7B3A

Crystal structure of PamZ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis of antibiotic self-resistance in a bee larvae pathogen.

Dang, T.Loll, B.Muller, S.Skobalj, R.Ebeling, J.Bulatov, T.Gensel, S.Gobel, J.Wahl, M.C.Genersch, E.Mainz, A.Sussmuth, R.D.

(2022) Nat Commun 13: 2349-2349

  • DOI: https://doi.org/10.1038/s41467-022-29829-w
  • Primary Citation of Related Structures:  
    7B3A

  • PubMed Abstract: 

    Paenibacillus larvae, the causative agent of the devastating honey-bee disease American Foulbrood, produces the cationic polyketide-peptide hybrid paenilamicin that displays antibacterial and antifungal activity. Its biosynthetic gene cluster contains a gene coding for the N-acetyltransferase PamZ. We show that PamZ acts as self-resistance factor in Paenibacillus larvae by deactivation of paenilamicin. Using tandem mass spectrometry, nuclear magnetic resonance spectroscopy and synthetic diastereomers, we identified the N-terminal amino group of the agmatinamic acid as the N-acetylation site. These findings highlight the pharmacophore region of paenilamicin, which we very recently identified as a ribosome inhibitor. Here, we further determined the crystal structure of PamZ:acetyl-CoA complex at 1.34 Å resolution. An unusual tandem-domain architecture provides a well-defined substrate-binding groove decorated with negatively-charged residues to specifically attract the cationic paenilamicin. Our results will help to understand the mode of action of paenilamicin and its role in pathogenicity of Paenibacillus larvae to fight American Foulbrood.


  • Organizational Affiliation

    Institut für Chemie, Technische Universität Berlin, Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative Acyl-transferase domain protein280Paenibacillus larvae subsp. larvaeMutation(s): 0 
Gene Names: ERICIII_02339ERICV_02787
UniProt
Find proteins for A0A2L1TND5 (Paenibacillus larvae subsp. larvae)
Explore A0A2L1TND5 
Go to UniProtKB:  A0A2L1TND5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2L1TND5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.966α = 90
b = 70.107β = 106.947
c = 54.552γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description