1N2Z | pdb_00001n2z

2.0 Angstrom structure of BtuF, the vitamin B12 binding protein of E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.210 (Depositor) 
  • R-Value Work: 
    0.189 (Depositor) 
  • R-Value Observed: 
    0.189 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1N2Z

This is version 2.1 of the entry. See complete history

Literature

The structure of Escherichia coli BtuF and binding to its cognate ATP binding cassette transporter

Borths, E.L.Locher, K.P.Lee, A.T.Rees, D.C.

(2002) Proc Natl Acad Sci U S A 99: 16642-16647

  • DOI: https://doi.org/10.1073/pnas.262659699
  • Primary Citation Related Structures: 
    1N2Z

  • PubMed Abstract: 

    Bacterial binding protein-dependent ATP binding cassette (ABC) transporters facilitate uptake of essential nutrients. The crystal structure of Escherichia coli BtuF, the protein that binds vitamin B12 and delivers it to the periplasmic surface of the ABC transporter BtuCD, reveals a bi-lobed fold resembling that of the ferrichrome binding protein FhuD. B12 is bound in the "base-on" conformation in a deep cleft formed at the interface between the two lobes of BtuF. A stable complex between BtuF and BtuCD (with the stoichiometry BtuC2D2F) is demonstrated to form in vitro and was modeled using the individual crystal structures. Two surface glutamates from BtuF may interact with arginine residues on the periplasmic surface of the BtuCD transporter. These glutamate and arginine residues are conserved among binding proteins and ABC transporters mediating iron and B12 uptake, suggesting that they may have a role in docking and the transmission of conformational changes.


  • Organizational Affiliation
    • Howard Hughes Medical Institute and Division of Chemistry and Chemical Engineering, Mail Code 114-96, California Institute of Technology, Pasadena, CA 91125, USA.

Macromolecule Content 

  • Total Structure Weight: 59.69 kDa 
  • Atom Count: 4,416 
  • Modeled Residue Count: 490 
  • Deposited Residue Count: 490 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Vitamin B12 transport protein btuF
A, B
245Escherichia coliMutation(s): 0 
Gene Names: btuf
UniProt
Find proteins for P37028 (Escherichia coli (strain K12))
Explore P37028 
Go to UniProtKB:  P37028
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37028
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CNC

Query on CNC



Download:Ideal Coordinates CCD File
GA [auth B],
T [auth A]
CYANOCOBALAMIN
C63 H89 Co N14 O14 P
SYZBZQWSWIJYAR-UVKKECPRSA-M
PG4

Query on PG4



Download:Ideal Coordinates CCD File
U [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
CD

Query on CD



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
C [auth A]
CA [auth B]
D [auth A]
AA [auth B],
BA [auth B],
C [auth A],
CA [auth B],
D [auth A],
DA [auth B],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
EA [auth B]
FA [auth B]
P [auth A]
Q [auth A]
R [auth A]
EA [auth B],
FA [auth B],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.210 (Depositor) 
  • R-Value Work:  0.189 (Depositor) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.066α = 90
b = 133.066β = 90
c = 67.687γ = 120

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2021-08-18
    Changes: Advisory, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-10-09
    Changes: Data collection, Structure summary