5FI9

Closed form of murine Acid Sphingomyelinase in complex with bisphosphonate inhibitor AbPA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.543 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of mammalian acid sphingomyelinase.

Gorelik, A.Illes, K.Heinz, L.X.Superti-Furga, G.Nagar, B.

(2016) Nat Commun 7: 12196-12196

  • DOI: 10.1038/ncomms12196
  • Primary Citation of Related Structures:  5FIB, 5FIC, 5HQN

  • PubMed Abstract: 
  • Acid sphingomyelinase (ASMase, ASM, SMPD1) converts sphingomyelin into ceramide, modulating membrane properties and signal transduction. Inactivating mutations in ASMase cause Niemann-Pick disease, and its inhibition is also beneficial in models of d ...

    Acid sphingomyelinase (ASMase, ASM, SMPD1) converts sphingomyelin into ceramide, modulating membrane properties and signal transduction. Inactivating mutations in ASMase cause Niemann-Pick disease, and its inhibition is also beneficial in models of depression and cancer. To gain a better understanding of this critical therapeutic target, we determined crystal structures of mammalian ASMase in various conformations. The catalytic domain adopts a calcineurin-like fold with two zinc ions and a hydrophobic track leading to the active site. Strikingly, the membrane interacting saposin domain assumes either a closed globular conformation independent from the catalytic domain, or an open conformation, which establishes an interface with the catalytic domain essential for activity. Structural mapping of Niemann-Pick mutations reveals that most of them likely destabilize the protein's fold. This study sheds light on the molecular mechanism of ASMase function, and provides a platform for the rational development of ASMase inhibitors and therapeutic use of recombinant ASMase.


    Organizational Affiliation

    Department of Biochemistry, McGill University, Montreal, Quebec, Canada H3G 0B1.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sphingomyelin phosphodiesterase
A, B
538Mus musculusGene Names: Smpd1 (Asm)
EC: 3.1.4.12
Find proteins for Q04519 (Mus musculus)
Go to UniProtKB:  Q04519
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NT8
Query on NT8

Download SDF File 
Download CCD File 
A, B
(1-azanyl-1-phosphono-decyl)phosphonic acid
C10 H25 N O6 P2
TWYYYYAFACTHMV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.543 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.201 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 57.394α = 80.47
b = 72.018β = 71.52
c = 74.420γ = 83.60
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-08-03
    Type: Database references