Adenylation domain structure from NRPS-like Delta-Poly-L-Ornithine synthetase (D-Ornithine bound)

Experimental Data Snapshot

  • Resolution: 2.51 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

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Structural and functional insights into delta-poly-L-ornithine polymer biosynthesis from Acinetobacter baumannii.

Patel, K.D.Gulick, A.M.

(2023) Commun Biol 6: 982-982

  • DOI: https://doi.org/10.1038/s42003-023-05362-4
  • Primary Citation of Related Structures:  
    8G95, 8G96, 8G97, 8G98

  • PubMed Abstract: 

    Cationic homo-polyamino acid (CHPA) peptides containing isopeptide bonds of diamino acids have been identified from Actinomycetes strains. However, none has been reported from other bacteria. Here, we report a δ-poly-L-ornithine synthetase from Acinetobacter baumannii, which we name PosA. Surprisingly, structural analysis of the adenylation domain and biochemical assay shows L-ornithine as the substrate for PosA. The product from the enzymatic reaction was purified and identified as poly-L-ornithine composed of 7-12 amino acid units. Chemical labeling of the polymer confirmed the isopeptide linkage of δ-poly-L-ornithine. We examine the biological activity of chemically synthesized 12-mer δ-poly-L-ornithine, illustrating that the polymer may act as an anti-fungal agent. Structures of the isolated adenylation domain from PosA are presented with several diamino acids and biochemical assays identify important substrate binding residues. Structurally-guided genome-mining led to the identification of homologs with different substrate binding residues that could activate additional substrates. A homolog from Bdellovibrionales sp. shows modest activity with L-arginine but not with any diamino acids observed to be substrates for previously examined CHPA synthetases. Our study indicates the possibility that additional CHPAs may be produced by various microbes, supporting the further exploration of uncharacterized natural products.

  • Organizational Affiliation

    Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, NY, 14203, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dimodular nonribosomal peptide synthase
A, B
413Acinetobacter baumannii AB307-0294Mutation(s): 0 
Gene Names: dhbF_1ABBFA_00818
Find proteins for A0A5K6CNB8 (Acinetobacter baumannii (strain AB307-0294))
Explore A0A5K6CNB8 
Go to UniProtKB:  A0A5K6CNB8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5K6CNB8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ORD (Subject of Investigation/LOI)
Query on ORD

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B]
C5 H12 N2 O2
Query on GOL

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C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B]
C3 H8 O3
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.51 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.837α = 90
b = 93.928β = 90
c = 152.257γ = 90
Software Package:
Software NamePurpose
Cootmodel building
AutoProcessdata reduction
autoPROCdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM136235

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Database references