1USQ

Complex of E. Coli DraE adhesin with Chloramphenicol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

High Resolution Studies of the Afa/Dr Adhesin Drae and its Interaction with Chloramphenicol

Pettigrew, D.Anderson, K.L.Billington, J.Cota, E.Simpson, P.Urvil, P.Rabuzin, F.Roversi, P.Nowicki, B.Du Merle, L.Le Bouguenec, C.Matthews, S.Lea, S.M.

(2004) J Biol Chem 279: 46851

  • DOI: https://doi.org/10.1074/jbc.M409284200
  • Primary Citation of Related Structures:  
    1USQ, 1USZ, 1UT1, 1UT2

  • PubMed Abstract: 

    Pathogenic Escherichia coli expressing Afa/Dr adhesins are able to cause both urinary tract and diarrheal infections. The Afa/Dr adhesins confer adherence to epithelial cells via interactions with the human complement regulating protein, decay accelerating factor (DAF or CD55). Two of the Afa/Dr adhesions, AfaE-III and DraE, differ from each other by only three residues but are reported to have several different properties. One such difference is disruption of the interaction between DraE and CD55 by chloramphenicol, whereas binding of AfaE-III to CD55 is unaffected. Here we present a crystal structure of a strand-swapped trimer of wild type DraE. We also present a crystal structure of this trimer in complex with chloramphenicol, as well as NMR data supporting the binding position of chloramphenicol within the crystal. The crystal structure reveals the precise atomic basis for the sensitivity of DraE-CD55 binding to chloramphenicol and demonstrates that in contrast to other chloramphenicol-protein complexes, drug binding is mediated via recognition of the chlorine "tail" rather than via intercalation of the benzene rings into a hydrophobic pocket.


  • Organizational Affiliation

    Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DR HEMAGGLUTININ STRUCTURAL SUBUNIT
A, B, C, D, E
A, B, C, D, E, F
149Escherichia coliMutation(s): 3 
UniProt
Find proteins for P24093 (Escherichia coli)
Explore P24093 
Go to UniProtKB:  P24093
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24093
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLM
Query on CLM

Download Ideal Coordinates CCD File 
FA [auth E]
K [auth A]
KA [auth F]
Q [auth B]
V [auth C]
FA [auth E],
K [auth A],
KA [auth F],
Q [auth B],
V [auth C],
Z [auth D]
CHLORAMPHENICOL
C11 H12 Cl2 N2 O5
WIIZWVCIJKGZOK-RKDXNWHRSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth E]
CA [auth E]
G [auth A]
GA [auth F]
AA [auth D],
BA [auth E],
CA [auth E],
G [auth A],
GA [auth F],
H [auth A],
HA [auth F],
L [auth A],
M [auth B],
N [auth B],
R [auth C],
S [auth C],
W [auth D],
X [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
DA [auth E]
EA [auth E]
I [auth A]
IA [auth F]
J [auth A]
DA [auth E],
EA [auth E],
I [auth A],
IA [auth F],
J [auth A],
JA [auth F],
O [auth B],
P [auth B],
T [auth C],
U [auth C],
Y [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.969α = 90
b = 118.969β = 90
c = 57.416γ = 120
Software Package:
Software NamePurpose
TNTrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-31
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Refinement description