7Y3V image
Deposition Date 2022-06-13
Release Date 2023-04-05
Last Version Date 2023-11-29
Entry Detail
PDB ID:
7Y3V
Keywords:
Title:
Crystal structure of CdpNPT in complex with harmane
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.43 Å
R-Value Free:
0.23
R-Value Work:
0.21
R-Value Observed:
0.23
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cyclic dipeptide N-prenyltransferase
Gene (Uniprot):cdpNPT
Chain IDs:A, B, C, D
Chain Length:404
Number of Molecules:4
Biological Source:Aspergillus fumigatus
Primary Citation
Catalytic potential of a fungal indole prenyltransferase toward beta-carbolines, harmine and harman, and their prenylation effects on antibacterial activity.
J.Biosci.Bioeng. 134 311 317 (2022)
PMID: 35931602 DOI: 10.1016/j.jbiosc.2022.07.004

Abstact

The prenylation of compounds has attracted much attention, since it often adds bioactivity to non-prenylated compounds. We employed an enzyme assay with CdpNPT, an indole prenyltransferase from Aspergillus fumigatus with two naturally occurring β-carbolines, harmine (3) and harman (4) as prenyl acceptors, in the presence of dimethylallyl diphosphate (DMAPP) as the prenyl donor. The enzyme accepted these two prenyl acceptor substrates to produce 6-(3',3'-dimethylallyl)harmine (5) from 3 and 9-(3',3'-dimethylallyl)harman (6) and 6-(3',3'-dimethylallyl)harman (7) from 4. The X-ray crystal structure analysis of the CdpNPT (38-440) truncated mutant complexed with 4, and docking simulation studies of DMAPP to the crystal structure of the CdpNPT (38-440) mutant, suggested that CdpNPT could employ the two-step prenylation mechanism to produce 7, while the enzyme produced 6 with either one- or two-step prenylation mechanisms. Furthermore, the antibacterial assays revealed that the 3',3'-dimethylallylation of 3 and 4, as well as harmol (1), at C-6 enhanced the activities against Staphylococcus aureus and Bacillus subtilis.

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