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 

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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' components (or EcfT/A/A' proteins; ECF module) ...

    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 EcfA2A290Levilactobacillus 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))
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Go to UniProtKB:  Q03PY6
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03PY6
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Energy-coupling factor transporter ATP-binding protein EcfA1B279Levilactobacillus 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))
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Go to UniProtKB:  Q03PY5
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UniProt GroupQ03PY5
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Entity ID: 3
MoleculeChainsSequence 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))
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Entity ID: 4
MoleculeChainsSequence 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))
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Go to UniProtKB:  Q03PY7
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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