6ET8

Crystal structure of AlbA in complex with albicidin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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This is version 1.2 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: https://doi.org/10.1038/s41467-018-05551-4
  • Primary Citation of Related Structures:  
    6ET8

  • 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 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, Biologische Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Albicidin resistance protein
A, B
222Klebsiella oxytocaMutation(s): 0 
Gene Names: albA
UniProt
Find proteins for Q8KRS7 (Klebsiella oxytoca)
Explore Q8KRS7 
Go to UniProtKB:  Q8KRS7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KRS7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.07α = 90
b = 123.35β = 90
c = 159.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Structure summary