1APA

X-RAY STRUCTURE OF A POKEWEED ANTIVIRAL PROTEIN, CODED BY A NEW GENOMIC CLONE, AT 0.23 NM RESOLUTION. A MODEL STRUCTURE PROVIDES A SUITABLE ELECTROSTATIC FIELD FOR SUBSTRATE BINDING.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

X-ray structure of a pokeweed antiviral protein, coded by a new genomic clone, at 0.23 nm resolution. A model structure provides a suitable electrostatic field for substrate binding.

Ago, H.Kataoka, J.Tsuge, H.Habuka, N.Inagaki, E.Noma, M.Miyano, M.

(1994) Eur J Biochem 225: 369-374

  • DOI: 10.1111/j.1432-1033.1994.00369.x
  • Primary Citation of Related Structures:  
    1APA

  • PubMed Abstract: 
  • We have determined the crystal structure of alpha-pokeweed antiviral protein, a member of ribosome-inactivating proteins, at 0.23 nm resolution, by the molecular-replacement method. The crystals belong to the space group P2(1)2(1)2 with unit-cell dimensions a = 4 ...

    We have determined the crystal structure of alpha-pokeweed antiviral protein, a member of ribosome-inactivating proteins, at 0.23 nm resolution, by the molecular-replacement method. The crystals belong to the space group P2(1)2(1)2 with unit-cell dimensions a = 4.71, b = 11.63 and c = 4.96 nm, and contain one protein molecule/asymmetric unit based on a crystal volume/unit protein molecular mass of 2.1 x 10(-3) nm3/Da. The crystallographic residual value was reduced to 17.2% (0.6-0.23 nm resolution) with root-mean-square deviations in bond lengths of 1.9 pm and bond angles of 2.2 degrees. The C alpha-C alpha distance map shows that alpha-pokeweed antiviral protein is composed of three modules, the N-terminal (Ala1-Leu76), the central (Tyr77-Lys185) and the C-terminal (Tyr186-Thr266) modules. The substrate-binding site is formed as a cleft between the central and C-terminal modules and all the active residues exist on the central module. The electrostatic potential around the substrate-binding site shows that the central and C-terminal module sides of this cleft have a negatively and a positively charged region, respectively. This charge distribution in the protein seems to provide a suitable interaction with the substrate rRNA.


    Related Citations: 
    • Expression of a Pokeweed Antiviral Protein in Escherichia Coli and its Characterization
      Kataoka, J., Ago, H., Habuka, N., Furuno, M., Masuta, C., Miyano, M., Koiwai, A.
      (1993) FEBS Lett 320: 31
    • Isolation and Analysis of a Genomic Clone Encoding a Pokeweed Antiviral Protein
      Kataoka, J., Habuka, N., Masuta, C., Miyano, M., Koiwai, A.
      (1992) Plant Mol Biol 20: 879

    Organizational Affiliation

    Life Science Research Laboratory, Japan Tobacco, Inc., Kanagawa.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POKEWEED ANTIVIRAL PROTEINA266Phytolacca americanaMutation(s): 0 
EC: 3.2.2.22
Find proteins for Q03464 (Phytolacca americana)
Explore Q03464 
Go to UniProtKB:  Q03464
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.1α = 90
b = 116.3β = 90
c = 49.6γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other