8KA0

Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin and a nicotinamide adenine dinucleotide (NAD+)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41467-024-50650-0
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RDTND-RID CBD
A, C, E, G
416Vibrio vulnificusMutation(s): 1 
Gene Names: CRN52_02910
EC: 3.4.22
UniProt
Find proteins for A0A2S3R7M0 (Vibrio vulnificus)
Explore A0A2S3R7M0 
Go to UniProtKB:  A0A2S3R7M0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2S3R7M0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-2
B, D, F, H
151Homo sapiensMutation(s): 0 
Gene Names: CALM2CAM2CAMB
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP24 (Homo sapiens)
Explore P0DP24 
Go to UniProtKB:  P0DP24
PHAROS:  P0DP24
GTEx:  ENSG00000143933 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP24
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
I [auth A],
L [auth C],
Q [auth E],
V [auth G]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
M [auth C],
P [auth D],
R [auth F],
U [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
J [auth B]
K [auth B]
N [auth D]
O [auth D]
S [auth F]
J [auth B],
K [auth B],
N [auth D],
O [auth D],
S [auth F],
T [auth F],
W [auth H],
X [auth H]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.222α = 90
b = 48.931β = 95.7
c = 178.603γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentKorea, Republic Ofthe Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program (KGM1382312)
Other governmentKorea, Republic Ofthe Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program (KGM2112335)

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Database references