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- PDB-8zhs: Structure of Mbp-Bte1 fusion protein -

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Basic information

Entry
Database: PDB / ID: 8zhs
TitleStructure of Mbp-Bte1 fusion protein
Components
  • C-terminal Bte1
  • Maltose/maltodextrin-binding periplasmic protein,N-terminal Bte1
KeywordsANTITOXIN / antibacterial toxin
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Uncharacterized protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Bacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsXu, J.H. / Chen, Z. / Gao, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Host Microbe / Year: 2025
Title: A human gut bacterium antagonizes neighboring bacteria by altering their protein-folding ability.
Authors: Bentley Lim / Jinghua Xu / Igor H Wierzbicki / Carlos G Gonzalez / Zhe Chen / David J Gonzalez / Xiang Gao / Andrew L Goodman /
Abstract: Antagonistic interactions play a key role in determining microbial community dynamics. Here, we report that one of the most widespread contact-dependent effectors in human gut microbiomes, Bte1, ...Antagonistic interactions play a key role in determining microbial community dynamics. Here, we report that one of the most widespread contact-dependent effectors in human gut microbiomes, Bte1, directly targets the PpiD-YfgM periplasmic chaperone complex in related microbes. Structural, biochemical, and genetic characterization of this interaction reveals that Bte1 reverses the activity of the chaperone complex, promoting substrate aggregation and toxicity. Using Bacteroides, we show that Bte1 is active in the mammalian gut, conferring a fitness advantage to expressing strains. Recipient cells targeted by Bte1 exhibit sensitivity to membrane-compromising conditions, and human gut microbes can use this effector to exploit pathogen-induced inflammation in the gut. Further, Bte1 allelic variation in gut metagenomes provides evidence for an arms race between Bte1-encoding and immunity-encoding strains in humans. Together, these studies demonstrate that human gut microbes alter the protein-folding capacity of neighboring cells and suggest strategies for manipulating community dynamics.
History
DepositionMay 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,N-terminal Bte1
B: Maltose/maltodextrin-binding periplasmic protein,N-terminal Bte1
C: C-terminal Bte1
D: C-terminal Bte1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,82014
Polymers137,8994
Non-polymers92110
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16360 Å2
ΔGint-97 kcal/mol
Surface area50580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.175, 253.874, 56.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,N-terminal Bte1 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 55985.680 Da / Num. of mol.: 2 / Mutation: D108A/K109A/E198A/N199A/K265A
Source method: isolated from a genetically manipulated source
Details: Sequence reference of MBP for strain 'Acinetobacter baumannii' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id P0AEX9.
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Gene: malE, b4034, JW3994, BF9343_1937 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEX9, UniProt: Q5LDT7
#2: Protein C-terminal Bte1


Mass: 12963.899 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Gene: BF9343_1937 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5LDT7
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
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: 2.75 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 10% v/v 2-Propanol, 0.1 M BICINE pH 8.5 and 30% w/v PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.4→42.13 Å / Num. obs: 55319 / % possible obs: 93.21 % / Redundancy: 10.3 % / Biso Wilson estimate: 40.3 Å2 / CC1/2: 0.99 / Net I/σ(I): 1.56
Reflection shellResolution: 2.4→2.5 Å / Num. unique obs: 4190 / CC1/2: 0.53

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
Blu-Icedata collection
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→42.13 Å / SU ML: 0.2881 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.5905
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2378 2000 3.62 %
Rwork0.1876 53314 -
obs0.1895 55314 93.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.72 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9561 0 60 418 10039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00799845
X-RAY DIFFRACTIONf_angle_d1.173513336
X-RAY DIFFRACTIONf_chiral_restr0.06361450
X-RAY DIFFRACTIONf_plane_restr0.00841689
X-RAY DIFFRACTIONf_dihedral_angle_d12.31473593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.37531050.27252795X-RAY DIFFRACTION69.18
2.46-2.530.27621200.26733222X-RAY DIFFRACTION80.51
2.53-2.60.34111290.25113411X-RAY DIFFRACTION84.51
2.6-2.690.27781370.24793661X-RAY DIFFRACTION90.43
2.69-2.780.30761410.23723759X-RAY DIFFRACTION94.2
2.78-2.90.27411470.21883912X-RAY DIFFRACTION96.41
2.9-3.030.29271470.21453925X-RAY DIFFRACTION97.35
3.03-3.190.29461500.21334011X-RAY DIFFRACTION98.37
3.19-3.390.25511500.20233998X-RAY DIFFRACTION98.6
3.39-3.650.22841510.17924031X-RAY DIFFRACTION99.36
3.65-4.010.22931540.15984099X-RAY DIFFRACTION99.32
4.02-4.60.19341540.14934083X-RAY DIFFRACTION99.6
4.6-5.790.2031560.15874167X-RAY DIFFRACTION99.54
5.79-42.130.18991590.17494240X-RAY DIFFRACTION97.04

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