7D4J

ddATP complex of cyclic trinucleotide synthase CdnD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal structure and functional implication of a bacterial cyclic AMP-AMP-GMP synthetase.

Ko, T.P.Wang, Y.C.Tsai, C.L.Yang, C.S.Hou, M.H.Chen, Y.

(2021) Nucleic Acids Res 49: 4725-4737

  • DOI: https://doi.org/10.1093/nar/gkab165
  • Primary Citation of Related Structures:  
    7D48, 7D4J, 7D4O, 7D4S, 7D4U

  • PubMed Abstract: 

    Mammalian cyclic GMP-AMP synthase (cGAS) and its homologue dinucleotide cyclase in Vibrio cholerae (VcDncV) produce cyclic dinucleotides (CDNs) that participate in the defense against viral infection. Recently, scores of new cGAS/DncV-like nucleotidyltransferases (CD-NTases) were discovered, which produce various CDNs and cyclic trinucleotides (CTNs) as second messengers. Here, we present the crystal structures of EcCdnD, a CD-NTase from Enterobacter cloacae that produces cyclic AMP-AMP-GMP, in its apo-form and in complex with ATP, ADP and AMPcPP, an ATP analogue. Despite the similar overall architecture, the protein shows significant structural variations from other CD-NTases. Adjacent to the donor substrate, another nucleotide is bound to the acceptor binding site by a non-productive mode. Isothermal titration calorimetry results also suggest the presence of two ATP binding sites. GTP alone does not bind to EcCdnD, which however binds to pppApG, a possible intermediate. The enzyme is active on ATP or a mixture of ATP and GTP, and the best metal cofactor is Mg2+. The conserved residues Asp69 and Asp71 are essential for catalysis, as indicated by the loss of activity in the mutants. Based on structural analysis and comparison with VcDncV and RNA polymerase, a tentative catalytic pathway for the CTN-producing EcCdnD is proposed.


  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic AMP-AMP-GMP synthase389Enterobacter cloacaeMutation(s): 0 
Gene Names: cdnD02P853_02262
EC: 2.7.7
UniProt
Find proteins for P0DSP4 (Enterobacter hormaechei subsp. hoffmannii (strain UCI 50))
Explore P0DSP4 
Go to UniProtKB:  P0DSP4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DSP4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.173α = 90
b = 53.173β = 90
c = 345.758γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
HKL-2000data processing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia Sinica (Taiwan)Taiwan--

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2021-04-21
    Changes: Database references
  • Version 1.2: 2021-05-19
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references, Refinement description