4TQU

Crystal structure of a bacterial ABC transporter involved in the import of the acidic polysaccharide alginate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.204 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a Bacterial ABC Transporter Involved in the Import of an Acidic Polysaccharide Alginate

Maruyama, Y.Itoh, T.Kaneko, A.Nishitani, Y.Mikami, B.Hashimoto, W.Murata, K.

(2015) Structure 23: 1643-1654

  • DOI: 10.1016/j.str.2015.06.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The acidic polysaccharide alginate represents a promising marine biomass for the microbial production of biofuels, although the molecular and structural characteristics of alginate transporters remain to be clarified. In Sphingomonas sp. A1, the ATP- ...

    The acidic polysaccharide alginate represents a promising marine biomass for the microbial production of biofuels, although the molecular and structural characteristics of alginate transporters remain to be clarified. In Sphingomonas sp. A1, the ATP-binding cassette transporter AlgM1M2SS is responsible for the import of alginate across the cytoplasmic membrane. Here, we present the substrate-transport characteristics and quaternary structure of AlgM1M2SS. The addition of poly- or oligoalginate enhanced the ATPase activity of reconstituted AlgM1M2SS coupled with one of the periplasmic solute-binding proteins, AlgQ1 or AlgQ2. External fluorescence-labeled oligoalginates were specifically imported into AlgM1M2SS-containing proteoliposomes in the presence of AlgQ2, ATP, and Mg(2+). The crystal structure of AlgQ2-bound AlgM1M2SS adopts an inward-facing conformation. The interaction between AlgQ2 and AlgM1M2SS induces the formation of an alginate-binding tunnel-like structure accessible to the solvent. The translocation route inside the transmembrane domains contains charged residues suitable for the import of acidic saccharides.


    Organizational Affiliation

    Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AlgM1
M
301Sphingomonas spMutation(s): 0 
Gene Names: algM1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
Alginate transporter AlgM1M2SS with bound periplasmic protein AlgQ2
Find proteins for Q9KWT8 (Sphingomonas sp)
Go to UniProtKB:  Q9KWT8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
AlgM2
N
305Sphingomonas spMutation(s): 0 
Gene Names: algM2
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
Alginate transporter AlgM1M2SS with bound periplasmic protein AlgQ2
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
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
Alginate transporter AlgM1M2SS with bound periplasmic protein AlgQ2
Find proteins for Q9KWT9 (Sphingomonas sp)
Go to UniProtKB:  Q9KWT9
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
AlgQ2
Q
516Sphingomonas spMutation(s): 0 
Gene Names: algQ2
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
Alginate transporter AlgM1M2SS with bound periplasmic protein AlgQ2
Find proteins for Q9KWT5 (Sphingomonas sp)
Go to UniProtKB:  Q9KWT5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
Q
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAW
Query on MAW

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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: 3.204 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.367α = 90.00
b = 134.177β = 90.00
c = 273.798γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grants-in-Aid for Scientific Research from Japan Society for the Promotion of ScienceJapan--
Targeted Proteins Research Program from Ministry of Education, Culture, Sports, Science, and TechnologyJapan--

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-08-19
    Type: Database references
  • Version 1.2: 2015-09-16
    Type: Database references