6ET8

Crystal structure of AlbA in complex with albicidin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular insights into antibiotic resistance - how a binding protein traps albicidin.

Rostock, L.Driller, R.Gratz, S.Kerwat, D.von Eckardstein, L.Petras, D.Kunert, M.Alings, C.Schmitt, F.J.Friedrich, T.Wahl, M.C.Loll, B.Mainz, A.Sussmuth, R.D.

(2018) Nat Commun 9: 3095-3095

  • DOI: 10.1038/s41467-018-05551-4

  • PubMed Abstract: 
  • The worldwide emergence of antibiotic resistance poses a serious threat to human health. A molecular understanding of resistance strategies employed by bacteria is obligatory to generate less-susceptible antibiotics. Albicidin is a highly potent anti ...

    The worldwide emergence of antibiotic resistance poses a serious threat to human health. A molecular understanding of resistance strategies employed by bacteria is obligatory to generate less-susceptible antibiotics. Albicidin is a highly potent antibacterial compound synthesized by the plant-pathogenic bacterium Xanthomonas albilineans. The drug-binding protein AlbA confers albicidin resistance to Klebsiella oxytoca. Here we show that AlbA binds albicidin with low nanomolar affinity resulting in full inhibition of its antibacterial activity. We report on the crystal structure of the drug-binding domain of AlbA (AlbAS) in complex with albicidin. Both α-helical repeat domains of AlbAS are required to cooperatively clamp albicidin, which is unusual for drug-binding proteins of the MerR family. Structure-guided NMR binding studies employing synthetic albicidin derivatives give valuable information about ligand promiscuity of AlbAS. Our findings thus expand the general understanding of antibiotic resistance mechanisms and support current drug-design efforts directed at more effective albicidin analogs.


    Organizational Affiliation

    Institut für Chemie, Biophysikalische Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.,Helmholtz Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489, Berlin, Germany.,Institut für Chemie, Biologische Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany. suessmuth@chem.tu-berlin.de.,Institut für Chemie, Biologische Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany.,Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0751, USA.,Institut für Chemie und Biochemie, Strukturbiochemie, Freie Universität Berlin, Takustraße 6, 14195, Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Albicidin resistance protein
A, B
222Klebsiella oxytocaMutation(s): 0 
Gene Names: albA
Find proteins for Q8KRS7 (Klebsiella oxytoca)
Go to UniProtKB:  Q8KRS7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BWH
Query on BWH

Download SDF File 
Download CCD File 
A, B
albicidin
C44 H38 N6 O12
NZSWNNDHPOTJNH-VEJILBAHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BWHKd: 5.6 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 54.070α = 90.00
b = 123.350β = 90.00
c = 159.200γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
AutoSolphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2019-10-16
    Type: Data collection, Database references