8UC3

Cryo-EM structure of the AlbAB cyclodipeptide oxidase enzyme filament


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cyclodipeptide oxidase is an enzyme filament.

Andreas, M.P.Giessen, T.W.

(2024) Nat Commun 15: 3574-3574

  • DOI: https://doi.org/10.1038/s41467-024-48030-9
  • Primary Citation of Related Structures:  
    8UC3

  • PubMed Abstract: 

    Modified cyclic dipeptides represent a widespread class of secondary metabolites with diverse pharmacological activities, including antibacterial, antifungal, and antitumor. Here, we report the structural characterization of the Streptomyces noursei enzyme AlbAB, a cyclodipeptide oxidase (CDO) carrying out α,β-dehydrogenations during the biosynthesis of the antibiotic albonoursin. We show that AlbAB is a megadalton heterooligomeric enzyme filament containing covalently bound flavin mononucleotide cofactors. We highlight that AlbAB filaments consist of alternating dimers of AlbA and AlbB and that enzyme activity is crucially dependent on filament formation. We show that AlbA-AlbB interactions are highly conserved suggesting that other CDO-like enzymes are likely enzyme filaments. As CDOs have been employed in the structural diversification of cyclic dipeptides, our results will be useful for future applications of CDOs in biocatalysis and chemoenzymatic synthesis.


  • Organizational Affiliation

    Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Albonoursin synthaseA,
D [auth B]
196Streptomyces noursei ATCC 11455Mutation(s): 0 
Gene Names: albA
UniProt
Find proteins for Q8GED9 (Streptomyces noursei)
Explore Q8GED9 
Go to UniProtKB:  Q8GED9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GED9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein AlbBB [auth D],
C
105Streptomyces noursei ATCC 11455Mutation(s): 0 
Gene Names: albB
UniProt
Find proteins for Q8GED8 (Streptomyces noursei)
Explore Q8GED8 
Go to UniProtKB:  Q8GED8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GED8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2.1
MODEL REFINEMENTPHENIX1.20.1-4487
MODEL REFINEMENTCoot0.9.8.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM133325

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release