4OQD

Crystal structure of the tylM1 N,N-dimethyltransferase in complex with SAH and TDP-Qui3NMe2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Production of a novel N-monomethylated dideoxysugar.

Thoden, J.B.Holden, H.M.

(2014) Biochemistry 53: 1105-1107

  • DOI: 10.1021/bi500098a
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The importance of unusual deoxysugars in biology has become increasingly apparent over the past decade. Some, for example, play key roles in the physiological activities of the natural products to which they are attached. Here we describe a study of ...

    The importance of unusual deoxysugars in biology has become increasingly apparent over the past decade. Some, for example, play key roles in the physiological activities of the natural products to which they are attached. Here we describe a study of TylM1, a dimethyltransferase from Streptomyces fradiae involved in the production of dTDP-mycaminose. From this investigation, the manner in which the enzyme binds its dimethylated product has been revealed. More significantly, by providing the enzyme with an alternative substrate, it was possible to produce a monomethylated product not observed in nature. This has important ramifications for the production of unique carbohydrates that may prove useful in drug design.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
A, B, C, D
263Streptomyces fradiaeMutation(s): 0 
Gene Names: tylM1 (tylMI)
EC: 2.1.1.235
Find proteins for P95748 (Streptomyces fradiae)
Go to UniProtKB:  P95748
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QDM
Query on QDM

Download SDF File 
Download CCD File 
A, B, C, D
TDP-3,6-dideoxy-3-N,N-dimethylglucose
C18 H31 N3 O14 P2
IJJNPDQFXCRKOA-WHRNYZGVSA-N
 Ligand Interaction
SAH
Query on SAH

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 73.532α = 90.00
b = 92.050β = 106.10
c = 80.177γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-3000data scaling
HKL-3000data collection
HKL-3000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2014-03-19
    Type: Database references