5EBB

Structure of human sphingomyelinase phosphodiesterase like 3A (SMPDL3A) with Zn2+

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 

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This is version 1.3 of the entry. See complete history. 


Literature

The structure and catalytic mechanism of human sphingomyelin phosphodiesterase like 3a - an acid sphingomyelinase homologue with a novel nucleotide hydrolase activity.

Lim, S.M., Yeung, K., Tresaugues, L., Ling, T.H., Nordlund, P.

(2016) FEBS J 283: 1107-1123

  • DOI: 10.1111/febs.13655
  • Primary Citation of Related Structures:  
    2XS6, 5EBB, 5EBE

  • PubMed Abstract: 

    • Human sphingomyelinase phosphodiesterase like 3a (SMPDL3a) is a secreted enzyme that shares a conserved catalytic domain with human acid sphingomyelinase (aSMase), the enzyme carrying mutations causative of Niemann-Pick disease. We have solved the structure of SMPDL3a revealing a calcineurin-like fold ...

    Human sphingomyelinase phosphodiesterase like 3a (SMPDL3a) is a secreted enzyme that shares a conserved catalytic domain with human acid sphingomyelinase (aSMase), the enzyme carrying mutations causative of Niemann-Pick disease. We have solved the structure of SMPDL3a revealing a calcineurin-like fold. A dimetal site, glycosylation pattern and a disulfide bond network are likely to be conserved also in human aSMase. We show that the binuclear site of SMPDL3a is occupied by two Zn(2+) ions and that excess Zn(2+) leads to inhibition of enzyme activity through binding to additional sites. As an extension of recent biochemical work we uncovered that SMPDL3a catalyses the hydrolysis of several modified nucleotides that include cytidine 5'-diphosphocholine, cytidine diphosphate ethanolamine and ADP-ribose, but not the aSMase substrate, sphingomyelin. We subsequently determined the structure of SMPDL3a in complex with the product 5'-cytidine monophosphate (CMP), a structure that is consistent with several distinct coordination modes of the substrate/product in the active site during the reaction cycle. Based on the structure of CMP complexes, we propose a phosphoryl transfer mechanism for SMPDL3a. Finally, a homology model of human aSMase was constructed to allow for the mapping of selected Niemann-Pick disease mutations on a three-dimensional framework to guide further characterization of their effects on aSMase function.

    Organizational Affiliation: 

    Institute of Molecular and Cell Biology, A*STAR, Singapore city, Singapore.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acid sphingomyelinase-like phosphodiesterase 3aA, B, C410Homo sapiensMutation(s): 0 
Gene Names: SMPDL3A, ASML3A
EC: 3.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q92484 (Homo sapiens)
Explore Q92484 
Go to UniProtKB:  Q92484
PHAROS:  Q92484
GTEx:  ENSG00000172594 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92484
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B],
S [auth C],
T [auth C],
U [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
MLI
Query on MLI
Download Ideal Coordinates CCD File 
I [auth A],
O [auth B],
V [auth C]		MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
P [auth B],
W [auth C]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
J [auth B],
K [auth B],
Q [auth C],
D [auth A],
E [auth A],
J [auth B],
K [auth B],
Q [auth C],
R [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.79α = 90
b = 147.79β = 90
c = 139.9γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoSHARPphasing
Aimlessdata scaling
Cootmodel building
ARPmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research FoundationSingaporeNRF-CRP4-2008-02
Swedish Cancer SocietySweden--

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-02-03
    Changes: Database references
  • Version 1.2: 2016-03-30
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary