4XTC

Crystal structure of bacterial alginate ABC transporter in complex with alginate pentasaccharide-bound periplasmic protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


This is version 2.0 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: 10.1074/jbc.M117.793992
  • Primary Citation of Related Structures:  
    4XTC, 5H6U, 5H71, 4XIG

  • 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 ...

    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 whasimot@kais.kyoto-u.ac.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AlgM1 M301Sphingomonas sp. A1Mutation(s): 0 
Gene Names: algM1
Find proteins for Q9KWT8 (Sphingomonas sp)
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Go to UniProtKB:  Q9KWT8
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
AlgM2 N305Sphingomonas sp. A1Mutation(s): 0 
Gene Names: algM2
Find proteins for Q9KWT7 (Sphingomonas sp)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
AlgS ST363Sphingomonas sp. A1Mutation(s): 1 
Gene Names: algS
Find proteins for Q9KWT9 (Sphingomonas sp)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
AlgQ2 Q516Sphingomonas sp. A1Mutation(s): 0 
Gene Names: algQ2
Find proteins for Q9KWT5 (Sphingomonas sp)
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Go to UniProtKB:  Q9KWT5
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid
A
5 N/A Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.608α = 90
b = 132.963β = 90
c = 272.973γ = 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: 2016-03-02
    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