4TY0

Crystal structure of Vibrio cholerae DncV cyclic AMP-GMP synthase in complex with linear intermediate 5' pppA(3',5')pG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structure-Guided Reprogramming of Human cGAS Dinucleotide Linkage Specificity.

Kranzusch, P.J.Lee, A.S.Wilson, S.C.Solovykh, M.S.Vance, R.E.Berger, J.M.Doudna, J.A.

(2014) Cell 158: 1011-1021

  • DOI: https://doi.org/10.1016/j.cell.2014.07.028
  • Primary Citation of Related Structures:  
    4TXY, 4TXZ, 4TY0

  • PubMed Abstract: 

    Cyclic dinucleotides (CDNs) play central roles in bacterial pathogenesis and innate immunity. The mammalian enzyme cGAS synthesizes a unique cyclic dinucleotide (cGAMP) containing a 2'-5' phosphodiester linkage essential for optimal immune stimulation, but the molecular basis for linkage specificity is unknown. Here, we show that the Vibrio cholerae pathogenicity factor DncV is a prokaryotic cGAS-like enzyme whose activity provides a mechanistic rationale for the unique ability of cGAS to produce 2'-5' cGAMP. Three high-resolution crystal structures show that DncV and human cGAS generate CDNs in sequential reactions that proceed in opposing directions. We explain 2' and 3' linkage specificity and test this model by reprogramming the human cGAS active site to produce 3'-5' cGAMP, leading to selective stimulation of alternative STING adaptor alleles in cells. These results demonstrate mechanistic homology between bacterial signaling and mammalian innate immunity and explain how active site configuration controls linkage chemistry for pathway-specific signaling.


  • Organizational Affiliation

    Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute (HHMI), University of California, Berkeley, Berkeley, CA 94720, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic AMP-GMP synthase
A, B
413Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: dncVVC_0179
EC: 2.7.7.86
UniProt
Find proteins for Q9KVG7 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KVG7 
Go to UniProtKB:  Q9KVG7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KVG7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
38V
Query on 38V

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3-[[(2R,3S,4R,5R)-5-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxolan-2-yl]methoxy-[[oxidanyl(phosphonooxy)phosphoryl]methyl]phosphinic acid
C21 H30 N10 O19 P4
QFHKDAVOJDVDDK-XPWFQUROSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
I [auth B],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.329α = 90
b = 59.596β = 96.47
c = 102.163γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
G. Harold and Leila Y. Mathers FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-09-03
    Changes: Database references
  • Version 1.2: 2014-10-01
    Changes: Database references
  • Version 1.3: 2015-02-04
    Changes: Derived calculations
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Refinement description