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- PDB-8ja8: Crystal structure of Mycobacterium tuberculosis LpqY with trehalo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ja8 | |||||||||
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Title | Crystal structure of Mycobacterium tuberculosis LpqY with trehalose bound in a closed liganded form | |||||||||
![]() | Trehalose-binding lipoprotein LpqY | |||||||||
![]() | SUGAR BINDING PROTEIN | |||||||||
Function / homology | ![]() trehalose transmembrane transporter activity / trehalose transport / biological process involved in interaction with host / ATP-binding cassette (ABC) transporter complex / ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhang, B. / Liang, J. / Rao, Z. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular recognition of trehalose and trehalose analogues by LpqY-SugABC. Authors: Jingxi Liang / Fengjiang Liu / Peng Xu / Wei Shangguan / Tianyu Hu / Shule Wang / Xiaolin Yang / Zhiqi Xiong / Xiuna Yang / Luke W Guddat / Biao Yu / Zihe Rao / Bing Zhang / ![]() ![]() Abstract: Trehalose plays a crucial role in the survival and virulence of the deadly human pathogen (). The type I ATP-binding cassette (ABC) transporter LpqY-SugABC is the sole pathway for trehalose to enter ...Trehalose plays a crucial role in the survival and virulence of the deadly human pathogen (). The type I ATP-binding cassette (ABC) transporter LpqY-SugABC is the sole pathway for trehalose to enter . The substrate-binding protein, LpqY, which forms a stable complex with the translocator SugABC, recognizes and captures trehalose and its analogues in the periplasmic space, but the precise molecular mechanism for this process is still not well understood. This study reports a 3.02-Å cryoelectron microscopy structure of trehalose-bound LpqY-SugABC in the pretranslocation state, a crystal structure of LpqY in a closed form with trehalose bound and five crystal structures of LpqY in complex with different trehalose analogues. These structures, accompanied by substrate-stimulated ATPase activity data, reveal how LpqY recognizes and binds trehalose and its analogues, and highlight the flexibility in the substrate binding pocket of LpqY. These data provide critical insights into the design of trehalose analogues that could serve as potential molecular probe tools or as anti-TB drugs. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 108.7 KB | Display | ![]() |
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PDB format | ![]() | 78 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8ja7C ![]() 8ja9C ![]() 8jaaC ![]() 8jabC ![]() 8jacC ![]() 8jadC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 49803.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: H37Rv / Gene: lpqY Production host: ![]() ![]() ![]() References: UniProt: P9WGU9 | ||||
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#2: Polysaccharide | alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose![]() | ||||
#3: Chemical | ChemComp-SO4 / ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.5 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 50 mM Magnesium sulfate hydrate, 50 mM HEPES sodium pH 7.0 and 1.6 M Lithium sulfate monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CS-PAD XPP / Detector: PIXEL / Date: Dec 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.5→50 Å / Num. obs: 70508 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.13 |
Reflection shell | Resolution: 1.5→1.54 Å / Num. unique obs: 6972 / CC1/2: 0.835 |
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Processing
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Refinement | Method to determine structure![]() ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 32.09 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→45.2 Å
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Refine LS restraints |
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