4YP2

Cleavage of nicotinamide adenine dinucleotides by the ribosome inactivating protein from Momordica charantia


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cleavage of nicotinamide adenine dinucleotide by the ribosome-inactivating protein from Momordica charantia.

Vinkovic, M.Dunn, G.Wood, G.E.Husain, J.Wood, S.P.Gill, R.

(2015) Acta Crystallogr.,Sect.F 71: 1152-1155

  • DOI: 10.1107/S2053230X15013540
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The interaction of momordin, a type 1 ribosome-inactivating protein from Momordica charantia, with NADP(+) and NADPH has been investigated by X-ray diffraction analysis of complexes generated by co-crystallization and crystal soaking. It is known tha ...

    The interaction of momordin, a type 1 ribosome-inactivating protein from Momordica charantia, with NADP(+) and NADPH has been investigated by X-ray diffraction analysis of complexes generated by co-crystallization and crystal soaking. It is known that the proteins of this family readily cleave the adenine-ribose bond of adenosine and related nucleotides in the crystal, leaving the product, adenine, bound to the enzyme active site. Surprisingly, the nicotinamide-ribose bond of oxidized NADP(+) is cleaved, leaving nicotinamide bound in the active site in the same position but in a slightly different orientation to that of the five-membered ring of adenine. No binding or cleavage of NADPH was observed at pH 7.4 in these experiments. These observations are in accord with current views of the enzyme mechanism and may contribute to ongoing searches for effective inhibitors.


    Organizational Affiliation

    Astex Therapeutics, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosome-inactivating protein momordin I
B
246Momordica charantiaMutation(s): 0 
EC: 3.2.2.22
Find proteins for P16094 (Momordica charantia)
Go to UniProtKB:  P16094
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NCA
Query on NCA

Download SDF File 
Download CCD File 
B
NICOTINAMIDE
C6 H6 N2 O
DFPAKSUCGFBDDF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.140 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 130.100α = 90.00
b = 130.100β = 90.00
c = 37.570γ = 120.00
Software Package:
Software NamePurpose
xia2data reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-20
    Type: Initial release
  • Version 1.1: 2015-09-09
    Type: Database references