1Y3P

Structure of AlgQ1, alginate-binding protein, complexed with an alginate tetrasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Direct Evidence for Sphingomonas sp. A1 Periplasmic Proteins as Macromolecule-Binding Proteins Associated with the ABC Transporter: Molecular Insights into Alginate Transport in the Periplasm(,)

Momma, K.Mishima, Y.Hashimoto, W.Mikami, B.Murata, K.

(2005) Biochemistry 44: 5053-5064

  • DOI: 10.1021/bi047781r
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A Gram-negative bacterium, Sphingomonas sp. A1, has a macromolecule (alginate) import system consisting of a pit on the cell surface and an alginate-specific ATP-binding cassette importer in the inner membrane. Transport of alginate from the pit to t ...

    A Gram-negative bacterium, Sphingomonas sp. A1, has a macromolecule (alginate) import system consisting of a pit on the cell surface and an alginate-specific ATP-binding cassette importer in the inner membrane. Transport of alginate from the pit to the ABC importer is probably mediated by two periplasmic binding protein homologues (AlgQ1 and AlgQ2). Here we describe characteristics of binding of AlgQ1 and AlgQ2 to alginate and its oligosaccharides through surface plasmon resonance biosensor analysis, UV absorption difference spectroscopy, and X-ray crystallography. Both AlgQ1 and AlgQ2 were inducibly expressed in the periplasm of alginate-grown cells of strain A1. Biosensor analysis indicated that both proteins specifically bind alginate with a high degree of polymerization (>100) and that dissociation constants for alginate with an average molecular mass of 26 kDa are 2.3 x 10(-)(7) M for AlgQ1 and 1.5 x 10(-)(7) M for AlgQ2. An in vitro ATPase assay using the membrane complex, including the alginate ABC importer, suggested that both alginate-bound forms of AlgQ1 and AlgQ2 are closely associated with the importer. X-ray crystallography showed that AlgQ1 consisted of two domains separated by a deep cleft that binds alginate oligosaccharides through a conformational change in the two domains. These results directly show that alginate-binding proteins play an important role in the efficient transport of alginate macromolecules with different degrees of polymerization in the periplasm.


    Organizational Affiliation

    Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AlgQ1
A
490Sphingomonas spMutation(s): 0 
Gene Names: algQ1
Find proteins for Q9KWT6 (Sphingomonas sp)
Go to UniProtKB:  Q9KWT6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
LGU
Query on LGU

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Download CCD File 
A
ALPHA-L-GULURONATE
alpha-L-gulopyranuronic acid
C6 H10 O7
AEMOLEFTQBMNLQ-AZLKCVHYSA-N
 Ligand Interaction
MAV
Query on MAV

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Download CCD File 
A
alpha-D-mannopyranuronic acid
C6 H10 O7
AEMOLEFTQBMNLQ-BYHBOUFCSA-N
 Ligand Interaction
BEM
Query on BEM

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Download CCD File 
A
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: 2 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.830α = 90.00
b = 67.431β = 95.90
c = 62.957γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance