1D6A | pdb_00001d6a

STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN COMPLEXED WITH GUANINE

• PDB DOI: https://doi.org/10.2210/pdb1D6A/pdb

• Classification: HYDROLASE
• Organism(s): Phytolacca americana
• Mutation(s): No 


• Deposited: 1999-10-12 Released: 1999-12-16 
• Deposition Author(s): Kurinov, I.V., Rajamohan, F., Venkatachalam, T.K., Uckun, F.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.250 (Depositor) 
• R-Value Work: 
  0.190 (Depositor) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

X-ray crystallographic analysis of the structural basis for the interaction of pokeweed antiviral protein with guanine residues of ribosomal RNA.

Kurinov, I.V., Rajamohan, F., Venkatachalam, T.K., Uckun, F.M.

(1999) Protein Sci 8: 2399-2405

• PubMed: 10595542 
• DOI: https://doi.org/10.1110/ps.8.11.2399
• Primary Citation Related Structures: 
  1D6A


• PubMed Abstract: 
  

  Pokeweed antiviral protein (PAP) is a ribosome-inactivating protein (RIP), which enzymatically removes a single adenine base from a conserved, surface exposed loop sequence of ribosomal rRNA. We now present unprecedented experimental evidence that PAP can release not only adenine but guanine as well from Escherichia coli rRNA, albeit at a rate 20 times slower than for adenine. We also report X-ray structure analysis and supporting modeling studies for the interactions of PAP with guanine. Our modeling studies indicated that PAP can accommodate a guanine base in the active site pocket without large conformational changes. This prediction was experimentally confirmed, since a guanine base was visible in the active site pocket of the crystal structure of the PAP-guanine complex.

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Organizational Affiliation: 
• Department of Structural Biology, Hughes Institute, Roseville, Minnesota 55113, USA. [e-mail]

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: 58.99 kDa 
• Atom Count: 4,694 
• Modeled 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
GUN	C [auth A], D [auth B]	GUANINE C5 H5 N5 O UYTPUPDQBNUYGX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.250 (Depositor) 
• R-Value Work:  0.190 (Depositor) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.294	α = 68.664
b = 49.411	β = 81.036
c = 64.288	γ = 63.87

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-12-16 
Deposition Author(s): Kurinov, I.V., Rajamohan, F., Venkatachalam, T.K., Uckun, F.M.

Revision History  

• Version 1.0: 1999-12-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary