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- PDB-8ja7: Cryo-EM structure of Mycobacterium tuberculosis LpqY-SugABC in co... -

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Basic information

Entry
Database: PDB / ID: 8ja7
TitleCryo-EM structure of Mycobacterium tuberculosis LpqY-SugABC in complex with trehalose
Components
  • Trehalose import ATP-binding protein SugC
  • Trehalose transport system permease protein SugA
  • Trehalose transport system permease protein SugB
  • Trehalose-binding lipoprotein LpqY
KeywordsMEMBRANE PROTEIN / ABC transporter
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex, transmembrane substrate-binding subunit-containing / ABC-type carbohydrate transporter activity / Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate / trehalose transmembrane transporter activity / trehalose transport / biological process involved in interaction with host / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport ...ATP-binding cassette (ABC) transporter complex, transmembrane substrate-binding subunit-containing / ABC-type carbohydrate transporter activity / Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate / trehalose transmembrane transporter activity / trehalose transport / biological process involved in interaction with host / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space / ATP hydrolysis activity / protein homodimerization activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
MalK, OB fold domain / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / Bacterial extracellular solute-binding protein ...MalK, OB fold domain / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Trehalose transport system permease protein SugB / Trehalose transport system permease protein SugA / Trehalose-binding lipoprotein LpqY / Trehalose import ATP-binding protein SugC
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 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 transport system permease protein SugA
B: Trehalose transport system permease protein SugB
E: Trehalose-binding lipoprotein LpqY
C: Trehalose import ATP-binding protein SugC
D: Trehalose import ATP-binding protein SugC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,2616
Polymers197,9195
Non-polymers3421
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Trehalose transport system permease protein SugA


Mass: 33041.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: sugA
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WG03
#2: Protein Trehalose transport system permease protein SugB


Mass: 29145.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: sugB
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WG01
#3: 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
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WGU9
#4: Protein Trehalose import ATP-binding protein SugC / MtbSugC / Nucleotide-binding domain of SugABC transporter / NBD of SugABC transporter / SugABC ...MtbSugC / Nucleotide-binding domain of SugABC transporter / NBD of SugABC transporter / SugABC transporter ATPase SugC


Mass: 42964.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: sugC
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WQI3, Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate
#5: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: LpqY-SugABC / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Source (recombinant)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50775 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413887
ELECTRON MICROSCOPYf_angle_d0.57318947
ELECTRON MICROSCOPYf_dihedral_angle_d7.8868299
ELECTRON MICROSCOPYf_chiral_restr0.0432252
ELECTRON MICROSCOPYf_plane_restr0.0042437

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