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 
  • R-Value Observed: 0.197 

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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: https://doi.org/10.1016/j.chembiol.2016.06.008
  • Primary Citation of Related Structures:  
    5EDL

  • 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 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 as 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative HMP/thiamine permease protein YkoE197Bacillus subtilisMutation(s): 0 
Gene Names: ykoEBSU13230
Membrane Entity: Yes 
UniProt
Find proteins for O34738 (Bacillus subtilis (strain 168))
Explore O34738 
Go to UniProtKB:  O34738
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34738
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPG
Query on MPG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
C21 H40 O4
JPJYKWFFJCWMPK-GDCKJWNLSA-N
VIB
Query on VIB

Download Ideal Coordinates CCD File 
B [auth A]3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM
C12 H17 N4 O S
JZRWCGZRTZMZEH-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
VIB Binding MOAD:  5EDL Kd: 4.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.713α = 90
b = 70.713β = 90
c = 196.839γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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