› 4wgk

X-ray diffraction
2.58Å resolution

Crystal structure of human neutral ceramidase with Zn-bound phosphate

Released:
DOI: 10.2210/pdb4wgk/pdb
PDB entry 4wgk coloured by chain, front view.
PDB entry 4wgk coloured by chain, side view.
PDB entry 4wgk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Basis for Ceramide Recognition and Hydrolysis by Human Neutral Ceramidase.
Airola MV, Allen WJ, Pulkoski-Gross MJ, Obeid LM, Rizzo RC, Hannun YA
Structure 23 1482-1491 (2015)
PMID: 26190575

Function and Biology Details

Reaction catalysed: 
N-acylsphingosine + H(2)O = a carboxylate + sphingosine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192546 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Neutral ceramidase soluble form Chains: A, B
Molecule details ›
Chains: A, B
Length: 688 amino acids
Theoretical weight: 75.98 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9NR71 (Residues: 99-780; Coverage: 87%)
Gene names: ASAH2, HNAC1
Sequence domains:
Structure domains: Neutral/alkaline non-lysosomal ceramidase, C-terminal domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
7 bound ligands:
Ligand ZN 2 x ZN
Ligand CA 2 x CA
Ligand NAG 5 x NAG
Ligand PO4 2 x PO4
Ligand CIT 4 x CIT
Ligand CL 1 x CL
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21
Unit cell:
a: 73.48Å b: 156.63Å c: 80.33Å
α: 90° β: 108.04° γ: 90°
R-values:
R R work R free
0.18 0.178 0.223
Expression system: Spodoptera frugiperda

Quick links

Citations

10 review citations

Sphingolipids and their metabolism in physiology and disease.
Hannun et al. (2018)
9 more

5 mentions without citation

Role of Ceramidases in Sphingolipid Metabolism and Human Diseases.
Parveen et al. (2019)
4 more