2WK1

Structure of the O-methyltransferase NovP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Crystal Structure of the Novobiocin Biosynthetic Enzyme Novp: The First Representative Structure for the Tylf O-Methyltransferase Superfamily.

Gomez Garcia, I.Stevenson, C.E.M.Uson, I.Freel Meyers, C.L.Walsh, C.T.Lawson, D.M.

(2010) J.Mol.Biol. 395: 390

  • DOI: 10.1016/j.jmb.2009.10.045

  • PubMed Abstract: 
  • NovP is an S-adenosyl-l-methionine-dependent O-methyltransferase that catalyzes the penultimate step in the biosynthesis of the aminocoumarin antibiotic novobiocin. Specifically, it methylates at 4-OH of the noviose moiety, and the resultant methoxy ...

    NovP is an S-adenosyl-l-methionine-dependent O-methyltransferase that catalyzes the penultimate step in the biosynthesis of the aminocoumarin antibiotic novobiocin. Specifically, it methylates at 4-OH of the noviose moiety, and the resultant methoxy group is important for the potency of the mature antibiotic: previous crystallographic studies have shown that this group interacts directly with the target enzyme DNA gyrase, which is a validated drug target. We have determined the high-resolution crystal structure of NovP from Streptomyces spheroides as a binary complex with its desmethylated cosubstrate S-adenosyl-l-homocysteine. The structure displays a typical class I methyltransferase fold, in addition to motifs that are consistent with a divalent-metal-dependent mechanism. This is the first representative structure of a methyltransferase from the TylF superfamily, which includes a number of enzymes implicated in the biosynthesis of antibiotics and other therapeutics. The NovP structure reveals a number of distinctive structural features that, based on sequence conservation, are likely to be characteristic of the superfamily. These include a helical 'lid' region that gates access to the cosubstrate binding pocket and an active center that contains a 3-Asp putative metal binding site. A further conserved Asp likely acts as the general base that initiates the reaction by deprotonating the 4-OH group of the noviose unit. Using in silico docking, we have generated models of the enzyme-substrate complex that are consistent with the proposed mechanism. Furthermore, these models suggest that NovP is unlikely to tolerate significant modifications at the noviose moiety, but could show increasing substrate promiscuity as a function of the distance of the modification from the methylation site. These observations could inform future attempts to utilize NovP for methylating a range of glycosylated compounds.


    Related Citations: 
    • Structure Determination of the O-Methyltransferase Novp Using the 'Free Lunch Algorithm' as Implemented in Shelxe.
      Uson, I.,Stevenson, C.E.M.,Lawson, D.M.,Sheldrick, G.M.
      (2007) Acta Crystallogr.,Sect.D 63: 1069
    • Crystallization and Preliminary X-Ray Analysis of the O-Methyltransferase Novp from the Novobiocin-Biosynthetic Cluster of Streptomyces Spheroides.
      Stevenson, C.E.M.,Freel Meyers, C.L.,Walsh, C.T.,Lawson, D.M.
      (2007) Acta Crystallogr.,Sect.F 63: 236


    Organizational Affiliation

    Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NOVP
A
282Streptomyces niveusMutation(s): 0 
Gene Names: novP
EC: 2.1.1.285
Find proteins for Q9L9F2 (Streptomyces niveus)
Go to UniProtKB:  Q9L9F2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.145 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 51.813α = 90.00
b = 46.038β = 104.97
c = 61.220γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-15
    Type: Initial release
  • Version 1.1: 2011-06-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance