4XIG

Crystal structure of bacterial alginate ABC transporter determined through humid air and glue-coating method


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

A solute-binding protein in the closed conformation induces ATP hydrolysis in a bacterial ATP-binding cassette transporter involved in the import of alginate.

Kaneko, A.Uenishi, K.Maruyama, Y.Mizuno, N.Baba, S.Kumasaka, T.Mikami, B.Murata, K.Hashimoto, W.

(2017) J Biol Chem 292: 15681-15690

  • DOI: https://doi.org/10.1074/jbc.M117.793992
  • Primary Citation of Related Structures:  
    4XIG, 4XTC, 5H6U, 5H71

  • PubMed Abstract: 

    The Gram-negative bacterium Sphingomonas sp. A1 incorporates alginate into cells via the cell-surface pit without prior depolymerization by extracellular enzymes. Alginate import across cytoplasmic membranes thereby depends on the ATP-binding cassette transporter AlgM1M2SS (a heterotetramer of AlgM1, AlgM2, and AlgS), which cooperates with the periplasmic solute-binding protein AlgQ1 or AlgQ2; however, several details of AlgM1M2SS-mediated alginate import are not well-understood. Herein, we analyzed ATPase and transport activities of AlgM1M2SS after reconstitution into liposomes with AlgQ2 and alginate oligosaccharide substrates having different polymerization degrees (PDs). Longer alginate oligosaccharides (PD ≥ 5) stimulated the ATPase activity of AlgM1M2SS but were inert as substrates of AlgM1M2SS-mediated transport, indicating that AlgM1M2SS-mediated ATP hydrolysis can be stimulated independently of substrate transport. Using X-ray crystallography in the presence of AlgQ2 and long alginate oligosaccharides (PD 6-8) and with the humid air and glue-coating method, we determined the crystal structure of AlgM1M2SS in complex with oligosaccharide-bound AlgQ2 at 3.6 Å resolution. The structure of the ATP-binding cassette transporter in complex with non-transport ligand-bound periplasmic solute-binding protein revealed that AlgM1M2SS and AlgQ2 adopt inward-facing and closed conformations, respectively. These in vitro assays and structural analyses indicated that interactions between AlgM1M2SS in the inward-facing conformation and periplasmic ligand-bound AlgQ2 in the closed conformation induce ATP hydrolysis by the ATP-binding protein AlgS. We conclude that substrate-bound AlgQ2 in the closed conformation initially interacts with AlgM1M2SS, the AlgM1M2SS-AlgQ2 complex then forms, and this formation is followed by ATP hydrolysis.


  • Organizational Affiliation

    From the Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, and.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AlgM1A [auth M]301Sphingomonas sp.Mutation(s): 0 
Gene Names: algM1
Membrane Entity: Yes 
UniProt
Find proteins for Q9KWT8 (Sphingomonas sp)
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Go to UniProtKB:  Q9KWT8
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UniProt GroupQ9KWT8
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AlgM2B [auth N]305Sphingomonas sp.Mutation(s): 0 
Gene Names: algM2
Membrane Entity: Yes 
UniProt
Find proteins for Q9KWT7 (Sphingomonas sp)
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Go to UniProtKB:  Q9KWT7
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UniProt GroupQ9KWT7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
AlgSC [auth S],
E [auth T]
363Sphingomonas sp. A1Mutation(s): 1 
Gene Names: algS
UniProt
Find proteins for Q9KWT9 (Sphingomonas sp)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
AlgQ2D [auth Q]516Sphingomonas sp. A1Mutation(s): 0 
Gene Names: algQ2
Membrane Entity: Yes 
UniProt
Find proteins for Q9KWT5 (Sphingomonas sp)
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Go to UniProtKB:  Q9KWT5
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UniProt GroupQ9KWT5
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Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acidF [auth A]4N/A
Glycosylation Resources
GlyTouCan:  G76472TU
GlyCosmos:  G76472TU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.175α = 90
b = 133.412β = 90
c = 272.687γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2017-08-09
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2020-01-01
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations, Structure summary