4YP2 | pdb_00004yp2

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

• PDB DOI: https://doi.org/10.2210/pdb4YP2/pdb

• Classification: HYDROLASE
• Organism(s): Momordica charantia
• Mutation(s): No 


• Deposited: 2015-03-12 Released: 2015-05-20 
• Deposition Author(s): Vinkovic, M., Hussain, J., Wood, G.E., Gill, R., Wood, S.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.168 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

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 F Struct Biol Commun 71: 1152-1155

• PubMed: 26323301 
• DOI: https://doi.org/10.1107/S2053230X15013540
• Primary Citation Related Structures: 
  4YP2, 5CF9


• 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 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.

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Organizational Affiliation: 
• Astex Therapeutics, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, England.
School of Biological Science, University of Southampton, Highfield, Southampton SO16 7PX, England.
Poole Hospital NHS Foundation Trust, Longfleet Road, Poole BH15 2JB, England.
Department of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, England.
Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.74 kDa 
• Atom Count: 2,264 
• Modeled Residue Count: 246 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome-inactivating protein momordin I	A [auth B]	246	Momordica charantia	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P16094 (Momordica charantia) Explore P16094  Go to UniProtKB:  P16094
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NCA	C [auth B]	NICOTINAMIDE C6 H6 N2 O DFPAKSUCGFBDDF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.168 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.1	α = 90
b = 130.1	β = 90
c = 37.57	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
PDB_EXTRACT	data extraction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-20 
Deposition Author(s): Vinkovic, M., Hussain, J., Wood, G.E., Gill, R., Wood, S.P.

Revision History  

• Version 1.0: 2015-05-20
  Type: Initial release
  
• Version 1.1: 2015-09-09
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-11-13
  Changes: Structure summary