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 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 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: https://doi.org/10.1016/j.bbrc.2017.07.087
  • Primary Citation of Related Structures:  
    5XVK, 5XVQ

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nicotinamide N-methyltransferase
A, B
284Mus musculusMutation(s): 0 
Gene Names: Nnmt
EC: 2.1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for O55239 (Mus musculus)
Explore O55239 
Go to UniProtKB:  O55239
IMPC:  MGI:1099443
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO55239
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.138α = 90
b = 71.699β = 90
c = 157.042γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Database references
  • Version 2.0: 2018-03-14
    Changes: Non-polymer description, Structure summary
  • Version 2.1: 2019-12-04
    Changes: Data collection
  • Version 2.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description