7YIW

The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (ALPL) at Acidic pH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The structural pathology for hypophosphatasia caused by malfunctional tissue non-specific alkaline phosphatase.

Yu, Y.Rong, K.Yao, D.Zhang, Q.Cao, X.Rao, B.Xia, Y.Lu, Y.Shen, Y.Yao, Y.Xu, H.Ma, P.Cao, Y.Qin, A.

(2023) Nat Commun 14: 4048-4048

  • DOI: https://doi.org/10.1038/s41467-023-39833-3
  • Primary Citation of Related Structures:  
    7YIV, 7YIW, 7YIX

  • PubMed Abstract: 

    Hypophosphatasia (HPP) is a metabolic bone disease that manifests as developmental abnormalities in bone and dental tissues. HPP patients exhibit hypo-mineralization and osteopenia due to the deficiency or malfunction of tissue non-specific alkaline phosphatase (TNAP), which catalyzes the hydrolysis of phosphate-containing molecules outside the cells, promoting the deposition of hydroxyapatite in the extracellular matrix. Despite the identification of hundreds of pathogenic TNAP mutations, the detailed molecular pathology of HPP remains unclear. Here, to address this issue, we determine the crystal structures of human TNAP at near-atomic resolution and map the major pathogenic mutations onto the structure. Our study reveals an unexpected octameric architecture for TNAP, which is generated by the tetramerization of dimeric TNAPs, potentially stabilizing the TNAPs in the extracellular environments. Moreover, we use cryo-electron microscopy to demonstrate that the TNAP agonist antibody (JTALP001) forms a stable complex with TNAP by binding to the octameric interface. The administration of JTALP001 enhances osteoblast mineralization and promoted recombinant TNAP-rescued mineralization in TNAP knockout osteoblasts. Our findings elucidate the structural pathology of HPP and highlight the therapeutic potential of the TNAP agonist antibody for osteoblast-associated bone disorders.


  • Organizational Affiliation

    Department of Orthopedics, Shanghai Key Laboratory of Orthopedics Implant, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alkaline phosphatase, tissue-nonspecific isozyme503Homo 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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
CB [auth H]
DB [auth H]
EA [auth D]
FA [auth D]
IB [auth F]
CB [auth H],
DB [auth H],
EA [auth D],
FA [auth D],
IB [auth F],
JB [auth F],
KA [auth C],
LA [auth C],
OB [auth E],
PB [auth E],
QA [auth B],
RA [auth B],
WA [auth G],
XA [auth G],
Y [auth A],
Z [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth A]
BB [auth G]
DA [auth A]
FB [auth H]
HA [auth D]
BA [auth A],
BB [auth G],
DA [auth A],
FB [auth H],
HA [auth D],
HB [auth H],
JA [auth D],
LB [auth F],
NA [auth C],
NB [auth F],
PA [auth C],
RB [auth E],
TA [auth B],
TB [auth E],
VA [auth B],
ZA [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AB [auth G]
CA [auth A]
GB [auth H]
IA [auth D]
MB [auth F]
AB [auth G],
CA [auth A],
GB [auth H],
IA [auth D],
MB [auth F],
OA [auth C],
SB [auth E],
UA [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A]
EB [auth H]
GA [auth D]
KB [auth F]
MA [auth C]
AA [auth A],
EB [auth H],
GA [auth D],
KB [auth F],
MA [auth C],
QB [auth E],
SA [auth B],
YA [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.364α = 90
b = 166.525β = 90
c = 181.605γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description