4OQE | pdb_00004oqe

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

• PDB DOI: https://doi.org/10.2210/pdb4OQE/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces fradiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-02-08 Released: 2014-02-26 
• Deposition Author(s): Thoden, J.B., Holden, H.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.277 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Production of a novel N-monomethylated dideoxysugar.

Thoden, J.B., Holden, H.M.

(2014) Biochemistry 53: 1105-1107

• PubMed: 24512254 
• DOI: https://doi.org/10.1021/bi500098a
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.97 kDa 
• Atom Count: 3,995 
• Modeled Residue Count: 479 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase	A, B	263	Streptomyces fradiae	Mutation(s): 0  Gene Names: tylM1, tylMI EC: 2.1.1.235
UniProt
Find proteins for P95748 (Streptomyces fradiae) Explore P95748  Go to UniProtKB:  P95748

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MMF	D [auth A], F [auth B]	dTDP-3-N-methylamino-3,6-dideoxygalactose C17 H29 N3 O14 P2 CDWXXXLIBVLVLM-KYQZRJCOSA-N
SAH	C [auth A], E [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.277 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.885	α = 90
b = 92.938	β = 97.29
c = 77.879	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
PHASER	phasing
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-26 
Deposition Author(s): Thoden, J.B., Holden, H.M.

Revision History  

• 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