8KA2 | pdb_00008ka2

Crystal structure of the RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) from Vibrio vulnificus

• PDB DOI: https://doi.org/10.2210/pdb8KA2/pdb

• Classification: TOXIN
• Organism(s): Vibrio vulnificus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-08-02 Released: 2024-07-10 
• Deposition Author(s): Lee, Y., Choi, S., Hwang, J., Kim, M.H.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.38 Å
• R-Value Free: 
  0.322 (Depositor), 0.317 (DCC) 
• R-Value Work: 
  0.286 (Depositor), 0.284 (DCC) 
• R-Value Observed: 
  0.288 (Depositor) 

Literature

Dissemination of pathogenic bacteria is reinforced by a MARTX toxin effector duet.

Choi, S., Lee, Y., Park, S., Jang, S.Y., Park, J., Oh, D.W., Kim, S.M., Kim, T.H., Lee, G.S., Cho, C., Kim, B.S., Lee, D., Kim, E.H., Cheong, H.K., Moon, J.H., Song, J.J., Hwang, J., Kim, M.H.

(2024) Nat Commun 15: 6218-6218

• PubMed: 39043696 
• DOI: https://doi.org/10.1038/s41467-024-50650-0
• Primary Citation Related Structures: 
  8K9Z, 8KA0, 8KA1, 8KA2


• PubMed Abstract: 
  

  Multiple bacterial genera take advantage of the multifunctional autoprocessing repeats-in-toxin (MARTX) toxin to invade host cells. Secretion of the MARTX toxin by Vibrio vulnificus, a deadly opportunistic pathogen that causes primary septicemia, the precursor of sepsis, is a major driver of infection; however, the molecular mechanism via which the toxin contributes to septicemia remains unclear. Here, we report the crystal and cryo-electron microscopy (EM) structures of a toxin effector duet comprising the domain of unknown function in the first position (DUF1)/Rho inactivation domain (RID) complexed with human targets. These structures reveal how the duet is used by bacteria as a potent weapon. The data show that DUF1 acts as a RID-dependent transforming NADase domain (RDTND) that disrupts NAD ⁺ homeostasis by hijacking calmodulin. The cryo-EM structure of the RDTND-RID duet complexed with calmodulin and Rac1, together with immunological analyses in vitro and in mice, provide mechanistic insight into how V. vulnificus uses the duet to suppress ROS generation by depleting NAD(P) ⁺ and modifying Rac1 in a mutually-reinforcing manner that ultimately paralyzes first line immune responses, promotes dissemination of invaders, and induces sepsis. These data may allow development of tools or strategies to combat MARTX toxin-related human diseases.

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Organizational Affiliation: 
• Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea.
Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.
Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Korea.
Core Research Facility & Analysis Center, KRIBB, Daejeon, 34141, Korea.
Graduate School of Medical Science and Engineering, KAIST, Daejeon, 34141, Korea.
Department of Biology Education, Chonnam National University, Gwangju, 61186, Korea.
College of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Korea.
College of Pharmacy, Chungbuk National University, Cheongju, Chungbuk, 28644, Korea.
Department of Food Science and Biotechnology, Ewha Womans University, Seoul, 03760, Korea.
Korea Basic Science Institute, Cheongju, Chungbuk, 28119, Korea.
Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea. [e-mail].
Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 95.27 kDa 
• Atom Count: 5,848 
• Modeled Residue Count: 729 
• Deposited Residue Count: 838 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RDTND-RID CBD	A, B	419	Vibrio vulnificus	Mutation(s): 0  Gene Names: CRN52_02910 EC: 3.4.22
UniProt
Find proteins for A0A2S3R7M0 (Vibrio vulnificus) Explore A0A2S3R7M0  Go to UniProtKB:  A0A2S3R7M0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.38 Å
• R-Value Free:  0.322 (Depositor), 0.317 (DCC) 
• R-Value Work:  0.286 (Depositor), 0.284 (DCC) 
• R-Value Observed: 0.288 (Depositor) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 207.726	α = 90
b = 207.726	β = 90
c = 54.647	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Lee, Y., Choi, S., Hwang, J., Kim, M.H.

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Funding Organization	Location	Grant Number
Other government		the Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program(KGM1382312)
Other government		the Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program(KGM2112335)

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release
  
• Version 1.1: 2024-08-07
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Structure summary