5VEM | pdb_00005vem

Human ectonucleotide pyrophosphatase / phosphodiesterase 5 (ENPP5, NPP5)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.227 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5VEM

Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

A key tyrosine substitution restricts nucleotide hydrolysis by the ectoenzyme NPP5.

Gorelik, A.Randriamihaja, A.Illes, K.Nagar, B.

(2017) FEBS J 284: 3718-3726

  • DOI: https://doi.org/10.1111/febs.14266
  • Primary Citation Related Structures: 
    5VEM, 5VEN, 5VEO

  • PubMed Abstract: 

    The ecto-nucleotide pyrophosphatase/phosphodiesterase (NPP) family of proteins mediates purinergic signaling by degrading extracellular nucleotides and also participates in phospholipid metabolism. NPP5 (ENPP5) is the least characterized member of this group and its specific role is unknown. This enzyme does not display activity on certain nucleotides and on other typical NPP substrates. In order to gain insights into its function, we determined the crystal structure of human and murine NPP5. Structural comparison with close homologs revealed a key phenylalanine to tyrosine substitution that prevents efficient hydrolysis of nucleotide diphosphates and triphosphates; reversal of this mutation enabled degradation of these molecules. Interestingly, NPP5 is able to cleave nicotinamide adenine dinucleotide (NAD), suggesting a potential role of this enzyme in NAD-based neurotransmission. An NPP5-specific metal binding motif is found adjacent to the active site, although its significance is unclear. These findings expand our understanding of substrate specificity within the NPP family. Structural data are available in the Protein Data Bank under the accession numbers 5VEM, 5VEN, and 5VEO.


  • Organizational Affiliation
    • Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Canada.

Macromolecule Content 

  • Total Structure Weight: 149 kDa 
  • Atom Count: 9,771 
  • Modeled Residue Count: 1,140 
  • Deposited Residue Count: 1,248 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ectonucleotide pyrophosphatase/phosphodiesterase family member 5
A, B, C
416Homo sapiensMutation(s): 0 
Gene Names: ENPP5UNQ550/PRO1107
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJA9 (Homo sapiens)
Explore Q9UJA9 
Go to UniProtKB:  Q9UJA9
PHAROS:  Q9UJA9
GTEx:  ENSG00000112796 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UJA9
Glycosylation
Glycosylation Sites: 3Go to GlyGen: Q9UJA9-1
Sequence Annotations
Expand
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
D, F, G, H
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G86851RC
GlyCosmos: G86851RC
GlyGen: G86851RC

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
L [auth A]
M [auth A]
N [auth A]
R [auth B]
S [auth B]
L [auth A],
M [auth A],
N [auth A],
R [auth B],
S [auth B],
T [auth B],
X [auth C],
Y [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
O [auth B]
P [auth B]
I [auth A],
J [auth A],
K [auth A],
O [auth B],
P [auth B],
Q [auth B],
U [auth C],
V [auth C],
W [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.227 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.411α = 90
b = 109.411β = 90
c = 134.82γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP-133535

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.2: 2017-11-22
    Changes: Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence, Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary