6WG5

Human ectonucleoside triphosphate diphosphohydrolase 4 (ENTPD4, NTPDase 4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the nucleotide-metabolizing enzyme NTPDase4.

Gorelik, A.Labriola, J.M.Illes, K.Nagar, B.

(2020) Protein Sci 29: 2054-2061

  • DOI: 10.1002/pro.3926
  • Primary Citation of Related Structures:  
    6WG5

  • PubMed Abstract: 
  • The ecto-nucleoside triphosphate diphosphohydrolases (NTPDases) are a family of enzymes found on the cell surface and in the lumen of certain organelles, that are major regulators of purinergic signaling. Their intracellular roles, however, have not been clearly defined ...

    The ecto-nucleoside triphosphate diphosphohydrolases (NTPDases) are a family of enzymes found on the cell surface and in the lumen of certain organelles, that are major regulators of purinergic signaling. Their intracellular roles, however, have not been clearly defined. NTPDase4 (UDPase, ENTPD4) is a Golgi protein potentially involved in nucleotide recycling as part of protein glycosylation, and is also found in lysosomes, where its purpose is unknown. To further our understanding of NTPDase4 function, we determined its crystal structure. The enzyme adopts a wide open, inactive conformation. Differences in the nucleotide-binding site relative to its homologs could account for its substrate selectivity. The putative membrane-interacting loop of cell-surface NTPDases is drastically altered in NTPDase4, potentially affecting its interdomain dynamics at the Golgi membrane.


    Organizational Affiliation

    Department of Biochemistry, McGill University, Montreal, Quebec, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ectonucleoside triphosphate diphosphohydrolase 4 A512Homo sapiensMutation(s): 0 
Gene Names: ENTPD4KIAA0392LALP70LYSAL1
EC: 3.6.1.6
Find proteins for Q9Y227 (Homo sapiens)
Explore Q9Y227 
Go to UniProtKB:  Q9Y227
NIH Common Fund Data Resources
PHAROS:  Q9Y227
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.378α = 90
b = 101.82β = 90
c = 129.644γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references
  • Version 1.2: 2020-10-07
    Changes: Database references