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: 3.20 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 2.0 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:  
    4TQU, 4TQV

  • 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-binding cassette transporter AlgM1M2SS is responsible for the import of alginate across the cytoplasmic membrane ...

    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. Electronic address: k-murata@lif.setsunan.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AlgM1A [auth M]301Sphingomonas sp.Mutation(s): 0 
Gene Names: algM1
Membrane Entity: Yes 
UniProt
Find proteins for Q9KWT8 (Sphingomonas sp)
Explore Q9KWT8 
Go to UniProtKB:  Q9KWT8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
AlgM2B [auth N]305Sphingomonas sp.Mutation(s): 0 
Gene Names: algM2
Membrane Entity: Yes 
UniProt
Find proteins for Q9KWT7 (Sphingomonas sp)
Explore Q9KWT7 
Go to UniProtKB:  Q9KWT7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
AlgSC [auth S], E [auth T]363Sphingomonas sp.Mutation(s): 1 
Gene Names: algS
UniProt
Find proteins for Q9KWT9 (Sphingomonas sp)
Explore Q9KWT9 
Go to UniProtKB:  Q9KWT9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
AlgQ2D [auth Q]516Sphingomonas sp.Mutation(s): 0 
Gene Names: algQ2
Membrane Entity: Yes 
UniProt
Find proteins for Q9KWT5 (Sphingomonas sp)
Explore Q9KWT5 
Go to UniProtKB:  Q9KWT5
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D 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 Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G76472TU
GlyCosmos:  G76472TU
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth Q]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.367α = 90
b = 134.177β = 90
c = 273.798γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report




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  (Full details and data files)

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-08-19
    Changes: Database references
  • Version 1.2: 2015-09-16
    Changes: Database references
  • Version 1.3: 2020-01-29
    Changes: Data collection, Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary