8YSS

Crystal structure of the apo form of Deinococcus wulumuqiensis CD-NTase DwCdnB

Summary for 8YSS

• Entry DOI: 10.2210/pdb8yss/pdb
• Descriptor: Nucleotidyltransferase (2 entities in total)
• Functional Keywords: cd-ntase, transferase
• Biological source: Deinococcus wulumuqiensis
• Total number of polymer chains: 1
• Total formula weight: 39499.29

Authors

Wang, Y.-C.,Yang, C.-S.,Hou, M.-H.,Chen, Y. (deposition date: 2024-03-23, release date: 2025-01-29)

Primary citation

Yang, C.S.,Shie, M.Y.,Huang, S.W.,Wang, Y.C.,Hou, M.H.,Chen, C.J.,Chen, Y.
Structural insights into signaling promiscuity of the CBASS anti-phage defense system from a radiation-resistant bacterium.
Int.J.Biol.Macromol., 295:139534-139534, 2025

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 revealed similar binding modes; however, in the presence of Mn, the UTP/CTP rotates and flips into the donor pocket and make extensive contacts with additional five residues, suggesting essential role of Mn 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.

PubMed: 39761885
DOI: 10.1016/j.ijbiomac.2025.139534

Experimental method

X-RAY DIFFRACTION (1.83 Å)