1MRK

STUDIES ON CRYSTAL STRUCTURES ACTIVE CENTER GEOMETRY AND DEPURINE MECHANISM OF TWO RIBOSOME-INACTIVATING PROTEINS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Studies on crystal structures, active-centre geometry and depurinating mechanism of two ribosome-inactivating proteins.

Huang, Q.Liu, S.Tang, Y.Jin, S.Wang, Y.

(1995) Biochem.J. 309: 285-298

  • Primary Citation of Related Structures:  1MRG, 1MRH, 1MRI, 1MRJ

  • PubMed Abstract: 
  • Two ribosome-inactivating proteins, trichosanthin and alpha-momorcharin, have been studied in the forms of complexes with ATP or formycin, by an X-ray-crystallographic method at 1.6-2.0 A (0.16-0.20 nm) resolution. The native alpha-momorcharin had be ...

    Two ribosome-inactivating proteins, trichosanthin and alpha-momorcharin, have been studied in the forms of complexes with ATP or formycin, by an X-ray-crystallographic method at 1.6-2.0 A (0.16-0.20 nm) resolution. The native alpha-momorcharin had been studied at 2.2 A resolution. Structures of trichosanthin were determined by a multiple isomorphous replacement method. Structures of alpha-momorcharin were determined by a molecular replacement method using refined trichosanthin as the searching model. Small ligands in all these complexes have been recognized and built on the difference in electron density. All these structures have been refined to achieve good results, both in terms of crystallography and of ideal geometry. These two proteins show considerable similarity in their three-dimensional folding and to that of related proteins. On the basis of these structures, detailed geometries of the active centres of these two proteins are described and are compared with those of related proteins. In all complexes the interactions between ligand atoms and protein atoms, including hydrophobic forces, aromatic stacking interactions and hydrogen bonds, are found to be specific towards the adenine base. The relationship between the sequence conservation of ribosome-inactivating proteins and their active-centre geometry was analysed. A depurinating mechanism of ribosome-inactivating proteins is proposed on the basis of these results. The N-7 atom of the substrate base group is proposed to be protonated by an acidic residue in the active centre.


    Related Citations: 
    • Active Center Geometry and Depurine Mechanism of Two Ribosome-Inactivating Proteins
      Tang, Y.,Huang, Q.
      (1994) Prog.Nat.Sci. 4: 527


    Organizational Affiliation

    Department of Chemistry, Peking University, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-TRICHOSANTHIN
A
247Trichosanthes kirilowiiEC: 3.2.2.22
Find proteins for P09989 (Trichosanthes kirilowii)
Go to UniProtKB:  P09989
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMC
Query on FMC

Download SDF File 
Download CCD File 
A
(1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol
C10 H13 N5 O4
KBHMEHLJSZMEMI-KSYZLYKTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.240α = 90.00
b = 76.740β = 90.00
c = 79.250γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-02-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance