Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 102.77 kDa 
• Atom Count: 7,187 
• Modelled Residue Count: 785 
• Deposited Residue Count: 858 
• Unique protein chains: 1

 5EGH

Structure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase in complex with phosphocholine

• PDB DOI: 10.2210/pdb5EGH/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2015-10-27 Released: 2016-03-09 
• Deposition Author(s): Morita, J., Kano, K., Kato, K., Takita, H., Ishitani, R., Nishimasu, H., Nureki, O., Aoki, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.211 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

Structure and biological function of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase

Morita, J., Kano, K., Kato, K., Takita, H., Sakagami, H., Yamamoto, Y., Mihara, E., Ueda, H., Sato, T., Tokuyama, H., Arai, H., Asou, H., Takagi, J., Ishitani, R., Nishimasu, H., Nureki, O., Aoki, J.

(2016) Sci Rep 6: 20995-20995

• PubMed: 26888014 
• DOI: 10.1038/srep20995
• Primary Citation of Related Structures:  
  5EGE, 5EGH


• PubMed Abstract: 
  

Choline is an essential nutrient for all living cells and is produced extracellularly by sequential degradation of phosphatidylcholine (PC). However, little is known about how choline is produced extracellularly. Here, we report that ENPP6, a choline-specific phosphodiesterase, hydrolyzes glycerophosphocholine (GPC), a degradation product of PC, as a physiological substrate and participates in choline metabolism. ENPP6 is highly expressed in liver sinusoidal endothelial cells and developing oligodendrocytes, which actively incorporate choline and synthesize PC. ENPP6-deficient mice exhibited fatty liver and hypomyelination, well known choline-deficient phenotypes. The choline moiety of GPC was incorporated into PC in an ENPP6-dependent manner both in vivo and in vitro. The crystal structure of ENPP6 in complex with phosphocholine revealed that the choline moiety of the phosphocholine is recognized by a choline-binding pocket formed by conserved aromatic and acidic residues. The present study provides the molecular basis for ENPP6-mediated choline metabolism at atomic, cellular and tissue levels.

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Organizational Affiliation: 

AMED (Japan Agency for Medical Research and Development)-CREST (Core Research for Evolutional Science and Technology), 1-7-1, Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ectonucleotide pyrophosphatase/phosphodiesterase family member 6	A, B	429	Mus musculus	Mutation(s): 2  Gene Names: Enpp6 EC: 3.1.4 (PDB Primary Data), 3.1.4.38 (PDB Primary Data)
UniProt
Find proteins for Q8BGN3 (Mus musculus) Explore Q8BGN3  Go to UniProtKB:  Q8BGN3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E, G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D, F	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G28454KX GlyCosmos:  G28454KX GlyGen:  G28454KX

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	N [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PC	L [auth A], R [auth B]	PHOSPHOCHOLINE C5 H15 N O4 P YHHSONZFOIEMCP-UHFFFAOYSA-O
ZN	H [auth A], I [auth A], O [auth B], P [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	J [auth A], K [auth A], M [auth A], Q [auth B], S [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.211 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.62	α = 60.59
b = 68.849	β = 86.99
c = 69.761	γ = 68.1

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
MOLREP	phasing
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Morita, J., Kano, K., Kato, K., Takita, H., Ishitani, R., Nishimasu, H., Nureki, O., Aoki, J.

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary