4XIG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.402 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • PubMed Abstract: 
  • The Gram-negative bacterium <i>Sphingomonas </i> 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-bindin ...

    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

    the Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan.,From the Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, and.,the Japan Synchrotron Radiation Research Institute (JASRI), Sayo-gun, Hyogo 679-5198, Japan.,the Laboratory of Food Microbiology, Department of Life Science, Faculty of Science and Engineering, Setsunan University, Neyagawa, Osaka 572-8508, Japan, and.,From the Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, and whasimot@kais.kyoto-u.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AlgM1
M
301Sphingomonas spMutation(s): 0 
Gene Names: algM1
Find proteins for Q9KWT8 (Sphingomonas sp)
Go to UniProtKB:  Q9KWT8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
AlgM2
N
305Sphingomonas spMutation(s): 0 
Gene Names: algM2
Find proteins for Q9KWT7 (Sphingomonas sp)
Go to UniProtKB:  Q9KWT7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
AlgS
S, T
363Sphingomonas spMutation(s): 1 
Gene Names: algS
Find proteins for Q9KWT9 (Sphingomonas sp)
Go to UniProtKB:  Q9KWT9
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
AlgQ2
Q
516Sphingomonas spMutation(s): 0 
Gene Names: algQ2
Find proteins for Q9KWT5 (Sphingomonas sp)
Go to UniProtKB:  Q9KWT5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAW
Query on MAW

Download SDF File 
Download CCD File 
Q
4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid
C6 H8 O6
IAKKJSVSFCTLRY-NVFHJIOMSA-N
 Ligand Interaction
BEM
Query on BEM

Download SDF File 
Download CCD File 
Q
beta-D-mannuronic acid
(2S,3S,4S,5S,6R)-3,4,5,6-tetrahydroxyoxane-2-carboxylic acid
C6 H10 O7
AEMOLEFTQBMNLQ-SYJWYVCOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.402 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.175α = 90.00
b = 133.412β = 90.00
c = 272.687γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2017-08-09
    Type: Data collection, Database references, Derived calculations
  • Version 1.2: 2020-01-01
    Type: Database references