7LJN | pdb_00007ljn

Structure of the Bradyrhizobium diazoefficiens CD-NTase CdnG in complex with GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.218 (Depositor), 0.177 (DCC) 
  • R-Value Work: 
    0.197 (Depositor) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Molecular basis of CD-NTase nucleotide selection in CBASS anti-phage defense.

Govande, A.A.Duncan-Lowey, B.Eaglesham, J.B.Whiteley, A.T.Kranzusch, P.J.

(2021) Cell Rep 35: 109206-109206

  • DOI: https://doi.org/10.1016/j.celrep.2021.109206
  • Primary Citation Related Structures: 
    7LJL, 7LJM, 7LJN, 7LJO

  • PubMed Abstract: 

    cGAS/DncV-like nucleotidyltransferase (CD-NTase) enzymes are signaling proteins that initiate antiviral immunity in animal cells and cyclic-oligonucleotide-based anti-phage signaling system (CBASS) phage defense in bacteria. Upon phage recognition, bacterial CD-NTases catalyze synthesis of cyclic-oligonucleotide signals, which activate downstream effectors and execute cell death. How CD-NTases control nucleotide selection to specifically induce defense remains poorly defined. Here, we combine structural and nucleotide-analog interference-mapping approaches to identify molecular rules controlling CD-NTase specificity. Structures of the cyclic trinucleotide synthase Enterobacter cloacae CdnD reveal coordinating nucleotide interactions and a possible role for inverted nucleobase positioning during product synthesis. We demonstrate that correct nucleotide selection in the CD-NTase donor pocket results in the formation of a thermostable-protein-nucleotide complex, and we extend our analysis to establish specific patterns governing selectivity for each of the major bacterial CD-NTase clades A-H. Our results explain CD-NTase specificity and enable predictions of nucleotide second-messenger signals within diverse antiviral systems.


  • Organizational Affiliation
    • Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.

Macromolecule Content 

  • Total Structure Weight: 187.34 kDa 
  • Atom Count: 12,830 
  • Modeled Residue Count: 1,353 
  • Deposited Residue Count: 1,664 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CD-NTase
A, B, C, D
416Bradyrhizobium diazoefficiensMutation(s): 0 
Gene Names: blr0072
EC: 2.7.7.85
UniProt
Find proteins for Q89Y83 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110))
Explore Q89Y83 
Go to UniProtKB:  Q89Y83
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ89Y83
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
(Subject of Investigation/LOI)

Query on GTP



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C],
K [auth D]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.218 (Depositor), 0.177 (DCC) 
  • R-Value Work:  0.197 (Depositor) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.996α = 90
b = 68.687β = 108.405
c = 112.432γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references
  • Version 1.3: 2024-04-03
    Changes: Refinement description