Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.22 kDa 
• Atom Count: 3173 
• Residue Count: 373 
• Unique protein chains: 1

4XJ1

Crystal structure of Vibrio cholerae DncV apo form

• DOI: 10.2210/pdb4XJ1/pdb

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


• Deposited: 2015-01-08 Released: 2015-04-29 
• Deposition Author(s): Kato, K., Ishii, R., Ishitani, R., Nureki, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.204 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

Literature

Structural Basis for the Catalytic Mechanism of DncV, Bacterial Homolog of Cyclic GMP-AMP Synthase

Kato, K., Ishii, R., Hirano, S., Ishitani, R., Nureki, O.

(2015) Structure 23: 843-850

• PubMed: 25865248 
• DOI: 10.1016/j.str.2015.01.023
• Primary Citation of Related Structures:  
  4XJ6, 4XJ1, 4XJ3, 4XJ4, 4XJ5


• PubMed Abstract: 
  

Cyclic dinucleotides (CDNs) play key roles as second messengers and signaling molecules in bacteria and metazoans. The newly identified dinucleotide cyclase in Vibrio cholerae (DncV) produces three different CDNs containing two 3'-5' phosphodiester bonds, and its predominant product is cyclic GMP-AMP, whereas mammalian cyclic GMP-AMP synthase (cGAS) produces only cyclic GMP-AMP containing mixed 2'-5' phosphodiester bonds. We report the crystal structures of V. cholerae and Escherichia coli DncV in complex with various nucleotides in the pre-reaction states. The high-resolution structures revealed that DncV preferably recognizes ATP and GTP as acceptor and donor nucleotides, respectively, in the first nucleotidyl transfer reaction. Considering the recently reported intermediate structures, our pre-reaction state structures provide the precise mechanism of 3'-5' linked cyclic AMP-GMP production in bacteria. A comparison with cGAS in the pre-reaction states suggests that the orientation of the acceptor nucleotide primarily determines the distinct linkage specificities between DncV and cGAS.

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Organizational Affiliation: 

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic AMP-GMP synthase	A	389	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: dncV, VC_0179 EC: 2.7.7
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
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.204 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.998	α = 90
b = 50.742	β = 93.07
c = 73.072	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-01-08 
• Released Date: 2015-04-29 
Deposition Author(s): Kato, K., Ishii, R., Ishitani, R., Nureki, O.

Revision History 

• Version 1.0: 2015-04-29
  Type: Initial release
  
• Version 1.1: 2015-05-20
  Changes: Database references
• Version 1.2: 2020-02-05
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy