4OQD

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

PDB DOI: https://doi.org/10.2210/pdb4OQD/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.216
R-Value Work: 0.181
R-Value Observed: 0.182

Starting Model: experimental
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Ligand Structure Quality Assessment

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

PubMed: 24512254 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 117.99 kDa
Atom Count: 8,244
Modelled Residue Count: 960
Deposited Residue Count: 1,052
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase	A, B, C, D	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P95748
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QDM Query on QDM Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	TDP-3,6-dideoxy-3-N,N-dimethylglucose C₁₈ H₃₁ N₃ O₁₄ P₂ IJJNPDQFXCRKOA-WHRNYZGVSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.216
R-Value Work: 0.181
R-Value Observed: 0.182
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.532	α = 90
b = 92.05	β = 106.1
c = 80.177	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-02-26

Deposition Author(s):

Thoden, J.B.

Holden, H.M.

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