2Z4U

Crystal structure of wild type PD-L4 from Phytolacca dioica leaves


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.122 

wwPDB Validation 3D Report Full Report


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:  

  • 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 d ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosome-inactivating protein PD-L4
A
261Phytolacca dioicaMutation(s): 0 
EC: 3.2.2.22
Find proteins for P84854 (Phytolacca dioica)
Go to UniProtKB:  P84854
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.122 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.521α = 90.00
b = 58.813β = 90.00
c = 98.774γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
Ilphasing
SHELXL-97refinement
HKL-2000data scaling
HKL-2000data reduction
Ilmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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