5XVQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

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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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nicotinamide N-methyltransferase (NNMT)
A, B
284Macaca mulattaMutation(s): 0 
Gene Names: NNMTEGK_06915
UniProt
Find proteins for F7ERX8 (Macaca mulatta)
Explore F7ERX8 
Go to UniProtKB:  F7ERX8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF7ERX8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.071α = 90
b = 65.028β = 89.97
c = 91.144γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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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: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary