8G97 | pdb_00008g97

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

PDB DOI: https://doi.org/10.2210/pdb8G97/pdb

Classification: LIGASE
Organism(s): Acinetobacter baumannii AB307-0294
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-02-21 Released: 2023-10-04
Deposition Author(s): Patel, K.D., Gulick, A.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free:
0.240 (Depositor), 0.241 (DCC)
R-Value Work:
0.194 (Depositor), 0.203 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

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

PubMed: 37752201 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s42003-023-05362-4
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 92.82 kDa
Atom Count: 6,435
Modeled Residue Count: 803
Deposited Residue Count: 826
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dimodular nonribosomal peptide synthase	A, B	413	Acinetobacter baumannii AB307-0294	Mutation(s): 0 Gene Names: dhbF_1, ABBFA_00818 EC: 6.3
UniProt
Find proteins for A0A5K6CNB8 (Acinetobacter baumannii (strain AB307-0294)) Explore A0A5K6CNB8 Go to UniProtKB: A0A5K6CNB8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5K6CNB8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ORD (Subject of Investigation/LOI) Query on ORD Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A]	I [auth A], L [auth B]	D-ORNITHINE C₅ H₁₂ N₂ O₂ AHLPHDHHMVZTML-SCSAIBSYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]