5BSZ

X-ray structure of the sugar N-methyltransferase KedS8 from Streptoalloteichus sp ATCC 53650


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular architecture of KedS8, a sugar N-methyltransferase from Streptoalloteichus sp. ATCC 53650.

Delvaux, N.A.Thoden, J.B.Holden, H.M.

(2015) Protein Sci. 24: 1593-1599

  • DOI: 10.1002/pro.2742

  • PubMed Abstract: 
  • Kedarcidin, produced by Streptoalloteichus sp. ATCC 53650, is a fascinating chromoprotein of 114 amino acid residues that displays both antibiotic and anticancer activity. The chromophore responsible for its chemotherapeutic activity is an ansa-bridg ...

    Kedarcidin, produced by Streptoalloteichus sp. ATCC 53650, is a fascinating chromoprotein of 114 amino acid residues that displays both antibiotic and anticancer activity. The chromophore responsible for its chemotherapeutic activity is an ansa-bridged enediyne with two attached sugars, l-mycarose, and l-kedarosamine. The biosynthesis of l-kedarosamine, a highly unusual trideoxysugar, is beginning to be revealed through bioinformatics approaches. One of the enzymes putatively involved in the production of this carbohydrate is referred to as KedS8. It has been proposed that KedS8 is an N-methyltransferase that utilizes S-adenosylmethionine as the methyl donor and a dTDP-linked C-4' amino sugar as the substrate. Here we describe the three-dimensional architecture of KedS8 in complex with S-adenosylhomocysteine. The structure was solved to 2.0 Å resolution and refined to an overall R-factor of 17.1%. Unlike that observed for other sugar N-methyltransferases, KedS8 adopts a novel tetrameric quaternary structure due to the swapping of β-strands at the N-termini of its subunits. The structure presented here represents the first example of an N-methyltransferase that functions on C-4' rather than C-3' amino sugars.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-methyltransferase
A
250Streptoalloteichus sp. ATCC 53650Mutation(s): 0 
Find proteins for K4P132 (Streptoalloteichus sp. ATCC 53650)
Go to UniProtKB:  K4P132
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
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
THM
Query on THM

Download SDF File 
Download CCD File 
A
THYMIDINE
DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE
C10 H14 N2 O5
IQFYYKKMVGJFEH-XLPZGREQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.168 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 63.254α = 90.00
b = 81.004β = 90.00
c = 126.916γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SAINTdata reduction
REFMACrefinement
SADABSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2015-10-14
    Type: Database references