1RL0
Crystal structure of a new ribosome-inactivating protein (RIP): dianthin 30
Summary for 1RL0
| Entry DOI | 10.2210/pdb1rl0/pdb |
| Descriptor | Antiviral protein DAP-30 (2 entities in total) |
| Functional Keywords | mixed beta-sheet, alpha and beta regions, hydrolase, plant protein |
| Biological source | Dianthus caryophyllus (clove pink) |
| Total number of polymer chains | 1 |
| Total formula weight | 28632.63 |
| Authors | Fermani, S.,Falini, G.,Ripamonti, A.,Bolognesi, A.,Polito, L.,Stirpe, F. (deposition date: 2003-11-24, release date: 2004-12-07, Last modification date: 2023-08-23) |
| Primary citation | Fermani, S.,Falini, G.,Ripamonti, A.,Polito, L.,Stirpe, F.,Bolognesi, A. The 1.4A structure of dianthin 30 indicates a role of surface potential at the active site of type 1 ribosome inactivating proteins J.Struct.Biol., 149:204-212, 2005 Cited by PubMed 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. PubMed: 15681236DOI: 10.1016/j.jsb.2004.11.007 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.4 Å) |
Structure validation
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