3WHO

X-ray-Crystallographic Structure of an RNase Po1 Exhibiting Anti-tumor Activity

• PDB DOI: https://doi.org/10.2210/pdb3WHO/pdb

• Classification: HYDROLASE
• Organism(s): Pleurotus ostreatus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-08-30 Released: 2014-07-02 
• Deposition Author(s): Kobayashi, H., Katsurtani, T., Hara, Y., Motoyoshi, N., Itagaki, T., Akita, F., Higashiura, A., Yamada, Y., Suzuki, M., Inokuchi, N.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.250 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 

Literature

X-ray crystallographic structure of RNase Po1 that exhibits anti-tumor activity.

Kobayashi, H., Katsutani, T., Hara, Y., Motoyoshi, N., Itagaki, T., Akita, F., Higashiura, A., Yamada, Y., Inokuchi, N., Suzuki, M.

(2014) Biol Pharm Bull 37: 968-978

• PubMed: 24882409 
• DOI: https://doi.org/10.1248/bpb.b13-00929
• Primary Citation of Related Structures:  
  3WHO


• PubMed Abstract: 
  

  RNase Po1 is a guanylic acid-specific ribonuclease member of the RNase T1 family from Pleurotus ostreatus. We previously reported that RNase Po1 inhibits the proliferation of human tumor cells, yet RNase T1 and other T1 family RNases are non-toxic. We determined the three-dimensional X-ray structure of RNase Po1 and compared it with that of RNase T1. The catalytic sites are conserved. However, there are three disulfide bonds, one more than in RNase T1. One of the additional disulfide bond is in the catalytic and binding site of RNase Po1, and makes RNase Po1 more stable than RNase T1. A comparison of the electrostatic potential of the molecular surfaces of these two proteins shows that RNase T1 is anionic whereas RNase Po1 is cationic, so RNase Po1 might bind to the plasma membrane electrostatically. We suggest that the structural stability and cationic character of RNase Po1 are critical to the anti-cancer properties of the protein.

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Organizational Affiliation: 

School of Pharmacy, Nihon University.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.19 kDa 
• Atom Count: 2,407 
• Modelled Residue Count: 303 
• Deposited Residue Count: 303 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanyl-specific ribonuclease Po1	A, B, C	101	Pleurotus ostreatus	Mutation(s): 1  EC: 4.6.1.24
UniProt
Find proteins for P81762 (Pleurotus ostreatus) Explore P81762  Go to UniProtKB:  P81762

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.250 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.557	α = 90
b = 75.557	β = 90
c = 34.803	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-07-02 
Deposition Author(s): Kobayashi, H., Katsurtani, T., Hara, Y., Motoyoshi, N., Itagaki, T., Akita, F., Higashiura, A., Yamada, Y., Suzuki, M., Inokuchi, N.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2014-07-02
  Type: Initial release
  
• Version 1.1: 2019-10-09
  Changes: Data collection, Database references
• Version 2.0: 2023-10-11
  Type: Coordinate replacement
  Reason: Sequence discrepancy
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary