3PFG

X-Ray crystal structure the N,N-dimethyltransferase TylM1 from Streptomyces fradiae in complex with SAM and dTDP-phenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.349 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular Architecture of TylM1 from Streptomyces fradiae: An N,N-Dimethyltransferase Involved in the Production of dTDP-d-mycaminose .

Carney, A.E.Holden, H.M.

(2011) Biochemistry 50: 780-787

  • DOI: 10.1021/bi101733y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • d-Mycaminose is an unusual dideoxy sugar found attached to the antibiotic tylosin, a commonly used veterinarian therapeutic. It is synthesized by the Gram-positive bacterium Streptomyces fradiae as a dTDP-linked sugar. The last step in its biosynthes ...

    d-Mycaminose is an unusual dideoxy sugar found attached to the antibiotic tylosin, a commonly used veterinarian therapeutic. It is synthesized by the Gram-positive bacterium Streptomyces fradiae as a dTDP-linked sugar. The last step in its biosynthesis involves the dimethylation of the hexose C-3' amino group by an S-adenosylmethionine (SAM) dependent enzyme referred to as TylM1. Here we report two high-resolution X-ray structures of TylM1, one in which the enzyme contains bound SAM and dTDP-phenol and the second in which the protein is complexed with S-adenosylhomocysteine (SAH) and dTDP-3-amino-3,6-dideoxyglucose, its natural substrate. Combined, these two structures, solved to 1.35 and 1.79 Å resolution, respectively, show the orientations of SAM and the dTDP-linked sugar substrate within the active site region. Specifically, the C-3' amino group of the hexose is in the correct position for an in-line attack at the reactive methyl group of SAM. Both Tyr 14 and Arg 241 serve to anchor the dTDP-linked sugar to the protein. To test the role of His 123 in catalysis, two site-directed mutant proteins were constructed, H123A and H123N. Both mutant proteins retained catalytic activity, albeit with reduced rates. Specifically, the k(cat)/K(m) was reduced to 1.8% and 0.37% for the H123A and H123N mutant proteins, respectively. High-resolution X-ray models showed that the observed perturbations in the kinetic constants were not due to major changes in their three-dimensional folds. Most likely the proton on the C-3' amino group is transferred to one of the water molecules lining the active site pocket as catalysis proceeds.


    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
N-methyltransferase
A
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

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

Download SDF File 
Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
TLO
Query on TLO

Download SDF File 
Download CCD File 
A
5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine
thymidine diphosphate phenol
C16 H20 N2 O11 P2
BANJVYKYIQPYKP-BFHYXJOUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.349 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.079α = 90.00
b = 41.382β = 121.21
c = 86.637γ = 90.00
Software Package:
Software NamePurpose
SADABSdata scaling
REFMACrefinement
PROTEUM PLUSdata collection
PHASERphasing
SAINTdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance