4RFS

Structure of a pantothenate energy coupling factor transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of a pantothenate transporter and implications for ECF module sharing and energy coupling of group II ECF transporters.

Zhang, M.Bao, Z.Zhao, Q.Guo, H.Xu, K.Wang, C.Zhang, P.

(2014) Proc Natl Acad Sci U S A 111: 18560-18565

  • DOI: 10.1073/pnas.1412246112
  • Primary Citation of Related Structures:  
    4RFS

  • PubMed Abstract: 
  • Energy-coupling factor (ECF) transporters are a unique group of ATP-binding cassette (ABC) transporters responsible for micronutrient uptake from the environment. Each ECF transporter is composed of an S component (or EcfS protein) and T/A/A' compone ...

    Energy-coupling factor (ECF) transporters are a unique group of ATP-binding cassette (ABC) transporters responsible for micronutrient uptake from the environment. Each ECF transporter is composed of an S component (or EcfS protein) and T/A/A' components (or EcfT/A/A' proteins; ECF module). Among the group II ECF transporters, several EcfS proteins share one ECF module; however, the underlying mechanism remains unknown. Here we report the structure of a group II ECF transporter-pantothenate transporter from Lactobacillus brevis (LbECF-PanT), which shares the ECF module with the folate and hydroxymethylpyrimidine transporters (LbECF-FolT and LbECF-HmpT). Structural and mutational analyses revealed the residues constituting the pantothenate-binding pocket. We found that although the three EcfS proteins PanT, FolT, and HmpT are dissimilar in sequence, they share a common surface area composed of the transmembrane helices 1/2/6 (SM1/2/6) to interact with the coupling helices 2/3 (CH2/3) of the same EcfT. CH2 interacts mainly with SM1 via hydrophobic interactions, which may modulate the sliding movement of EcfS. CH3 binds to a hydrophobic surface groove formed by SM1, SM2, and SM6, which may transmit the conformational changes from EcfA/A' to EcfS. We also found that the residues at the intermolecular surfaces in LbECF-PanT are essential for transporter activity, and that these residues may mediate intermolecular conformational transmission and/or affect transporter complex stability. In addition, we found that the structure of EcfT is conformationally dynamic, which supports its function as a scaffold to mediate the interaction of the ECF module with various EcfS proteins to form different transporter complexes.


    Organizational Affiliation

    National Key Laboratory of Plant Molecular Genetics and CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, and pengzhang01@sibs.ac.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Energy-coupling factor transporter ATP-binding protein EcfA2A290Lactobacillus brevisMutation(s): 0 
Gene Names: ecfA2
EC: 3.6.3
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Energy-Coupling Factor (ECF) Transporters
Protein: 
ECF-PanT energy-coupling factor pantothenate transporter
Find proteins for Q03PY6 (Lactobacillus brevis (strain ATCC 367 / JCM 1170))
Explore Q03PY6 
Go to UniProtKB:  Q03PY6
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Energy-coupling factor transporter ATP-binding protein EcfA1B279Lactobacillus brevisMutation(s): 0 
Gene Names: ecfA1
EC: 3.6.3 (PDB Primary Data), 7 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Energy-Coupling Factor (ECF) Transporters
Protein: 
ECF-PanT energy-coupling factor pantothenate transporter
Find proteins for Q03PY5 (Lactobacillus brevis (strain ATCC 367 / JCM 1170))
Explore Q03PY5 
Go to UniProtKB:  Q03PY5
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Substrate binding pritein SS203Lactobacillus brevisMutation(s): 0 
Gene Names: LVIS_0658
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Energy-Coupling Factor (ECF) Transporters
Protein: 
ECF-PanT energy-coupling factor pantothenate transporter
Find proteins for Q03SM0 (Lactobacillus brevis (strain ATCC 367 / JCM 1170))
Explore Q03SM0 
Go to UniProtKB:  Q03SM0
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Energy-coupling factor transporter transmembrane protein EcfTT280Lactobacillus brevisMutation(s): 0 
Gene Names: ecfT
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Energy-Coupling Factor (ECF) Transporters
Protein: 
ECF-PanT energy-coupling factor pantothenate transporter
Find proteins for Q03PY7 (Lactobacillus brevis (strain ATCC 367 / JCM 1170))
Explore Q03PY7 
Go to UniProtKB:  Q03PY7
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.726α = 90
b = 145.24β = 90
c = 157.141γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2015-01-28
    Changes: Database references