6FFV

The crystal structure of BtuM cobalamin transporter

• PDB DOI:  https://doi.org/10.2210/pdb6FFV/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Thiobacillus denitrificans
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2018-01-09 Released: 2018-08-08 
• Deposition Author(s): Rempel, S., Colucci, E., de Gier, J.W., Guskov, A., Slotboom, D.J.
• Funding Organization(s): NWO, European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.236 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

Cysteine-mediated decyanation of vitamin B12 by the predicted membrane transporter BtuM.

Rempel, S., Colucci, E., de Gier, J.W., Guskov, A., Slotboom, D.J.

(2018) Nat Commun 9: 3038-3038

• PubMed: 30072686 
• DOI: https://doi.org/10.1038/s41467-018-05441-9
• Primary Citation of Related Structures:  
  6FFV


• PubMed Abstract: 
  

  Uptake of vitamin B12 is essential for many prokaryotes, but in most cases the membrane proteins involved are yet to be identified. We present the biochemical characterization and high-resolution crystal structure of BtuM, a predicted bacterial vitamin B12 uptake system. BtuM binds vitamin B12 in its base-off conformation, with a cysteine residue as axial ligand of the corrin cobalt ion. Spectroscopic analysis indicates that the unusual thiolate coordination allows for decyanation of vitamin B12. Chemical modification of the substrate is a property other characterized vitamin B12-transport proteins do not exhibit.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 27.05 kDa 
• Atom Count: 1,863 
• Modelled Residue Count: 194 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BtuM	A	207	Thiobacillus denitrificans	Mutation(s): 0  Gene Names: Tbd_2719 Membrane Entity: Yes
UniProt
Find proteins for Q3SFD8 (Thiobacillus denitrificans (strain ATCC 25259)) Explore Q3SFD8  Go to UniProtKB:  Q3SFD8

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B12	B [auth A]	COBALAMIN C62 H89 Co N13 O14 P LKVIQTCSMMVGFU-DWSMJLPVSA-N
BNG	H [auth A], I [auth A], J [auth A]	nonyl beta-D-glucopyranoside C15 H30 O6 QFAPUKLCALRPLH-UXXRCYHCSA-N
PG4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	R [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.236 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.54	α = 90
b = 87.54	β = 90
c = 97.91	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
SHELXDE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Rempel, S., Colucci, E., de Gier, J.W., Guskov, A., Slotboom, D.J.

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Funding Organization	Location	Grant Number
NWO	Netherlands	865.11.001
European Research Council	Belgium	282083

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2018-08-15
  Changes: Data collection, Database references
• Version 1.2: 2018-09-19
  Changes: Data collection
• Version 1.3: 2019-11-20
  Changes: Derived calculations
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary