RCSB PDB - 8YSJ: Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with UMPNPP

 8YSJ

Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with UMPNPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.171 

Starting Model: experimental
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Literature

Structural insights into signaling promiscuity of the CBASS anti-phage defense system from a radiation-resistant bacterium.

Yang, C.S.Shie, M.Y.Huang, S.W.Wang, Y.C.Hou, M.H.Chen, C.J.Chen, Y.

(2025) Int J Biol Macromol 295: 139534-139534

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.139534
  • Primary Citation of Related Structures:  
    8YSC, 8YSD, 8YSE, 8YSG, 8YSI, 8YSJ, 8YSK, 8YSL, 8YSM, 8YSN, 8YSO, 8YSQ, 8YSR, 8YSS, 8YSU

  • PubMed Abstract: 

    Radiation-resistant bacteria are of great application potential in various fields, including bioindustry and bioremediation of radioactive waste. However, how radiation-resistant bacteria combat against invading phages is seldom addressed. Here, we present a series of crystal structures of a sensor and an effector of the cyclic oligonucleotide-based anti-phage signaling system (CBASS) from a radioresistant bacterium Deinococcus wulumuqiensis. We found that the sensor CD-NTase enzyme, DwCdnB, can bind all four ribonucleotides and synthesize a variety of cyclic di-nucleotides, including the novel second messenger 3'3'-cyclic di-CMP. Crystal structures of DwCdnB in complex with ATP and dATP provide structural explanations for specific recognition of ribonucleotides via metal coordination with ribose 2'-OH. Crystal structures of DwCdnB in complex with purine and/or pyrimidine nucleotides in the presence of Mg 2+ revealed similar binding modes; however, in the presence of Mn 2+ , the UTP/CTP rotates and flips into the donor pocket and make extensive contacts with additional five residues, suggesting essential role of Mn 2+ for catalytic production of cyclic di-pyrimidines. Finally, structural analysis of the downstream effector DwCap5 further provides a structural explanation for its non-specific recognition of a broad range of cyclic di-nucleotides. In sum, this work provides key structural insights into the immune mechanisms of radioresistant bacteria.


  • Organizational Affiliation

    Department of Food Science and Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleotidyltransferase348Deinococcus wulumuqiensisMutation(s): 0 
Gene Names: DVJ83_15700
UniProt
Find proteins for A0A345ILN6 (Deinococcus wulumuqiensis)
Explore A0A345ILN6 
Go to UniProtKB:  A0A345ILN6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A345ILN6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.171 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.346α = 74.396
b = 46.244β = 73.126
c = 61.058γ = 84.271
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 2KHClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan111-2311-B-039-001-MY3

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release