6FNP | pdb_00006fnp

Crystal structure of ECF-CbrT, a cobalamin transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.293 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 
    0.246 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6FNP

This is version 1.1 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: https://doi.org/10.7554/eLife.35828
  • Primary Citation 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. 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
    • Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 231.01 kDa 
  • Atom Count: 15,083 
  • Modeled Residue Count: 1,933 
  • Deposited Residue Count: 2,068 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Membrane protein
A, E
182Lactobacillus delbrueckiiMutation(s): 0 
Gene Names: AT236_00087CFL1_01875LBUL87_0070SB57_03475
Membrane Entity: Yes 
UniProt
Find proteins for Q1G7W0 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14))
Explore Q1G7W0 
Go to UniProtKB:  Q1G7W0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1G7W0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Energy-coupling factor transporter ATP-binding protein EcfA1
B, F
300Lactobacillus delbrueckiiMutation(s): 0 
Gene Names: ecfA1cbiO1Ldb0424
EC: 3.6.3 (PDB Primary Data), 7 (UniProt)
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
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Energy-coupling factor transporter ATP-binding protein EcfA2
C, G
287Lactobacillus delbrueckiiMutation(s): 0 
Gene Names: ecfA2cbiO2Ldb0425
EC: 3.6.3 (PDB Primary Data), 7 (UniProt)
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
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Energy-coupling factor transporter transmembrane protein EcfT
D, H
265Lactobacillus delbrueckiiMutation(s): 0 
Gene Names: ecfTAT236_00396CFL1_00754SB57_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: 3.40 Å
  • R-Value Free:  0.293 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 0.246 (Depositor) 
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

View Full Validation Report



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
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description