5XVK

Crystal structure of mouse Nicotinamide N-methyltransferase (NNMT) bound with end product, 1-methyl Nicotinamide (MNA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Crystal structures of monkey and mouse nicotinamide N-methyltransferase (NNMT) bound with end product, 1-methyl nicotinamide

Swaminathan, S.Birudukota, S.Thakur, M.K.Parveen, R.Kandan, S.Juluri, S.Shaik, S.Anand, N.N.Burri, R.R.Kristam, R.Hallur, M.S.Rajagopal, S.Schreuder, H.Langer, T.Rudolph, C.Ruf, S.Dhakshinamoorthy, S.Gosu, R.Kannt, A.

(2017) Biochem. Biophys. Res. Commun. 491: 416-422

  • DOI: 10.1016/j.bbrc.2017.07.087
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nicotinamide N-methyltransferase (NNMT) is a S-adenosyl-l-methionine (SAM)-dependent enzyme that catalyzes N-methylation of nicotinamide (NA) and other pyridines to form N-methyl pyridinium ions. Here we report the first ternary complex X-ray crystal ...

    Nicotinamide N-methyltransferase (NNMT) is a S-adenosyl-l-methionine (SAM)-dependent enzyme that catalyzes N-methylation of nicotinamide (NA) and other pyridines to form N-methyl pyridinium ions. Here we report the first ternary complex X-ray crystal structures of monkey NNMT and mouse NNMT in bound form with the primary endogenous product, 1-methyl nicotinamide (MNA) and demethylated cofactor, S-adenosyl-homocysteine (SAH) determined at 2.30 Å and 1.88 Å respectively. The structural fold of these enzymes is identical to human NNMT. It is known that the primary endogenous product catalyzed by NNMT, MNA is a specific inhibitor of NNMT. Our data clearly indicates that the MNA binds to the active site and it would be trapped in the active site due to the formation of the bridge between the pole (long helix, α3) and long C-terminal loop. This might explain the mechanism of MNA acting as a feedback inhibitor of NNMT.


    Organizational Affiliation

    Department of Structural Biology, Jubilant Biosys Ltd, Bangalore 560022, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nicotinamide N-methyltransferase
A, B
284Mus musculusMutation(s): 0 
Gene Names: Nnmt
EC: 2.1.1.1
Find proteins for O55239 (Mus musculus)
Go to UniProtKB:  O55239
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8GC
Query on 8GC

Download SDF File 
Download CCD File 
A, B
3-carbamoyl-1-methylpyridin-1-ium
1-methylnicotinamide
C7 H9 N2 O
LDHMAVIPBRSVRG-UHFFFAOYSA-O
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.138α = 90.00
b = 71.699β = 90.00
c = 157.042γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-08-23
    Type: Database references
  • Version 2.0: 2018-03-14
    Type: Non-polymer description, Structure summary