5I8R

aSMase with zinc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.646 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Human acid sphingomyelinase structures provide insight to molecular basis of Niemann-Pick disease.

Zhou, Y.F.Metcalf, M.C.Garman, S.C.Edmunds, T.Qiu, H.Wei, R.R.

(2016) Nat Commun 7: 13082-13082

  • DOI: 10.1038/ncomms13082
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Acid sphingomyelinase (ASM) hydrolyzes sphingomyelin to ceramide and phosphocholine, essential components of myelin in neurons. Genetic alterations in ASM lead to ASM deficiency (ASMD) and have been linked to Niemann-Pick disease types A and B. Olipu ...

    Acid sphingomyelinase (ASM) hydrolyzes sphingomyelin to ceramide and phosphocholine, essential components of myelin in neurons. Genetic alterations in ASM lead to ASM deficiency (ASMD) and have been linked to Niemann-Pick disease types A and B. Olipudase alfa, a recombinant form of human ASM, is being developed as enzyme replacement therapy to treat the non-neurological manifestations of ASMD. Here we present the human ASM holoenzyme and product bound structures encompassing all of the functional domains. The catalytic domain has a metallophosphatase fold, and two zinc ions and one reaction product phosphocholine are identified in a histidine-rich active site. The structures reveal the underlying catalytic mechanism, in which two zinc ions activate a water molecule for nucleophilic attack of the phosphodiester bond. Docking of sphingomyelin provides a model that allows insight into the selectivity of the enzyme and how the ASM domains collaborate to complete hydrolysis. Mapping of known mutations provides a basic understanding on correlations between enzyme dysfunction and phenotypes observed in ASMD patients.


    Organizational Affiliation

    Department of Biochemistry &Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA.,Protein Engineering Department, Biologics Research, Sanofi, Framingham, Massachusetts 01701, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sphingomyelin phosphodiesterase
A, B, C
583Homo sapiensMutation(s): 0 
Gene Names: SMPD1 (ASM)
EC: 3.1.4.12
Find proteins for P17405 (Homo sapiens)
Go to Gene View: SMPD1
Go to UniProtKB:  P17405
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-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, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.646 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.248 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 191.020α = 90.00
b = 230.870β = 90.00
c = 252.320γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata reduction
HKL-2000data collection
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-02-19 
  • Released Date: 2016-09-07 
  • Deposition Author(s): Zhou, Y.F., Wei, R.R.

Revision History 

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2016-11-16
    Type: Database references