2QES

Crystal structure of the ribosome inactivating protein PDL4 from P. dioica leaves in complex with adenine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.116 

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This is version 1.1 of the entry. See complete history


Literature

Atomic resolution (1.1 A) structure of the ribosome-inactivating protein PD-L4 from Phytolacca dioica L. leaves

Ruggiero, A.Chambery, A.Di Maro, A.Parente, A.Berisio, R.

(2008) Proteins 71: 8-15

  • DOI: 10.1002/prot.21712
  • Primary Citation of Related Structures:  
    2QET, 2QES, 2Z4U, 2Z53

  • PubMed Abstract: 
  • The ribosome inactivating protein PD-L4 from Phytolacca dioica is a N-beta-glycosidase, probably involved in plant defence. The crystal structures of wild type PD-L4 and of the S211A PD-L4 mutant with significantly decreased catalytic activity were determined at atomic resolution ...

    The ribosome inactivating protein PD-L4 from Phytolacca dioica is a N-beta-glycosidase, probably involved in plant defence. The crystal structures of wild type PD-L4 and of the S211A PD-L4 mutant with significantly decreased catalytic activity were determined at atomic resolution. To determine the structural determinants for the reduced activity of S211A PD-L4, both forms have also been co-crystallized with adenine, the major product of PD-L4 catalytic reaction. In the structure of the S211A mutant, the cavity formed by the lack of the Ser hydroxyl group is filled by a water molecule; the insertion of this non-isosteric group leads to small albeit concerted changes in the tightly packed active site of the enzyme. These changes have been correlated to the different activity of the mutant enzyme. This work highlights the importance of atomic resolution studies for the deep understanding of enzymatic properties.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome-inactivating protein PD-L4 A261Phytolacca dioicaMutation(s): 0 
EC: 3.2.2.22
Find proteins for P84854 (Phytolacca dioica)
Explore P84854 
Go to UniProtKB:  P84854
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADE
Query on ADE

Download Ideal Coordinates CCD File 
A
ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.116 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.521α = 90
b = 58.813β = 90
c = 98.774γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
IlMilionemodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
IlMilionephasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance