9OUF | pdb_00009ouf

Crystal structure of an ADP-ribosyl hydrolase from Streptococcus parasanguinis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 
    0.197 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Antibacterial ADP-ribosyl cyclase toxins inhibit bacterial growth by rapidly depleting NAD(P).

Colautti, J.Kim, Y.Whitney, J.C.

(2025) J Biological Chem : 110491-110491

  • DOI: https://doi.org/10.1016/j.jbc.2025.110491
  • Primary Citation of Related Structures:  
    9OUF

  • PubMed Abstract: 

    In metazoans, enzymes belonging to the bifunctional ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase family regulate diverse cellular processes by synthesizing and hydrolyzing the intracellular second messenger cyclic ADP-ribose (cADPr), derived from the electron carrier nicotinamide adenine dinucleotide (NAD + ). However, bacterial enzymes belonging to this family have not been characterized. Here, we identify a bacterial ADP-ribosyl cyclase that is associated with the type VII secretion system and functions as an antibacterial toxin. This enzyme, which we name Tac1, inhibits bacterial growth by rapidly hydrolyzing NAD + and NADP + . We determine the X-ray crystal structure of Tac1 to a resolution of 1.4 Å, which reveals that this protein adopts the core catalytic fold of metazoan ADP-ribosyl cyclase enzymes. Using a combination of biochemical and mutagenesis approaches, we identify catalytic residues within the active site of Tac1 that are responsible for the formation of a cADPr catalytic intermediate and subsequent hydrolysis of this intermediate into linear ADP-ribose. A bioinformatic analysis reveals that Tac1 is the founding member of a widespread family of bacterial ADP-ribosyl cyclase enzymes, many of which are associated with interbacterial conflict systems. We also identify enzymes in this family that are not associated with biological conflict systems and demonstrate that they produce cADPr as their major product rather than linear ADP-ribose, suggesting that these enzymes serve a biological function distinct from interbacterial antagonism. Together, these findings demonstrate that ADP-ribosyl cyclase/cADPr hydrolase enzymes function as toxins in diverse bacterial conflict systems and suggest that cADPr may play a previously overlooked role in bacterial physiology.


  • Organizational Affiliation
    • Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease159Streptococcus parasanguinisMutation(s): 0 
Gene Names: SPLFYP13_01488
EC: 3.1
UniProt
Find proteins for A0AAJ1HBH3 (Streptococcus parasanguinis)
Explore A0AAJ1HBH3 
Go to UniProtKB:  A0AAJ1HBH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAJ1HBH3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free:  0.197 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.185α = 90
b = 59.151β = 90
c = 40.075γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
HKL-3000phasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaPJT-173486

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release