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 9S0V | pdb_00009s0v

The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (hTNAP) in complex with phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 
    0.266 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

TNAP dephosphorylates phosphocholine and phosphoethanolamine and participates in triglyceride transport from the liver to the bloodstream.

Drevet Mulard, E., Imam, I., Coureux, P.D., Briolay, A., Bessueille, L., Tarby, A., Balayssac, S., Narisawa, S., Lecornu, F., Gilard, V., Violot, S., Millan, J.L., Rautureau, G.J.P., Ballut, L., Magne, D.

(2025) Commun Biol 8: 1501-1501

  • DOI: https://doi.org/10.1038/s42003-025-08901-3
  • Primary Citation Related Structures: 
    9S0V

  • PubMed Abstract: 

    Tissue-nonspecific alkaline phosphatase (TNAP) is primarily known for its role in skeletal mineralization, through the hydrolysis of inorganic pyrophosphate (PP i ). Here we demonstrate that TNAP-knockout mice exhibit liver steatosis and reduced serum triglyceride levels, mirroring the effects of choline deficiency, which impairs phosphatidylcholine synthesis, an essential component of VLDL. In fasting WT mice, TNAP inhibition via SBI-425 administration decreases choline levels in blood and liver. Incubating mouse or human serum with SBI-425 inhibits the dephosphorylation of phosphocholine and phosphoethanolamine, an alternative substrate for hepatic phosphatidylcholine synthesis. In hepatocytes, TNAP inhibition impedes proliferation when the medium is supplemented with phosphocholine instead of choline. Recombinant TNAP hydrolyzes phosphocholine and phosphoethanolamine with similar efficiency than PP i . X-ray diffraction and cryo-EM identified the residues in TNAP's active site interacting with phosphocholine, PP i and the TNAP inhibitor. In summary, TNAP is the phosphatase enabling cellular choline uptake during fasting, participating in hepatic lipid metabolism.


  • Organizational Affiliation: 
    • UMR CNRS 5246, ICBMS, University Lyon, Université Claude Bernard Lyon 1, Lyon, France.

Macromolecule Content 

  • Total Structure Weight: 291.64 kDa 
  • Atom Count: 19,230 
  • Modeled Residue Count: 2,411 
  • Deposited Residue Count: 2,545 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alkaline phosphatase, tissue-nonspecific isozyme
A, B, C, D, E
509Homo sapiensMutation(s): 0 
Gene Names: ALPL
EC: 3.1.3.1 (PDB Primary Data), 3.9.1.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P05186 (Homo sapiens)
Explore P05186 
Go to UniProtKB:  P05186
PHAROS:  P05186
GTEx:  ENSG00000162551 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05186
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P05186-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, G, I, J, L
F, G, I, J, L, M, N, O, P, R
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H, K, Q, S
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
DA [auth B]
JA [auth C]
PA [auth D]
VA [auth E]
WA [auth E]
DA [auth B],
JA [auth C],
PA [auth D],
VA [auth E],
WA [auth E],
X [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4
(Subject of Investigation/LOI)

Query on PO4



Download:Ideal Coordinates CCD File
EA [auth B],
KA [auth C],
QA [auth D],
XA [auth E],
Y [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
AA [auth B]
FA [auth C]
GA [auth C]
LA [auth D]
MA [auth D]
AA [auth B],
FA [auth C],
GA [auth C],
LA [auth D],
MA [auth D],
RA [auth E],
SA [auth E],
T [auth A],
U [auth A],
Z [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
(Subject of Investigation/LOI)

Query on CA



Download:Ideal Coordinates CCD File
CA [auth B],
IA [auth C],
OA [auth D],
UA [auth E],
W [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
BA [auth B],
HA [auth C],
NA [auth D],
TA [auth E],
V [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free:  0.266 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.73α = 90
b = 297.7β = 90
c = 205.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)France--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release
  • Version 1.1: 2026-09-16
    Changes: Database references
  • Version 1.2: 2026-09-23
    Changes: Database references