5I8R

aSMase with zinc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.248 
  • R-Value Observed: 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
  • Structures With Same Primary Citation

  • 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

    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: SMPD1ASM
EC: 3.1.4.12
Find proteins for P17405 (Homo sapiens)
Go to UniProtKB:  P17405
NIH Common Fund Data Resources
PHAROS  P17405
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

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

Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 191.02α = 90
b = 230.87β = 90
c = 252.32γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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
    Changes: Database references