7MW8

Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

ENPP1's regulation of extracellular cGAMP is a ubiquitous mechanism of attenuating STING signaling.

Carozza, J.A.Cordova, A.F.Brown, J.A.AlSaif, Y.Bohnert, V.Cao, X.Mardjuki, R.E.Skariah, G.Fernandez, D.Li, L.

(2022) Proc Natl Acad Sci U S A 119: e2119189119-e2119189119

  • DOI: https://doi.org/10.1073/pnas.2119189119
  • Primary Citation of Related Structures:  
    7MW8, 7N1S

  • PubMed Abstract: 

    The metazoan innate immune second messenger 2′3′-cGAMP is present both inside and outside cells. However, only extracellular cGAMP can be negatively regulated by the extracellular hydrolase ENPP1. Here, we determine whether ENPP1’s regulation of extracellular cGAMP is a ubiquitous mechanism of attenuating stimulator of interferon genes (STING) signaling. We identified ENPP1H362A, a point mutation that cannot degrade the 2′-5′ linkage in cGAMP while maintaining otherwise normal function. The selectivity of this histidine is conserved down to bacterial nucleotide pyrophosphatase/phosphodiesterase (NPP), allowing structural analysis and suggesting an unexplored ancient history of 2′-5′ cyclic dinucleotides. Enpp1H362A mice demonstrated that extracellular cGAMP is not responsible for the devastating phenotype in ENPP1-null humans and mice but is responsible for antiviral immunity and systemic inflammation. Our data define extracellular cGAMP as a pivotal STING activator, identify an evolutionarily critical role for ENPP1 in regulating inflammation, and suggest a therapeutic strategy for viral and inflammatory conditions by manipulating ENPP1 activity.


  • Organizational Affiliation

    ChEM-H Institute, Stanford University, Stanford, CA 94301.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphodiesterase-nucleotide pyrophosphatase427Xanthomonas citriMutation(s): 1 
Gene Names: XAC3562_610174
UniProt
Find proteins for A0A0U5FM15 (Xanthomonas citri pv. citri)
Explore A0A0U5FM15 
Go to UniProtKB:  A0A0U5FM15
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U5FM15
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
pApG2synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
M [auth D]
N [auth D]
O [auth B]
P [auth B]
Q [auth C]
M [auth D],
N [auth D],
O [auth B],
P [auth B],
Q [auth C],
R [auth C],
S [auth A],
T [auth A],
U [auth E],
V [auth E],
W [auth F],
X [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.42α = 90
b = 66.719β = 116.25
c = 134.961γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States1209045-100-PAMNF

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description