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 1.2 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: https://doi.org/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' 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Energy-coupling factor transporter ATP-binding protein EcfA2290Levilactobacillus brevisMutation(s): 0 
Gene Names: ecfA2
EC: 3.6.3
Membrane Entity: Yes 
UniProt
Find proteins for Q03PY6 (Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947))
Explore Q03PY6 
Go to UniProtKB:  Q03PY6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03PY6
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 EcfA1279Levilactobacillus brevisMutation(s): 0 
Gene Names: ecfA1
EC: 3.6.3 (PDB Primary Data), 7 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q03PY5 (Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947))
Explore Q03PY5 
Go to UniProtKB:  Q03PY5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03PY5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Substrate binding pritein SC [auth S]203Levilactobacillus brevisMutation(s): 0 
Gene Names: LVIS_0658
Membrane Entity: Yes 
UniProt
Find proteins for Q03SM0 (Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947))
Explore Q03SM0 
Go to UniProtKB:  Q03SM0
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UniProt GroupQ03SM0
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Energy-coupling factor transporter transmembrane protein EcfTD [auth T]280Levilactobacillus brevisMutation(s): 0 
Gene Names: ecfT
Membrane Entity: Yes 
UniProt
Find proteins for Q03PY7 (Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947))
Explore Q03PY7 
Go to UniProtKB:  Q03PY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03PY7
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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  (Full details and data files)

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2015-01-28
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references