Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.69 kDa 
• Atom Count: 2578 
• Modelled Residue Count: 288 
• Deposited Residue Count: 301 
• Unique protein chains: 1

1ZWX

Crystal Structure of SmcL

• PDB DOI: 10.2210/pdb1ZWX/pdb

• Classification: HYDROLASE
• Organism(s): Listeria ivanovii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2005-06-06 Released: 2005-08-16 
• Deposition Author(s): Openshaw, A.E.A., Race, P.R., Monzo, H.J., Vasquez-Boland, J.A., Banfield, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.233 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

Crystal structure of SmcL, a bacterial neutral sphingomyelinase C from Listeria.

Openshaw, A.E.A., Race, P.R., Monzo, H.J., Vasquez-Boland, J.A., Banfield, M.J.

(2005) J Biol Chem 280: 35011-35017

• PubMed: 16093240 
• DOI: 10.1074/jbc.M506800200
• Primary Citation of Related Structures:  
  1ZWX


• PubMed Abstract: 
  

Sphingomyelinases C are enzymes that catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine. Various pathogenic bacteria produce secreted neutral sphingomyelinases C that act as membrane-damaging virulence factors. Mammalian neutral sphingomyelinases C, which display sequence homology to the bacterial enzymes, are involved in sphingolipid metabolism and signaling. This article describes the first structure to be determined for a member of the neutral sphingomyelinase C family, SmcL, from the intracellular bacterial pathogen Listeria ivanovii. The structure has been refined to 1.9-A resolution with phases derived by single isomorphous replacement with anomalous scattering techniques from a single iridium derivative. SmcL adopts a DNase I-like fold, and is the first member of this protein superfamily to have its structure determined that acts as a phospholipase. The structure reveals several unique features that adapt the protein to its phospholipid substrate. These include large hydrophobic beta-hairpin and hydrophobic loops surrounding the active site that may bind and penetrate the lipid bilayer to position sphingomyelin in a catalytically competent position. The structure also provides insight into the proposed general base/acid catalytic mechanism, in which His-325 and His-185 play key roles.

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Organizational Affiliation: 

Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne, NE2 4HH United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
sphingomyelinase-c	A	301	Listeria ivanovii	Mutation(s): 0  Gene Names: smcL EC: 3.1.4.12 Membrane Entity: Yes
UniProt
Find proteins for Q9RLV9 (Listeria ivanovii) Explore Q9RLV9  Go to UniProtKB:  Q9RLV9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.233 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.86	α = 90
b = 66.86	β = 90
c = 180.848	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-06-06 
• Released Date: 2005-08-16 
Deposition Author(s): Openshaw, A.E.A., Race, P.R., Monzo, H.J., Vasquez-Boland, J.A., Banfield, M.J.

Revision History  

• Version 1.0: 2005-08-16
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance