6FNP

Crystal structure of ECF-CbrT, a cobalamin transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Functional and structural characterization of an ECF-type ABC transporter for vitamin B12.

Santos, J.A.Rempel, S.Mous, S.T.Pereira, C.T.Ter Beek, J.de Gier, J.W.Guskov, A.Slotboom, D.J.

(2018) Elife 7

  • DOI: 10.7554/eLife.35828
  • Primary Citation of Related Structures:  
    6FNP

  • PubMed Abstract: 
  • Vitamin B12 (cobalamin) is the most complex B-type vitamin and is synthetized exclusively in a limited number of prokaryotes. Its biologically active variants contain rare organometallic bonds, which are used by enzymes in a variety of central metabolic pathways such as L-methionine synthesis and ribonucleotide reduction ...

    Vitamin B12 (cobalamin) is the most complex B-type vitamin and is synthetized exclusively in a limited number of prokaryotes. Its biologically active variants contain rare organometallic bonds, which are used by enzymes in a variety of central metabolic pathways such as L-methionine synthesis and ribonucleotide reduction. Although its biosynthesis and role as co-factor are well understood, knowledge about uptake of cobalamin by prokaryotic auxotrophs is scarce. Here, we characterize a cobalamin-specific ECF-type ABC transporter from Lactobacillus delbrueckii , ECF-CbrT, and demonstrate that it mediates the specific, ATP-dependent uptake of cobalamin. We solved the crystal structure of ECF-CbrT in an apo conformation to 3.4 Å resolution. Comparison with the ECF transporter for folate (ECF-FolT2) from the same organism, reveals how the identical ECF module adjusts to interact with the different substrate binding proteins FolT2 and CbrT. ECF-CbrT is unrelated to the well-characterized B12 transporter BtuCDF, but their biochemical features indicate functional convergence.


    Organizational Affiliation

    Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Membrane protein AE182Lactobacillus delbrueckiiMutation(s): 0 
Gene Names: AT236_00087CFL1_01875LBUL87_0070SB57_03475
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
Group II energy-coupling factor (ECF) transporter for vitamin B12, apo inward-facing state
Find proteins for Q1G7W0 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778))
Explore Q1G7W0 
Go to UniProtKB:  Q1G7W0
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 EcfA1 BF300Lactobacillus delbrueckiiMutation(s): 0 
Gene Names: ecfA1cbiO1Ldb0424
EC: 3.6.3 (PDB Primary Data), 7 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
Group II energy-coupling factor (ECF) transporter for vitamin B12, apo inward-facing state
Find proteins for Q1GBJ0 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778))
Explore Q1GBJ0 
Go to UniProtKB:  Q1GBJ0
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Energy-coupling factor transporter ATP-binding protein EcfA2 CG287Lactobacillus delbrueckiiMutation(s): 0 
Gene Names: ecfA2cbiO2Ldb0425
EC: 3.6.3
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
Group II energy-coupling factor (ECF) transporter for vitamin B12, apo inward-facing state
Find proteins for Q1GBI9 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778))
Explore Q1GBI9 
Go to UniProtKB:  Q1GBI9
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Energy-coupling factor transporter transmembrane protein EcfT DH265Lactobacillus delbrueckiiMutation(s): 0 
Gene Names: ecfTAT236_00396CFL1_00754SB57_06620
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
Group II energy-coupling factor (ECF) transporter for vitamin B12, apo inward-facing state
Find proteins for Q1GBI8 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778))
Explore Q1GBI8 
Go to UniProtKB:  Q1GBI8
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.246 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.47α = 72.57
b = 92.86β = 66.27
c = 105.51γ = 62.89
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NWONetherlands865.11.001

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release