Crystal structure of lactococcal OpuAC in its open conformation

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

Starting Model: experimental
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Ligand binding and crystal structures of the substrate-binding domain of the ABC transporter OpuA.

Wolters, J.C.Berntsson, R.P.Gul, N.Karasawa, A.Thunnissen, A.M.Slotboom, D.J.Poolman, B.

(2010) PLoS One 5: e10361-e10361

  • DOI: https://doi.org/10.1371/journal.pone.0010361
  • Primary Citation of Related Structures:  
    3L6G, 3L6H

  • PubMed Abstract: 

    The ABC transporter OpuA from Lactococcus lactis transports glycine betaine upon activation by threshold values of ionic strength. In this study, the ligand binding characteristics of purified OpuA in a detergent-solubilized state and of its substrate-binding domain produced as soluble protein (OpuAC) was characterized. The binding of glycine betaine to purified OpuA and OpuAC (K(D) = 4-6 microM) did not show any salt dependence or cooperative effects, in contrast to the transport activity. OpuAC is highly specific for glycine betaine and the related proline betaine. Other compatible solutes like proline and carnitine bound with affinities that were 3 to 4 orders of magnitude lower. The low affinity substrates were not noticeably transported by membrane-reconstituted OpuA. OpuAC was crystallized in an open (1.9 A) and closed-liganded (2.3 A) conformation. The binding pocket is formed by three tryptophans (Trp-prism) coordinating the quaternary ammonium group of glycine betaine in the closed-liganded structure. Even though the binding site of OpuAC is identical to that of its B. subtilis homolog, the affinity for glycine betaine is 4-fold higher. Ionic strength did not affect substrate binding to OpuA, indicating that regulation of transport is not at the level of substrate binding, but rather at the level of translocation. The overlap between the crystal structures of OpuAC from L.lactis and B.subtilis, comprising the classical Trp-prism, show that the differences observed in the binding affinities originate from outside of the ligand binding site.

  • Organizational Affiliation

    Biochemistry Department, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre, University of Groningen, Groningen, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Betaine ABC transporter permease and substrate binding protein256Lactococcus lactisMutation(s): 0 
Gene Names: busABLL1451L724L72477
Find proteins for Q7DAU8 (Lactococcus lactis subsp. lactis (strain IL1403))
Explore Q7DAU8 
Go to UniProtKB:  Q7DAU8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7DAU8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on B3P

Download Ideal Coordinates CCD File 
C11 H26 N2 O6
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.131α = 90
b = 68.131β = 90
c = 109.143γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description