5D3M

Folate ECF transporter: AMPPNP bound state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural insight in the toppling mechanism of an energy-coupling factor transporter.

Swier, L.J.Guskov, A.Slotboom, D.J.

(2016) Nat Commun 7: 11072-11072

  • DOI: https://doi.org/10.1038/ncomms11072
  • Primary Citation of Related Structures:  
    5D0Y, 5D3M, 5JSZ

  • PubMed Abstract: 

    Energy-coupling factor (ECF) transporters mediate uptake of micronutrients in prokaryotes. The transporters consist of an S-component that binds the transported substrate and an ECF module (EcfAA'T) that binds and hydrolyses ATP. The mechanism of transport is poorly understood but presumably involves an unusual step in which the membrane-embedded S-component topples over to carry the substrate across the membrane. In many ECF transporters, the S-component dissociates from the ECF module after transport. Subsequently, substrate-bound S-components out-compete the empty proteins for re-binding to the ECF module in a new round of transport. Here we present crystal structures of the folate-specific transporter ECF-FolT from Lactobacillus delbrueckii. Interaction of the ECF module with FolT stabilizes the toppled state, and simultaneously destroys the high-affinity folate-binding site, allowing substrate release into the cytosol. We hypothesize that differences in the kinetics of toppling can explain how substrate-loaded FolT out-competes apo-FolT for association with the ECF module.


  • Organizational Affiliation

    Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Energy-coupling factor transporter ATP-binding protein EcfA1
A, E
298Lactobacillus delbrueckiiMutation(s): 0 
Gene Names: ecfA1cbiO1Ldb0424
EC: 3.6.3
Membrane Entity: Yes 
UniProt
Find proteins for Q1GBJ0 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14))
Explore Q1GBJ0 
Go to UniProtKB:  Q1GBJ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1GBJ0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Energy-coupling factor transporter ATP-binding protein EcfA2
B, F
287Lactobacillus delbrueckiiMutation(s): 0 
Gene Names: ecfA2cbiO2Ldb0425
EC: 3.6.3
Membrane Entity: Yes 
UniProt
Find proteins for Q1GBI9 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14))
Explore Q1GBI9 
Go to UniProtKB:  Q1GBI9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1GBI9
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
S-component for folate
C, G
184Lactobacillus delbrueckiiMutation(s): 0 
Gene Names: Ldb1625
Membrane Entity: Yes 
UniProt
Find proteins for Q1G929 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14))
Explore Q1G929 
Go to UniProtKB:  Q1G929
Entity Groups  
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UniProt GroupQ1G929
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Energy-coupling factor transporter transmembrane protein EcfT
D, H
265Lactobacillus delbrueckiiMutation(s): 0 
Gene Names: cbiQecfTLBVIB27_01965LBVIB44_01960SB57_06620
Membrane Entity: Yes 
UniProt
Find proteins for Q1GBI8 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14))
Explore Q1GBI8 
Go to UniProtKB:  Q1GBI8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1GBI8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.07α = 84.67
b = 97.26β = 64.78
c = 105.45γ = 62.59
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council282083

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-04-13
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Author supporting evidence, Data collection, Database references, Refinement description