3LE7 image
Deposition Date 2010-01-14
Release Date 2010-04-14
Last Version Date 2024-11-20
Entry Detail
PDB ID:
3LE7
Keywords:
Title:
Crystal structure of PD-L1 from P. dioica in complex with adenine
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.65 Å
R-Value Free:
0.24
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
C 1 2 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome-inactivating protein PD-L1/PD-L2
Chain IDs:A, B
Chain Length:261
Number of Molecules:2
Biological Source:Phytolacca dioica
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ASN B ASN GLYCOSYLATION SITE
Primary Citation
The role of the glycan moiety on the structure-function relationships of PD-L1, type 1 ribosome-inactivating protein from P. dioica leaves
Mol Biosyst 6 570 579 (2010)
PMID: 20174685 DOI: 10.1039/b919801f

Abstact

N-glycosylation is one of the major naturally occurring covalent co-translational modifications of proteins in plants, being involved in proteins structure, folding, stability and biological activity. In the present work the influence of carbohydrate moieties on the structure-function relationships of type 1 ribosome-inactivating proteins (RIPs) was investigated. To this aim, PD-Ls, RIPs isolated from Phytolacca dioica L. leaves, differing for their glycosylation degree, were used as an experimental system. In particular, comparative structural and biological analyses were performed using native and unglycosylated recombinant PD-L1, the most glycosylated P. dioica RIP isoform. The glycans influence on protein synthesis inhibition and adenine polynucleotide glycosidase activity was investigated. The interaction with adenine, the product of the de-adenylation reaction, was also investigated for native and recombinant PD-L1 by fluorescence spectroscopy. Furthermore, the crystal structure of PD-L1 in complex with adenine was determined. Our data confirm that the absence of glycan moieties did not affect the biological activity in terms of protein synthesis inhibition. However, the removal of carbohydrate chains significantly increased the deadenylation capability, likely as a consequence of the increased accessibility of substrates to the active site pocket. Furthermore, preliminary data on cellular uptake showed that all PD-L isoforms were internalized and, for the first time, that the vesicular distribution within cells could be influenced by the protein glycosylation degree.

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