5EDL

Crystal structure of an S-component of ECF transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structure of a Group I Energy Coupling Factor Vitamin Transporter S Component in Complex with Its Cognate Substrate.

Josts, I.Almeida Hernandez, Y.Andreeva, A.Tidow, H.

(2016) Cell Chem Biol 23: 827-836

  • DOI: 10.1016/j.chembiol.2016.06.008

  • PubMed Abstract: 
  • Energy coupling factor (ECF) transporters are responsible for the uptake of essential scarce nutrients in prokaryotes. This ATP-binding cassette transporter family comprises two subgroups that share a common architecture forming a tripartite membrane ...

    Energy coupling factor (ECF) transporters are responsible for the uptake of essential scarce nutrients in prokaryotes. This ATP-binding cassette transporter family comprises two subgroups that share a common architecture forming a tripartite membrane protein complex consisting of a translocation component and ATP hydrolyzing module and a substrate-capture (S) component. Here, we present the crystal structure of YkoE from Bacillus subtilis, the S component of the previously uncharacterized group I ECF transporter YkoEDC. Structural and biochemical analyses revealed the constituent residues of the thiamine-binding pocket as well asĀ an unexpected mode of vitamin recognition. In addition, our experimental and bioinformatics data demonstrate major differences between YkoE and group II ECF transporters and indicate how group I vitamin transporter S components have diverged from other group I and group II ECF transporters.


    Organizational Affiliation

    The Hamburg Centre for Ultrafast Imaging (CUI), Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany; Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany.,MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.,The Hamburg Centre for Ultrafast Imaging (CUI), Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany; Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany. Electronic address: tidow@chemie.uni-hamburg.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative HMP/thiamine permease protein YkoE
A
197Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: ykoE
Find proteins for O34738 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34738
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VIB
Query on VIB

Download SDF File 
Download CCD File 
A
3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM
THIAMIN; VITAMIN B1
C12 H17 N4 O S
JZRWCGZRTZMZEH-UHFFFAOYSA-N
 Ligand Interaction
MPG
Query on MPG

Download SDF File 
Download CCD File 
A
[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
C21 H40 O4
JPJYKWFFJCWMPK-GDCKJWNLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VIBKd: 4.5 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.195 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 70.713α = 90.00
b = 70.713β = 90.00
c = 196.839γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
SHELXDEphasing
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-10-21 
  • Released Date: 2016-08-17 
  • Deposition Author(s): Josts, I., Tidow, H.

Revision History 

  • Version 1.0: 2016-08-17
    Type: Initial release