4OQE

Crystal structure of the tylM1 N,N-dimethyltransferase in complex with SAH and TDP-Fuc3NMe

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 

Starting Model: experimental
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This is version 1.2 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: https://doi.org/10.1021/bi500098a
  • Primary Citation of Related Structures:  
    4OQD, 4OQE

  • 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 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
A, B
263Streptomyces fradiaeMutation(s): 0 
Gene Names: tylM1, tylMI
EC: 2.1.1.235
UniProt
Find proteins for P95748 (Streptomyces fradiae)
Explore P95748 
Go to UniProtKB:  P95748
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP95748
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.885α = 90
b = 92.938β = 97.29
c = 77.879γ = 90
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
PHASERphasing
REFMACrefinement
SAINTdata reduction
SADABSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2014-03-19
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description