1. The 1.4Å structure of dianthin 30 indicates a role of surface potential at the active site of type 1 ribosome inactivating proteins
- Author
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Giuseppe Falini, Alberto Ripamonti, Andrea Bolognesi, Letizia Polito, Simona Fermani, Fiorenzo Stirpe, FERMANI S., FALINI G., RIPAMONTI A., POLITO L., STIRPE F., and BOLOGNESI A.
- Subjects
Models, Molecular ,Protein Folding ,endocrine system ,Molecular Sequence Data ,Sequence alignment ,Protein Structure, Secondary ,chemistry.chemical_compound ,X-Ray Diffraction ,Structural Biology ,Protein biosynthesis ,Amino Acid Sequence ,Plant Proteins ,Protein Synthesis Inhibitors ,Binding Sites ,Sequence Homology, Amino Acid ,biology ,Ribosome-inactivating protein ,Water ,Active site ,Ribosomal RNA ,Protein Structure, Tertiary ,Ricin ,Biochemistry ,chemistry ,Plant protein ,Ribosome Inactivating Proteins, Type 1 ,biology.protein ,Crystallization ,Ribosomes ,DNA - Abstract
Ribosome inactivating proteins (RIPs) are plant proteins with enzymatic activity identified as rRNA N-glycosidase (EC 3.2.2.22), which cleaves the N-glycosidic bond of a specific adenine on the ricin/sarcin region of rRNA, thus causing inhibition of protein synthesis. They also depurinate extensively DNA and other polynucleotides. The three-dimensional structure of dianthin 30, a type 1 (single-chain) RIP of Dianthus caryophyllus (leaves), is now described at 1.4 angstroms, a resolution never achieved before for any RIP. The fold typical of RIPs is conserved, despite some differences in the loop regions. The general structure comparison by superimposed alpha-carbon (249 atoms) and the sequence alignment by structure for dianthin 30 and saporin-S6 give a root mean square deviation of 0.625 angstroms. Despite the differences reported for the biological activities of the two RIPs, their structures fit quite well and both show a protein segment containing strands beta7, beta8, and beta9 shorter than other RIPs. However, the surface electrostatic potential in the active site region neatly distinguishes dianthin 30 from saporin-S6. The possible relationship between the charge distribution and the behavior of the proteins toward different substrates is discussed.
- Published
- 2005