3RLB

Crystal structure at 2.0 A of the S-component for thiamin from an ECF-type ABC transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structural basis of modularity in ECF-type ABC transporters.

Erkens, G.B.Berntsson, R.P.Fulyani, F.Majsnerowska, M.Ter Beek, J.Poolman, B.Slotboom, D.J.

(2011) Nat Struct Mol Biol 18: 755-760

  • DOI: 10.1038/nsmb.2073
  • Primary Citation of Related Structures:  
    3RLB

  • PubMed Abstract: 
  • Energy coupling factor (ECF) transporters are used for the uptake of vitamins in Prokarya. They consist of an integral membrane protein that confers substrate specificity (the S-component) and an energizing module that is related to ATP-binding casse ...

    Energy coupling factor (ECF) transporters are used for the uptake of vitamins in Prokarya. They consist of an integral membrane protein that confers substrate specificity (the S-component) and an energizing module that is related to ATP-binding cassette (ABC) transporters. S-components for different substrates often do not share detectable sequence similarity but interact with the same energizing module. Here we present the crystal structure of the thiamine-specific S-component ThiT from Lactococcus lactis at 2.0 Å. Extensive protein-substrate interactions explain its high binding affinity for thiamine (K(d) ~10(-10) M). ThiT has a fold similar to that of the riboflavin-specific S-component RibU, with which it shares only 14% sequence identity. Two alanines in a conserved motif (AxxxA) located on the membrane-embedded surface of the S-components mediate the interaction with the energizing module. Based on these findings, we propose a general transport mechanism for ECF transporters.


    Organizational Affiliation

    University of Groningen, Groningen Biomolecular Science and Biotechnology Institute, Groningen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ThiTAB192Lactococcus lactis subsp. cremoris NZ9000Mutation(s): 0 
Gene Names: LLNZ_01755
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BNG
Query on BNG

Download CCD File 
A, B
nonyl beta-D-glucopyranoside
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
 Ligand Interaction
VIB
Query on VIB

Download CCD File 
A, B
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VIBKd :  0.12000000476837158   nM  PDBBind
VIBKd:  0.12000000476837158   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.654α = 90
b = 84.654β = 95.81
c = 127.301γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-07-20
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary