title: The 1.4 anstroms structure of dianthin 30 indicates a role of surface potential at the active site of type 1 ribosome inactivating proteins.
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.
authors.affiliation: Dipartimento di Chimica G. Ciamician, Alma Mater Studiorum Universita' di Bologna, via Selmi 2, I-40126 Bologna, Italy.
authors.forename: Simona
authors.initials: S
authors.lastname: Fermani
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Falini
authors.forename: Alberto
authors.initials: A
authors.lastname: Ripamonti
authors.forename: Letizia
authors.initials: L
authors.lastname: Polito
authors.forename: Fiorenzo
authors.initials: F
authors.lastname: Stirpe
authors.forename: Andrea
authors.initials: A
authors.lastname: Bolognesi
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D003460:Crystallization; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000737:chemistry / Q000494:pharmacology*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011500:Protein Synthesis Inhibitors / Q000494:pharmacology*; D054789:Ribosome Inactivating Proteins, Type 1; D012270:Ribosomes / Q000187:drug effects*; D017386:Sequence Homology, Amino Acid; D014867:Water / Q000737:chemistry; D014961:X-Ray Diffraction
chemical_list: D010940:Plant Proteins; D011500:Protein Synthesis Inhibitors; D054789:Ribosome Inactivating Proteins, Type 1; D014867:Water