1J1N

Structure Analysis of AlgQ2, A Macromolecule(Alginate)-Binding Periplasmic Protein Of Sphingomonas Sp. A1., Complexed with an Alginate Tetrasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of AlgQ2, a macromolecule (alginate)-binding protein of Sphingomonas sp. A1, complexed with an alginate tetrasaccharide at 1.6-A resolution

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

(2003) J.BIOL.CHEM. 278: 6552-6559

  • DOI: 10.1074/jbc.M209932200

  • PubMed Abstract: 
  • Sphingomonas sp. A1 possesses a high molecular weight (HMW) alginate uptake system composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate ...

    Sphingomonas sp. A1 possesses a high molecular weight (HMW) alginate uptake system composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by the periplasmic HMW alginate-binding proteins AlgQ1 and AlgQ2. We determined the crystal structure of AlgQ2 complexed with an alginate tetrasaccharide using an alginate-free (apo) form as a search model and refined it at 1.6-A resolution. One tetrasaccharide was found between the N and C-terminal domains, which are connected by three extended hinge loops. The tetrasaccharide complex took on a closed domain form, in contrast to the open domain form of the apo form. The tetrasaccharide was bound in the cleft between the domains through van der Waals interactions and the formation of hydrogen bonds. Among the four sugar residues, the nonreducing end residue was located at the bottom of the cleft and exhibited the largest number of interactions with the surrounding amino acid residues, suggesting that AlgQ2 mainly recognizes and binds to the nonreducing part of a HMW alginate and delivers the polymer to the ABC transporter through conformational changes (open and closed forms) of the two domains.


    Related Citations: 
    • Crystal structure of AlgQ2, a macromolecule (alginate)-binding protein of Sphingomonas sp. A1 at 2.0A resolution
      Momma, K.,Mikami, B.,Mishima, Y.,Hashimoto, W.,Murata, K.
      (2002) J.Mol.Biol. 316: 1051


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AlgQ2
A, B
492Sphingomonas sp.Gene Names: algQ2
Find proteins for Q9KWT5 (Sphingomonas sp.)
Go to UniProtKB:  Q9KWT5
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

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

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

Download SDF File 
Download CCD File 
A, B
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: 1.6 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 95.630α = 90.00
b = 53.881β = 107.53
c = 114.924γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance