8C7P

Tagless BtuM in complex with cyanocobalamin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.225 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Cobalamin decyanation by the membrane transporter BtuM.

Martinez Felices, J.M.Barreto, Y.B.Thangaratnarajah, C.Whittaker, J.J.Alencar, A.M.Guskov, A.Slotboom, D.J.

(2024) Structure 32: 1165-1173.e3

  • DOI: https://doi.org/10.1016/j.str.2024.04.014
  • Primary Citation of Related Structures:  
    8C7P

  • PubMed Abstract: 

    BtuM is a bacterial cobalamin transporter that binds the transported substrate in the base-off state, with a cysteine residue providing the α-axial coordination of the central cobalt ion via a sulfur-cobalt bond. Binding leads to decyanation of cobalamin variants with a cyano group as the β-axial ligand. Here, we report the crystal structures of untagged BtuM bound to two variants of cobalamin, hydroxycobalamin and cyanocobalamin, and unveil the native residue responsible for the β-axial coordination, His28. This coordination had previously been obscured by non-native histidines of His-tagged BtuM. A model in which BtuM initially binds cobinamide reversibly with low affinity (K D  = 4.0 μM), followed by the formation of a covalent bond (rate constant of 0.163 s -1 ), fits the kinetics data of substrate binding and decyanation of the cobalamin precursor cobinamide by BtuM. The covalent binding mode suggests a mechanism not used by any other transport protein.


  • Organizational Affiliation

    Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cobalamin ABC transporter199Thiobacillus denitrificans ATCC 25259Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3SFD8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B12 (Subject of Investigation/LOI)
Query on B12

Download Ideal Coordinates CCD File 
B [auth A]COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.225 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.318α = 90
b = 91.318β = 90
c = 77.391γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
Cootmodel building
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentNetherlands--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release
  • Version 1.1: 2024-08-21
    Changes: Database references