7Y3V
Crystal structure of CdpNPT in complex with harmane
Summary for 7Y3V
| Entry DOI | 10.2210/pdb7y3v/pdb |
| Descriptor | Cyclic dipeptide N-prenyltransferase, PHOSPHATE ION, 1-methyl-9H-pyrido[3,4-b]indole, ... (4 entities in total) |
| Functional Keywords | prenyltransferases, cyclic dipeptide n-prenyltransferase, transferase |
| Biological source | Aspergillus fumigatus |
| Total number of polymer chains | 4 |
| Total formula weight | 185409.32 |
| Authors | Nakashima, Y.,Morita, H. (deposition date: 2022-06-13, release date: 2023-04-05, Last modification date: 2023-11-29) |
| Primary citation | Hamdy, S.A.,Kodama, T.,Nakashima, Y.,Han, X.,Morita, H. 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 Cited by PubMed Abstract: 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. PubMed: 35931602DOI: 10.1016/j.jbiosc.2022.07.004 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.43 Å) |
Structure validation
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