4GTX

Crystal structure of mouse Enpp1 in complex with TMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.201 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of Enpp1, an extracellular glycoprotein involved in bone mineralization and insulin signaling.

Kato, K.Nishimasu, H.Okudaira, S.Mihara, E.Ishitani, R.Takagi, J.Aoki, J.Nureki, O.

(2012) Proc.Natl.Acad.Sci.USA 109: 16876-16881

  • DOI: 10.1073/pnas.1208017109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Enpp1 is a membrane-bound glycoprotein that regulates bone mineralization by hydrolyzing extracellular nucleotide triphosphates to produce pyrophosphate. Enpp1 dysfunction causes human diseases characterized by ectopic calcification. Enpp1 also inhib ...

    Enpp1 is a membrane-bound glycoprotein that regulates bone mineralization by hydrolyzing extracellular nucleotide triphosphates to produce pyrophosphate. Enpp1 dysfunction causes human diseases characterized by ectopic calcification. Enpp1 also inhibits insulin signaling, and an Enpp1 polymorphism is associated with insulin resistance. However, the precise mechanism by which Enpp1 functions in these cellular processes remains elusive. Here, we report the crystal structures of the extracellular region of mouse Enpp1 in complex with four different nucleotide monophosphates, at resolutions of 2.7-3.2 Å. The nucleotides are accommodated in a pocket formed by an insertion loop in the catalytic domain, explaining the preference of Enpp1 for an ATP substrate. Structural mapping of disease-associated mutations indicated the functional importance of the interdomain interactions. A structural comparison of Enpp1 with Enpp2, a lysophospholipase D, revealed marked differences in the domain arrangements and active-site architectures. Notably, the Enpp1 mutant lacking the insertion loop lost the nucleotide-hydrolyzing activity but instead gained the lysophospholipid-hydrolyzing activity of Enpp2. Our findings provide structural insights into how the Enpp family proteins evolved to exert their diverse cellular functions.


    Organizational Affiliation

    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I
A, B
823Mus musculusMutation(s): 1 
Gene Names: Enpp1 (Npps, Pc1, Pdnp1), Enpp2 (Npps2, Pdnp2)
EC: 3.1.4.39
Find proteins for P06802 (Mus musculus)
Go to UniProtKB:  P06802
Find proteins for Q9R1E6 (Mus musculus)
Go to UniProtKB:  Q9R1E6
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
TMP
Query on TMP

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A, B
THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N
 Ligand Interaction
NAG
Query on NAG

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A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.201 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.218 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 105.723α = 90.00
b = 105.723β = 90.00
c = 174.442γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
BSSdata collection
SCALEPACKdata scaling
PHENIXrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2017-08-23
    Type: Source and taxonomy
  • Version 1.2: 2017-11-15
    Type: Refinement description
  • Version 1.3: 2018-06-20
    Type: Data collection, Source and taxonomy