4DVE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1073/pnas.1203219109
  • Primary Citation of Related Structures:  
    4DVE

  • 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) ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Biotin transporter BioYA, B, C198Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: bioYllmg_1964
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Energy-Coupling Factor (ECF) Transporters
Protein: 
BioY, S component of the Biotin Transporter
Find proteins for A2RMJ9 (Lactococcus lactis subsp. cremoris (strain MG1363))
Explore A2RMJ9 
Go to UniProtKB:  A2RMJ9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BTNKd :  0.30000001192092896   nM  PDBBind
BTNKd:  0.30000001192092896   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
SHARPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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