3H5K
Crystal structure of the ribosome inactivating protein PDL1
Summary for 3H5K
| Entry DOI | 10.2210/pdb3h5k/pdb |
| Related | 2qet 2z4u 2z53 |
| Descriptor | Ribosome-inactivating protein PD-L1/PD-L2, 2-acetamido-2-deoxy-beta-D-glucopyranose, 1,2-ETHANEDIOL, ... (4 entities in total) |
| Functional Keywords | protein, ribosome inactivation, disulfide bond, glycoprotein, hydrolase, plant defense, protein synthesis inhibitor, toxin |
| Biological source | Phytolacca dioica (Bella sombra tree) |
| Total number of polymer chains | 2 |
| Total formula weight | 59072.62 |
| Authors | Ruggiero, A.,Di Maro, A.,Severino, V.,Chambery, A.,Berisio, R. (deposition date: 2009-04-22, release date: 2009-10-13, Last modification date: 2024-10-30) |
| Primary citation | Ruggiero, A.,Di Maro, A.,Severino, V.,Chambery, A.,Berisio, R. Crystal structure of PD-L1, a ribosome inactivating protein from Phytolacca dioica L. Leaves with the property to induce DNA cleavage Biopolymers, 91:1135-1142, 2009 Cited by PubMed Abstract: The structure of the highly glycosylated type 1 ribosome inactivating protein PD-L1 was determined by X-ray crystallography. This protein belongs to a group of four PD-Ls (PD-L1-4) expressed in Phytolacca dioica leaves. Of these, PD-L1 and PD-L2 are endowed with the ability to cleave double strand DNA, a property which is not shared by the other two components of the family. Single crystals of native PD-L1, the most glycosylated, were obtained using seeding techniques and phase determination was achieved using molecular replacement. To investigate the role of glycosylation in the different functionality of these proteins, we performed DNA cleavage assays on the E. coli plasmid pBR322. These experiments revealed that DNA cleaving ability does not depend on the level of glycosylation of PD-L1, since there is no difference in the activities displayed by native PD-L1 and a recombinant non-glycosylated form. Besides, confirming that DNA cleavage by PD-L1 cannot be attributed to contaminations, these data unambiguously show that functional changes between PD-L1 and PD-L4 are solely to be attributed to their sequence differences. On the basis of the comparison of PD-L1 and PD-L4 crystal structures, we propose possible structural determinants responsible for their different functional behavior. PubMed: 19452522DOI: 10.1002/bip.21260 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.45 Å) |
Structure validation
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