4TXY | pdb_00004txy

Crystal structure of Vibrio cholerae DncV cyclic AMP-GMP synthase, a prokaryotic cGAS homolog

• PDB DOI: https://doi.org/10.2210/pdb4TXY/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-07 Released: 2014-08-13 
• Deposition Author(s): Kranzusch, P.J., Lee, A.S.Y., Wilson, S.C., Solovykh, M.S., Vance, R.E., Berger, J.M., Doudna, J.A.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), G. Harold and Leila Y. Mathers Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.250 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

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

• PubMed: 25131990 
• DOI: https://doi.org/10.1016/j.cell.2014.07.028
• Primary Citation 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.

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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.
Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.
Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Department of Biophysics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address: [e-mail].
Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute (HHMI), University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 93.98 kDa 
• Atom Count: 5,912 
• Modeled Residue Count: 739 
• Deposited Residue Count: 826 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic AMP-GMP synthase	A, B	413	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: dncV, VC_0179 EC: 2.7.7.86 (PDB Primary Data), 2.7.7 (UniProt)
UniProt
Find proteins for Q9KVG7 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KVG7  Go to UniProtKB:  Q9KVG7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.250 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.167	α = 90
b = 59.116	β = 95.48
c = 102.539	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-08-13 
Deposition Author(s): Kranzusch, P.J., Lee, A.S.Y., Wilson, S.C., Solovykh, M.S., Vance, R.E., Berger, J.M., Doudna, J.A.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
G. Harold and Leila Y. Mathers Foundation	United States	--

Revision History  

• 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, Structure summary
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references, Refinement description