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- PDB-8wct: The crystal structure of the CHASE4 domain of iron-sensetive memb... -

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Basic information

Entry
Database: PDB / ID: 8wct
TitleThe crystal structure of the CHASE4 domain of iron-sensetive membrane protein (IsmP,Uniprot ID:Q9I243)
ComponentsBifunctional diguanylate cyclase/phosphodiesterase
KeywordsMEMBRANE PROTEIN / CHEASE4 domain / iron-sensetive
Function / homology
Function and homology information


CHASE4 / CHASE4 domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. ...CHASE4 / CHASE4 domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Bifunctional diguanylate cyclase/phosphodiesterase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, C.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2024
Title: A c-di-GMP signaling module controls responses to iron in Pseudomonas aeruginosa.
Authors: Xueliang Zhan / Kuo Zhang / Chenchen Wang / Qiao Fan / Xiujia Tang / Xi Zhang / Ke Wang / Yang Fu / Haihua Liang /
Abstract: Cyclic dimeric guanosine monophosphate (c-di-GMP) serves as a bacterial second messenger that modulates various processes including biofilm formation, motility, and host-microbe symbiosis. Numerous ...Cyclic dimeric guanosine monophosphate (c-di-GMP) serves as a bacterial second messenger that modulates various processes including biofilm formation, motility, and host-microbe symbiosis. Numerous studies have conducted comprehensive analysis of c-di-GMP. However, the mechanisms by which certain environmental signals such as iron control intracellular c-di-GMP levels are unclear. Here, we show that iron regulates c-di-GMP levels in Pseudomonas aeruginosa by modulating the interaction between an iron-sensing protein, IsmP, and a diguanylate cyclase, ImcA. Binding of iron to the CHASE4 domain of IsmP inhibits the IsmP-ImcA interaction, which leads to increased c-di-GMP synthesis by ImcA, thus promoting biofilm formation and reducing bacterial motility. Structural characterization of the apo-CHASE4 domain and its binding to iron allows us to pinpoint residues defining its specificity. In addition, the cryo-electron microscopy structure of ImcA in complex with a c-di-GMP analog (GMPCPP) suggests a unique conformation in which the compound binds to the catalytic pockets and to the membrane-proximal side located at the cytoplasm. Thus, our results indicate that a CHASE4 domain directly senses iron and modulates the crosstalk between c-di-GMP metabolic enzymes.
History
DepositionSep 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional diguanylate cyclase/phosphodiesterase
B: Bifunctional diguanylate cyclase/phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3423
Polymers54,2502
Non-polymers921
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.431, 75.205, 104.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)

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Components

#1: Protein Bifunctional diguanylate cyclase/phosphodiesterase / Iron-sensetive membrane protein


Mass: 27125.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA2072 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I243
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate lithium, 20% PEG3350, 0.1 M Bis-Tris propane, pH 7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 40453 / % possible obs: 99.9 % / Redundancy: 11.4 % / Biso Wilson estimate: 23.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.125 / Net I/σ(I): 13.84
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.9-2.020.55464750.980.581
2.02-2.150.3960860.9870.4091
2.15-2.330.28356500.9920.2971
2.33-2.550.21452390.9950.2241
2.55-2.850.15547630.9970.1621
2.85-3.290.10942230.9980.1151
3.29-4.020.07836070.9980.0821
4.02-5.670.06428370.9980.0671
1.9-1.950.0616760.9980.0641

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Processing

Software
NameVersionClassification
PHENIXdev_4788model building
PHENIXdev_4788refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42.79 Å / SU ML: 0.2299 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.1576
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2634 1973 4.88 %
Rwork0.2252 38480 -
obs0.2271 40453 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.72 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 6 388 3670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663345
X-RAY DIFFRACTIONf_angle_d0.94294537
X-RAY DIFFRACTIONf_chiral_restr0.0544500
X-RAY DIFFRACTIONf_plane_restr0.0074598
X-RAY DIFFRACTIONf_dihedral_angle_d12.06591192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.37531480.28552695X-RAY DIFFRACTION99.13
1.95-20.29661290.25082707X-RAY DIFFRACTION99.72
2-2.060.27811380.23782701X-RAY DIFFRACTION99.68
2.06-2.130.25611270.23392712X-RAY DIFFRACTION99.89
2.13-2.20.3081510.22652718X-RAY DIFFRACTION99.62
2.2-2.290.29191310.2272714X-RAY DIFFRACTION99.68
2.29-2.390.26431100.22362770X-RAY DIFFRACTION99.62
2.39-2.520.2771320.23252736X-RAY DIFFRACTION99.69
2.52-2.680.25421500.23892745X-RAY DIFFRACTION99.79
2.68-2.880.2711190.22842747X-RAY DIFFRACTION99.79
2.88-3.170.30611550.2262750X-RAY DIFFRACTION99.93
3.18-3.630.20741540.21352764X-RAY DIFFRACTION99.83
3.63-4.580.25071590.20742798X-RAY DIFFRACTION99.66
4.58-42.790.25861700.22312923X-RAY DIFFRACTION99.68

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