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- PDB-8jac: Crystal structure of Mycobacterium tuberculosis LpqY in complex w... -

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Basic information

Entry
Database: PDB / ID: 8jac
TitleCrystal structure of Mycobacterium tuberculosis LpqY in complex with trehalose analogue YB-16
ComponentsTrehalose-binding lipoprotein LpqY
KeywordsSUGAR BINDING PROTEIN
Function / homology
Function and homology information


trehalose transmembrane transporter activity / trehalose transport / biological process involved in interaction with host / ATP-binding cassette (ABC) transporter complex / periplasmic space / plasma membrane
Similarity search - Function
: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
alpha-D-glucopyranose / Chem-W4Z / Trehalose-binding lipoprotein LpqY
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, B. / Liang, J. / Rao, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171217 China
National Natural Science Foundation of China (NSFC)32200983 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
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
DepositionMay 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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: Trehalose-binding lipoprotein LpqY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5897
Polymers49,8031
Non-polymers7866
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-18 kcal/mol
Surface area17150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.748, 62.864, 143.906
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Trehalose-binding lipoprotein LpqY / SugABC transporter substrate-binding protein LpqY / SugABC transporter SBP LpqY


Mass: 49803.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: lpqY, Rv1235
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P9WGU9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-W4Z / N-[[(2R,3S,4S,5R,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl]ethanamide


Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Nonpolymer detailsYB-16 is 6-deoxy-6-acetamino-alpha,alpha-trehalose. It consists of W4Z and GLC.

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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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 31351 / % possible obs: 99.8 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.151 / Net I/σ(I): 13.79
Reflection shellResolution: 2.09→2.15 Å / Num. unique obs: 3067 / CC1/2: 0.813

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Processing

Software
NameVersionClassification
PHENIX1.16_3549: ???refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.34 Å / Cross valid method: THROUGHOUT
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.24 --
Rwork0.203 --
obs-31351 99.8 %
Displacement parametersBiso mean: 40.71 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 46 130 3454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00363399
X-RAY DIFFRACTIONf_angle_d0.61044658
X-RAY DIFFRACTIONf_chiral_restr0.0435535
X-RAY DIFFRACTIONf_plane_restr0.0062612
X-RAY DIFFRACTIONf_dihedral_angle_d15.722009

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