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- PDB-7uxr: Crystal structure of the BtTir TIR domain -

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Basic information

Entry
Database: PDB / ID: 7uxr
TitleCrystal structure of the BtTir TIR domain
ComponentsTIR domain protein
KeywordsHYDROLASE / cADPR isomer / NAD+ / bacterial TIR
Function / homologyTIR domain / Toll - interleukin 1 - resistance / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / hydrolase activity / signal transduction / 2' cyclic ADP-D-ribose synthase BtTIR
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsShi, Y. / Masic, V. / Mosaiab, T. / Vasquez, E. / Ve, T.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Science / Year: 2022
Title: Cyclic ADP ribose isomers: Production, chemical structures, and immune signaling.
Authors: Mohammad K Manik / Yun Shi / Sulin Li / Mark A Zaydman / Neha Damaraju / Samuel Eastman / Thomas G Smith / Weixi Gu / Veronika Masic / Tamim Mosaiab / James S Weagley / Steven J Hancock / ...Authors: Mohammad K Manik / Yun Shi / Sulin Li / Mark A Zaydman / Neha Damaraju / Samuel Eastman / Thomas G Smith / Weixi Gu / Veronika Masic / Tamim Mosaiab / James S Weagley / Steven J Hancock / Eduardo Vasquez / Lauren Hartley-Tassell / Nestoras Kargios / Natsumi Maruta / Bryan Y J Lim / Hayden Burdett / Michael J Landsberg / Mark A Schembri / Ivan Prokes / Lijiang Song / Murray Grant / Aaron DiAntonio / Jeffrey D Nanson / Ming Guo / Jeffrey Milbrandt / Thomas Ve / Bostjan Kobe /
Abstract: Cyclic adenosine diphosphate (ADP)-ribose (cADPR) isomers are signaling molecules produced by bacterial and plant Toll/interleukin-1 receptor (TIR) domains via nicotinamide adenine dinucleotide ...Cyclic adenosine diphosphate (ADP)-ribose (cADPR) isomers are signaling molecules produced by bacterial and plant Toll/interleukin-1 receptor (TIR) domains via nicotinamide adenine dinucleotide (oxidized form) (NAD) hydrolysis. We show that v-cADPR (2'cADPR) and v2-cADPR (3'cADPR) isomers are cyclized by O-glycosidic bond formation between the ribose moieties in ADPR. Structures of 2'cADPR-producing TIR domains reveal conformational changes that lead to an active assembly that resembles those of Toll-like receptor adaptor TIR domains. Mutagenesis reveals a conserved tryptophan that is essential for cyclization. We show that 3'cADPR is an activator of ThsA effector proteins from the bacterial antiphage defense system termed Thoeris and a suppressor of plant immunity when produced by the effector HopAM1. Collectively, our results reveal the molecular basis of cADPR isomer production and establish 3'cADPR in bacteria as an antiviral and plant immunity-suppressing signaling molecule.
History
DepositionMay 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 12, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TIR domain protein
B: TIR domain protein


Theoretical massNumber of molelcules
Total (without water)39,7922
Polymers39,7922
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-5 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.690, 43.127, 98.757
Angle α, β, γ (deg.)90.000, 90.040, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein TIR domain protein / TIR domain-containing protein


Mass: 19896.170 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: Btheta7330_00630, DW011_11495, DWY18_13615, GAN93_22170, SAMN02910322_04521
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0FGV9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES, pH 7.0, 0.2 M magnesium chloride, 16-22% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.42→43.13 Å / Num. obs: 59368 / % possible obs: 98.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 17.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Rrim(I) all: 0.072 / Net I/σ(I): 11.2
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.171 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2685 / CC1/2: 0.649 / Rpim(I) all: 0.478 / Rrim(I) all: 1.267 / % possible all: 88.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7UXU

7uxu


Resolution: 1.42→39.52 Å / SU ML: 0.181 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.9243
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2085 2011 3.39 %
Rwork0.189 57315 -
obs0.1897 59326 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.1 Å2
Refinement stepCycle: LAST / Resolution: 1.42→39.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 0 165 2451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00882393
X-RAY DIFFRACTIONf_angle_d1.05233250
X-RAY DIFFRACTIONf_chiral_restr0.0825349
X-RAY DIFFRACTIONf_plane_restr0.0079421
X-RAY DIFFRACTIONf_dihedral_angle_d12.7858871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.450.29131380.2973817X-RAY DIFFRACTION91.47
1.45-1.490.28841410.27244031X-RAY DIFFRACTION97.07
1.49-1.540.29581370.25434010X-RAY DIFFRACTION97.46
1.54-1.590.24091450.23254104X-RAY DIFFRACTION97.97
1.59-1.640.23431400.23244070X-RAY DIFFRACTION98.27
1.64-1.710.26541440.23084057X-RAY DIFFRACTION98.18
1.71-1.790.23931430.22454095X-RAY DIFFRACTION98.49
1.79-1.880.21231450.21214096X-RAY DIFFRACTION98.51
1.88-20.21381410.18634102X-RAY DIFFRACTION99.21
2-2.150.19171430.18794145X-RAY DIFFRACTION99.12
2.15-2.370.21881500.18344145X-RAY DIFFRACTION99.54
2.37-2.710.20011450.18244179X-RAY DIFFRACTION99.52
2.71-3.420.18451440.17664194X-RAY DIFFRACTION99.79
3.42-39.520.19261550.16164270X-RAY DIFFRACTION99.24

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