PCPD: Plant cytochrome P450 database and web-based tools for structural construction and ligand docking.
Database
Homologous modeling
Ligand docking
Plant P450 database
Web service
Journal
Synthetic and systems biotechnology
ISSN: 2405-805X
Titre abrégé: Synth Syst Biotechnol
Pays: China
ID NLM: 101694371
Informations de publication
Date de publication:
Jun 2021
Jun 2021
Historique:
received:
30
10
2020
revised:
25
03
2021
accepted:
16
04
2021
entrez:
17
5
2021
pubmed:
18
5
2021
medline:
18
5
2021
Statut:
epublish
Résumé
Plant cytochrome P450s play key roles in the diversification and functional modification of plant natural products. Although over 200,000 plant P450 gene sequences have been recorded, only seven crystalized P450 genes severely hampered the functional characterization, gene mining and engineering of important P450s. Here, we combined Rosetta homologous modeling and MD-based refinement to construct a high-resolution P450 structure prediction process (PCPCM), which was applied to 181 plant P450s with identified functions. Furthermore, we constructed a ligand docking process (PCPLD) that can be applied for plant P450s virtual screening. 10 examples of virtual screening indicated the process can reduce about 80% screening space for next experimental verification. Finally, we constructed a plant P450 database (PCPD: http://p450.biodesign.ac.cn/), which includes the sequences, structures and functions of the 181 plant P450s, and a web service based on PCPCM and PCPLD. Our study not only developed methods for the P450-specific structure analysis, but also introduced a universal approach that can assist the mining and functional analysis of P450 enzymes.
Identifiants
pubmed: 33997360
doi: 10.1016/j.synbio.2021.04.004
pii: S2405-805X(21)00023-5
pmc: PMC8094579
doi:
Types de publication
Journal Article
Langues
eng
Pagination
102-109Informations de copyright
© 2021 The Authors.
Déclaration de conflit d'intérêts
The authors declare no competing financial interests.
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