1PAG

THE 2.5 ANGSTROMS STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN

• PDB DOI: https://doi.org/10.2210/pdb1PAG/pdb

• Classification: PROTEIN SYNTHESIS INHIBITOR
• Organism(s): Phytolacca americana
• Mutation(s): No 


• Deposited: 1992-10-19 Released: 1994-01-31 
• Deposition Author(s): Monzingo, A.F., Collins, E.J., Ernst, S.R., Irvin, J.D., Robertus, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Work: 
  0.200 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

The 2.5 A structure of pokeweed antiviral protein.

Monzingo, A.F., Collins, E.J., Ernst, S.R., Irvin, J.D., Robertus, J.D.

(1993) J Mol Biol 233: 705-715

• PubMed: 8411176 
• DOI: https://doi.org/10.1006/jmbi.1993.1547
• Primary Citation of Related Structures:  
  1PAF, 1PAG


• PubMed Abstract: 
  

  The pokeweed antiviral protein (PAP), isolated from the leaves of Phytolacca americana, is one of a family of plant and bacterial ribosome-inhibiting proteins (RIPs) which act as specific N-glycosidases on rRNA. Here we report the three-dimensional structure of PAP determined to 2.5 A resolution by X-ray crystallography. After 14 rounds of refinement, the R factor is 0.17 for 5.0 to 2.5 A data. The protein is homologous with the A chain of ricin and exhibits a very similar folding pattern. The positions of key active site residues are also similar. We also report the 2.8 A structure of PAP complexed with a substrate analog, formycin 5'-monophosphate. As seen previously in ricin, the formycin ring is stacked between invariant tyrosines 72 and 123. Arg179 bonds to N-3 which is thought to be important in catalysis.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Texas, Austin 78712.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 59.38 kDa 
• Atom Count: 4,244 
• Modelled Residue Count: 524 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POKEWEED ANTIVIRAL PROTEIN	A, B	262	Phytolacca americana	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P10297 (Phytolacca americana) Explore P10297  Go to UniProtKB:  P10297

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMP	C [auth A], D [auth B]	FORMYCIN-5'-MONOPHOSPHATE C10 H14 N5 O7 P PBAHXXBYQACZMA-KSYZLYKTSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Work:  0.200 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.4	α = 80
b = 50.1	β = 113.2
c = 65.2	γ = 116.5

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-31 
Deposition Author(s): Monzingo, A.F., Collins, E.J., Ernst, S.R., Irvin, J.D., Robertus, J.D.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-10-16
  Changes: Structure summary