architecture and a catalytic Zn ²⁺ binding site in its core, similar to adiponectin receptors. Interestingly, we uncover a Ca ²⁺ binding site physically and functionally connected to the Zn ²⁺ providing a structural explanation for the known regulatory role of Ca ²⁺ on ACER3 enzymatic activity and for the loss of function in E33G-ACER3 mutant found in leukodystrophic patients.

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Organizational Affiliation: 
• IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France.
CBS, University of Montpellier, CNRS, INSERM, Montpellier, 34090, France.
Institute for chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany.
Chemistry Department, Faculty of Science, Suez Canal University, 41522, Ismailia, Egypt.
Macromolecular Crystallography, Swiss Light Source, Paul Scherrer Institut, 5232, Villigen PSI, Switzerland.
IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France. [e-mail].
IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 41.65 kDa 
• Atom Count: 3,039 
• Modeled Residue Count: 350 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alkaline ceramidase 3,Soluble cytochrome b562	A	350	Homo sapiens, Escherichia coli This entity is chimeric	Mutation(s): 0  Gene Names: ACER3, APHC, PHCA, cybC EC: 3.5.1 (PDB Primary Data), 3.5.1.23 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for Q9NUN7 (Homo sapiens) Explore Q9NUN7  Go to UniProtKB:  Q9NUN7
PHAROS:  Q9NUN7 GTEx:  ENSG00000078124
UniProt Groups	P0ABE7Q9NUN7

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLB	L [auth A]	(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-QJRAZLAKSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	M [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	N [auth A], O [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	I [auth A], J [auth A], K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.270 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.259 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.88	α = 90
b = 68.83	β = 90
c = 257.52	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-02 
Deposition Author(s): Leyrat, C., Vasiliauskaite-Brooks, I., Healey, R.D., Sounier, R., Grison, C., Hoh, F., Basu, S., Granier, S.

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Funding Organization	Location	Grant Number
European Commission	France	647687

Revision History  

• Version 1.0: 2019-01-02
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary