Crystal structure at 2.1 A of the S-component for biotin from an ECF-type ABC transporter

Experimental Data Snapshot

  • Resolution: 2.09 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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Structural divergence of paralogous S components from ECF-type ABC transporters.

Berntsson, R.P.Ter Beek, J.Majsnerowska, M.Duurkens, R.H.Puri, P.Poolman, B.Slotboom, D.J.

(2012) Proc Natl Acad Sci U S A 109: 13990-13995

  • DOI: https://doi.org/10.1073/pnas.1203219109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Energy coupling factor (ECF) proteins are ATP-binding cassette transporters involved in the import of micronutrients in prokaryotes. They consist of two nucleotide-binding subunits and the integral membrane subunit EcfT, which together form the ECF module and a second integral membrane subunit that captures the substrate (the S component). Different S components, unrelated in sequence and specific for different ligands, can interact with the same ECF module. Here, we present a high-resolution crystal structure at 2.1 Å of the biotin-specific S component BioY from Lactococcus lactis. BioY shares only 16% sequence identity with the thiamin-specific S component ThiT from the same organism, of which we recently solved a crystal structure. Consistent with the lack of sequence similarity, BioY and ThiT display large structural differences (rmsd = 5.1 Å), but the divergence is not equally distributed over the molecules: The S components contain a structurally conserved N-terminal domain that is involved in the interaction with the ECF module and a highly divergent C-terminal domain that binds the substrate. The domain structure explains how the S components with large overall structural differences can interact with the same ECF module while at the same time specifically bind very different substrates with subnanomolar affinity. Solitary BioY (in the absence of the ECF module) is monomeric in detergent solution and binds D-biotin with a high affinity but does not transport the substrate across the membrane.

  • Organizational Affiliation

    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Biotin transporter BioY
A, B, C
198Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
Gene Names: bioYllmg_1964
Membrane Entity: Yes 
Find proteins for A2RMJ9 (Lactococcus lactis subsp. cremoris (strain MG1363))
Explore A2RMJ9 
Go to UniProtKB:  A2RMJ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2RMJ9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BNG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
I [auth B]
J [auth B]
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
L [auth C]
nonyl beta-D-glucopyranoside
C15 H30 O6
Query on BTN

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
K [auth C]
C10 H16 N2 O3 S
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C
Binding Affinity Annotations 
IDSourceBinding Affinity
BTN PDBBind:  4DVE Kd: 0.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.09 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.825α = 90
b = 57.384β = 91.07
c = 166.865γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2012-10-17
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary