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- PDB-7uwg: The crystal structure of the TIR domain-containing protein from A... -

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Basic information

Entry
Database: PDB / ID: 7uwg
TitleThe crystal structure of the TIR domain-containing protein from Acinetobacter baumannii (AbTir)
ComponentsMolecular chaperone Tir
KeywordsHYDROLASE / 2' cADPR / NADase / Bacterial TIR
Function / homologyNAD catabolic process / TIR domain / NAD+ nucleosidase activity / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / signal transduction / Molecular chaperone Tir
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsManik, M.K. / Nanson, J.D. / Ve, T. / Kobe, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
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 3, 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

Downloads & links

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Assembly

Deposited unit
A: Molecular chaperone Tir
B: Molecular chaperone Tir
C: Molecular chaperone Tir
D: Molecular chaperone Tir
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,22110
Polymers62,4584
Non-polymers7636
Water4,270237
1
A: Molecular chaperone Tir
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7112
Polymers15,6151
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Molecular chaperone Tir
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0894
Polymers15,6151
Non-polymers4743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Molecular chaperone Tir
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7112
Polymers15,6151
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Molecular chaperone Tir
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7112
Polymers15,6151
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.683, 67.770, 72.167
Angle α, β, γ (deg.)90.000, 110.460, 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
Molecular chaperone Tir / TIR domain-containing protein


Mass: 15614.538 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: APD31_10100, H0529_09530 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0Q1J3X1
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C12H26O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 38.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 0.2 M LiSO4, and 25% PEG 3350

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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: Feb 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.16→47.86 Å / Num. obs: 25989 / % possible obs: 97.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 25.33 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.1 / Rrim(I) all: 0.14 / Net I/σ(I): 7.6
Reflection shellResolution: 2.16→2.24 Å / Rmerge(I) obs: 0.66 / Num. unique obs: 2180 / CC1/2: 0.77 / Rpim(I) all: 0.52

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lqc

4lqc


Resolution: 2.16→47.86 Å / SU ML: 0.2665 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.1275
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2295 2006 7.73 %
Rwork0.1906 23961 -
obs0.1937 25967 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.35 Å2
Refinement stepCycle: LAST / Resolution: 2.16→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4372 0 44 237 4653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274494
X-RAY DIFFRACTIONf_angle_d0.62486093
X-RAY DIFFRACTIONf_chiral_restr0.0441692
X-RAY DIFFRACTIONf_plane_restr0.0026770
X-RAY DIFFRACTIONf_dihedral_angle_d11.49911642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.220.28751310.24011630X-RAY DIFFRACTION94.52
2.22-2.280.30611480.23581683X-RAY DIFFRACTION95.66
2.28-2.340.31221350.22471693X-RAY DIFFRACTION97.49
2.34-2.420.27461430.22471703X-RAY DIFFRACTION97.62
2.42-2.50.29031400.2251710X-RAY DIFFRACTION97.73
2.5-2.60.26351490.21471712X-RAY DIFFRACTION97.74
2.6-2.720.25481360.21571688X-RAY DIFFRACTION97.38
2.72-2.870.26971490.20831702X-RAY DIFFRACTION98.35
2.87-3.050.25491370.19871735X-RAY DIFFRACTION98.37
3.05-3.280.23851430.21733X-RAY DIFFRACTION98.37
3.28-3.610.18851510.17581716X-RAY DIFFRACTION98.11
3.61-4.130.19011440.15591723X-RAY DIFFRACTION97.95
4.13-5.210.16371480.14881751X-RAY DIFFRACTION98.8
5.21-47.860.22631520.18751782X-RAY DIFFRACTION98.82

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