8JSJ

Crystal structure of an N-terminal cyclic nucleotide-binding domain of a PycTIR from Novosphingobium pentaromativorans

• PDB DOI: https://doi.org/10.2210/pdb8JSJ/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Novosphingobium pentaromativorans US6-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-06-20 Released: 2024-07-03 
• Deposition Author(s): Wang, Y.-C., Yang, C.-S., Hou, M.-H., Chen, Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 0.282 
• R-Value Work: 0.258 

Starting Model: in silico

Literature

Structural and functional characterization of cyclic pyrimidine-regulated anti-phage system.

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

(2024) Nat Commun 15: 5634-5634

• PubMed: 38965224 
• DOI: https://doi.org/10.1038/s41467-024-49861-2
• Primary Citation of Related Structures:  
  8JSF, 8JSJ, 8JSK, 8JSZ


• PubMed Abstract: 
  

  3',5'-cyclic uridine monophosphate (cUMP) and 3',5'-cyclic cytidine monophosphate (cCMP) have been established as bacterial second messengers in the phage defense system, named pyrimidine cyclase system for anti-phage resistance (Pycsar). This system consists of a pyrimidine cyclase and a cyclic pyrimidine receptor protein. However, the molecular mechanism underlying cyclic pyrimidine synthesis and recognition remains unclear. Herein, we determine the crystal structures of a uridylate cyclase and a cytidylate cyclase, revealing the conserved residues for cUMP and cCMP production, respectively. In addition, a distinct zinc-finger motif of the uridylate cyclase is identified to confer substantial resistance against phage infections. Furthermore, structural characterization of cUMP receptor protein PycTIR provides clear picture of specific cUMP recognition and identifies a conserved N-terminal extension that mediates PycTIR oligomerization and activation. Overall, our results contribute to the understanding of cyclic pyrimidine-mediated bacterial defense.

---

Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.02 kDa 
• Atom Count: 1,067 
• Modelled Residue Count: 134 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PycTIR	A	311	Novosphingobium pentaromativorans US6-1	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 0.282 
• R-Value Work: 0.258 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.115	α = 90
b = 87.115	β = 90
c = 93.349	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Wang, Y.-C., Yang, C.-S., Hou, M.-H., Chen, Y.

---

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	111-2311-B-039-001-MY3

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release
  
• Version 1.1: 2024-07-17
  Changes: Database references, Structure summary