3H5K

Crystal structure of the ribosome inactivating protein PDL1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of PD-L1, a ribosome inactivating protein from Phytolacca dioica L. Leaves with the property to induce DNA cleavage

Ruggiero, A., Di Maro, A., Severino, V., Chambery, A., Berisio, R.

(2009) Biopolymers 91: 1135-1142

  • DOI: 10.1002/bip.21260
  • Primary Citation of Related Structures:  
    3H5K

  • 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 endo ...

    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.

    Organizational Affiliation: 

    Istituto di Biostrutture e Bioimmagini, Napoli I-80134, Italy.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome-inactivating protein PD-L1/PD-L2 A, B261Phytolacca dioicaMutation(s): 0 
EC: 3.2.2.22
Find proteins for P84853 (Phytolacca dioica)
Explore P84853 
Go to UniProtKB:  P84853
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.011α = 90
b = 34.735β = 127.99
c = 120.63γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REMOmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REMOphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary