4R9U

Structure of vitamin B12 transporter BtuCD in a nucleotide-bound outward facing state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.785 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of AMP-PNP-bound BtuCD and mechanism of ATP-powered vitamin B12 transport by BtuCD-F.

Korkhov, V.M.Mireku, S.A.Veprintsev, D.B.Locher, K.P.

(2014) Nat.Struct.Mol.Biol. 21: 1097-1099

  • DOI: 10.1038/nsmb.2918

  • PubMed Abstract: 
  • The reaction mechanism of BtuCD-F-catalyzed vitamin B12 transport into Escherichia coli is currently unclear. Here we present the structure of the last missing state in the form of AMP-PNP-bound BtuCD, trapped by a disulfide cross-link. Our structura ...

    The reaction mechanism of BtuCD-F-catalyzed vitamin B12 transport into Escherichia coli is currently unclear. Here we present the structure of the last missing state in the form of AMP-PNP-bound BtuCD, trapped by a disulfide cross-link. Our structural and biochemical data allow a consistent mechanism to be formulated, thus rationalizing the roles of substrate, ATP and substrate-binding protein.


    Organizational Affiliation

    1] Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zurich, Zurich, Switzerland. [2] Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland.,Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zurich, Zurich, Switzerland.,Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin B12 import system permease protein BtuC
A, B
333Escherichia coli (strain K12)Mutation(s): 7 
Gene Names: btuC
Find proteins for P06609 (Escherichia coli (strain K12))
Go to UniProtKB:  P06609
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Vitamin B12 import ATP-binding protein BtuD
C, D
249Escherichia coli (strain K12)Mutation(s): 3 
Gene Names: btuD
EC: 7.6.2.8
Find proteins for P06611 (Escherichia coli (strain K12))
Go to UniProtKB:  P06611
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
C, D
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
LDA
Query on LDA

Download SDF File 
Download CCD File 
A, B
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.785 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 372.850α = 90.00
b = 113.210β = 94.92
c = 69.430γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
PHENIXmodel building
PHENIXrefinement
PHENIXphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2014-12-03
    Type: Database references
  • Version 1.2: 2014-12-17
    Type: Database references