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- PDB-8ka2: Crystal structure of the RID-dependent transforming NADase domain... -

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Basic information

Entry
Database: PDB / ID: 8ka2
TitleCrystal structure of the RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) from Vibrio vulnificus
ComponentsRDTND-RID CBD
KeywordsTOXIN / MARTX toxin / RDTND-RID / NADase
Function / homology
Function and homology information


Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / host cell cytosol / acyltransferase activity / ligase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cysteine-type peptidase activity / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane ...Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / host cell cytosol / acyltransferase activity / ligase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cysteine-type peptidase activity / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis / extracellular region / metal ion binding / membrane
Similarity search - Function
: / C-terminal repeat from RTX toxins / : / : / Pasteurella multocida toxin, C2 domain / RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / CGT/MARTX, cysteine protease (CPD) domain ...: / C-terminal repeat from RTX toxins / : / : / Pasteurella multocida toxin, C2 domain / RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Serralysin-like metalloprotease, C-terminal / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Multifunctional-autoprocessing repeats-in-toxin
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.38 Å
AuthorsLee, Y. / Choi, S. / Hwang, J. / Kim, M.H.
Funding support2items
OrganizationGrant numberCountry
Other governmentthe Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program(KGM1382312)
Other governmentthe Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program(KGM2112335)
CitationJournal: Nat Commun / Year: 2024
Title: Dissemination of pathogenic bacteria is reinforced by a MARTX toxin effector duet.
Authors: Sanghyeon Choi / Youngjin Lee / Shinhye Park / Song Yee Jang / Jongbin Park / Do Won Oh / Su-Man Kim / Tae-Hwan Kim / Ga Seul Lee / Changyi Cho / Byoung Sik Kim / Donghan Lee / Eun-Hee Kim / ...Authors: Sanghyeon Choi / Youngjin Lee / Shinhye Park / Song Yee Jang / Jongbin Park / Do Won Oh / Su-Man Kim / Tae-Hwan Kim / Ga Seul Lee / Changyi Cho / Byoung Sik Kim / Donghan Lee / Eun-Hee Kim / Hae-Kap Cheong / Jeong Hee Moon / Ji-Joon Song / Jungwon Hwang / Myung Hee Kim /
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 ...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.
History
DepositionAug 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RDTND-RID CBD
B: RDTND-RID CBD


Theoretical massNumber of molelcules
Total (without water)95,2682
Polymers95,2682
Non-polymers00
Water00
1
A: RDTND-RID CBD


Theoretical massNumber of molelcules
Total (without water)47,6341
Polymers47,6341
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RDTND-RID CBD


Theoretical massNumber of molelcules
Total (without water)47,6341
Polymers47,6341
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)207.726, 207.726, 54.647
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein RDTND-RID CBD / MARTX


Mass: 47633.836 Da / Num. of mol.: 2 / Fragment: MARTX toxin DUF1-RIDcbd region
Source method: isolated from a genetically manipulated source
Details: NCBI accession ID: WP_015728045.1; Additional N-terminus residues (GAM) from expression vector
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: CRN52_02910 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2S3R7M0, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 22% (w/v) PEG 3350 and 4% (v/v) Tacsimate (pH 6.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.38→50 Å / Num. obs: 17817 / % possible obs: 99.6 % / Redundancy: 6.2 % / CC1/2: 0.996 / Net I/σ(I): 11.1
Reflection shellResolution: 3.38→3.44 Å / Num. unique obs: 721 / CC1/2: 0.568

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.38→40.42 Å / Cor.coef. Fo:Fc: 0.814 / Cor.coef. Fo:Fc free: 0.764 / Cross valid method: THROUGHOUT / ESU R Free: 0.735 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32212 830 5.2 %RANDOM
Rwork0.28599 ---
obs0.28789 15125 82.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.18 Å20 Å2
2--0.37 Å2-0 Å2
3----1.19 Å2
Refinement stepCycle: 1 / Resolution: 3.38→40.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5848 0 0 0 5848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135963
X-RAY DIFFRACTIONr_bond_other_d0.0350.0175412
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.6388067
X-RAY DIFFRACTIONr_angle_other_deg2.3281.58412555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9915722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60123.249357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.17115997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.5851539
X-RAY DIFFRACTIONr_chiral_restr0.0790.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026742
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021279
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6225.8082909
X-RAY DIFFRACTIONr_mcbond_other3.6165.8082908
X-RAY DIFFRACTIONr_mcangle_it6.2798.6983624
X-RAY DIFFRACTIONr_mcangle_other6.2798.6983625
X-RAY DIFFRACTIONr_scbond_it2.8685.9563054
X-RAY DIFFRACTIONr_scbond_other2.8685.9563055
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1028.8434444
X-RAY DIFFRACTIONr_long_range_B_refined10.79468.9937266
X-RAY DIFFRACTIONr_long_range_B_other10.79368.9997267
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.384→3.471 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 3 -
Rwork0.333 85 -
obs--6.32 %

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