5MGZ | pdb_00005mgz

Streptomyces Spheroides NovO (8-demethylnovbiocic acid methyltransferase) with SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.202 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SAHClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Structural and Functional Basis of C-Methylation of Coumarin Scaffolds by NovO.

Sadler, J.C.Chung, C.H.Mosley, J.E.Burley, G.A.Humphreys, L.D.

(2017) ACS Chem Biol 12: 374-379

  • DOI: https://doi.org/10.1021/acschembio.6b01053
  • Primary Citation of Related Structures:  
    5MGZ

  • PubMed Abstract: 

    C-methylation of aromatic small molecules by C-methyltransferases (C-MTs) is an important biological transformation that involves C-C bond formation using S-adenosyl-l-methionine (SAM) as the methyl donor. Here, two advances in the mechanistic understanding of C-methylation of the 8-position of coumarin substrates catalyzed by the C-MT NovO from Streptomyces spheroides are described. First, a crystal structure of NovO reveals the Arg116-Asn117 and His120-Arg121 motifs are essential for coumarin substrate binding. Second, the active-site His120 is responsible for deprotonation of the phenolic 7-hydroxyl group on the coumarin substrate, activating the rate-determining methyl transfer step from SAM. This work expands our mechanistic knowledge of C-MTs, which could be used in the downstream development of engineered biocatalysts for small molecule C-alkylations.


  • Organizational Affiliation

    GlaxoSmithKline Medicines Research Centre , Gunnels Wood Road, Stevenage, SG1 2NY , United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
8-demethylnovobiocic acid C(8)-methyltransferase
A, B
236Streptomyces niveusMutation(s): 0 
Gene Names: novO
EC: 2.1.1.284
UniProt
Find proteins for Q9L9F3 (Streptomyces niveus)
Explore Q9L9F3 
Go to UniProtKB:  Q9L9F3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9L9F3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.202 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.724α = 90
b = 66.97β = 92.99
c = 80.563γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SAHClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references