6LCQ

Crystal structure of rice defensin OsAFP1

Summary for 6LCQ

• Entry DOI: 10.2210/pdb6lcq/pdb
• Descriptor: Defensin-like protein CAL1, PHOSPHATE ION (3 entities in total)
• Functional Keywords: rice, oryza sativa, defensin, antifungal, cysteine-stabilized alpha/beta structure, antifungal protein
• Biological source: Oryza sativa (Rice)
• Total number of polymer chains: 2
• Total formula weight: 12141.81

Authors

Ochiai, A.,Ogawa, K.,Fukuda, M.,Suzuki, M.,Ito, K.,Tanaka, T.,Sagehashi, Y.,Taniguchi, M. (deposition date: 2019-11-19, release date: 2020-04-01, Last modification date: 2024-10-16)

Primary citation

Ochiai, A.,Ogawa, K.,Fukuda, M.,Suzuki, M.,Ito, K.,Tanaka, T.,Sagehashi, Y.,Taniguchi, M.
Crystal structure of rice defensin OsAFP1 and molecular insight into lipid-binding.
J.Biosci.Bioeng., 130:6-13, 2020

PubMed Abstract: Defensins are antibacterial peptides that function in the innate immune system. OsAFP1, a defensin identified from Oryza sativa (rice), exhibits antimicrobial activity against rice pathogens. Intriguingly, OsAFP1 was also shown to demonstrate potent antifungal activity against the human pathogenic fungus Candida albicans by inducing apoptosis in target cells, suggesting that OsAFP1 represents a potential new antibiotic candidate; however, further analyses, particularly at the structural level, are required to elucidate the mechanistic underpinnings of OsAFP1 antifungal activity. Here, we determined the three-dimensional structure of OsAFP1 using X-ray crystallography. OsAFP1 features the cysteine-stabilized αβ structure highly conserved in plant defensins and presents a dimeric structure that appears necessary for antifungal activity. Superimposition of the OsAFP1 structure with that of Nicotiana alata NaD1 complexed with phosphatidic acid indicated that the target molecule is likely trapped between the S2-S3 loops of each OsAFP1 dimer. In lipid-binding analyses performed using nitrocellulose membranes immobilized with various membrane lipid components, OsAFP1 was found to bind to phosphatidylinositols (PIPs) harboring phosphate groups, particularly PI(3)P. These results indicate that OsAFP1 exerts antifungal activity by binding to PI(3)P contained in the C. albicans cell membrane, thereby applying cellular stress and inducing apoptosis. Furthermore, the OsAFP1 structure and site-specific-mutation analyses revealed that Arg1, His2, Leu4, Arg9, and Phe10 play critical roles in OsAFP1 dimer formation. Thus, our study provides novel insights into the antifungal mechanism of OsAFP1.

PubMed: 32192842
DOI: 10.1016/j.jbiosc.2020.02.011

Experimental method

X-RAY DIFFRACTION (1.62 Å)