3H5K: Crystal Structure Of The Ribosome Inactivating Protein Pdl1

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.
PDB ID: 3H5KDownload
MMDB ID: 77309
PDB Deposition Date: 2009/4/22
Updated in MMDB: 2009/10
Experimental Method:
x-ray diffraction
Resolution: 1.45  Å
Source Organism:
Similar Structures:
Biological Unit for 3H5K: monomeric; determined by author and by software (PISA)
Molecular Components in 3H5K
Label Count Molecule
Protein (1 molecule)
Ribosome-inactivating Protein Pd-l1pd-l2
Molecule annotation
Chemicals (2 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB