4U2Z

X-ray crystal structure of an Sco GlgEI-V279S/1,2,2-trifluromaltose complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Synthesis of 2-deoxy-2,2-difluoro-alpha-maltosyl fluoride and its X-ray structure in complex with Streptomyces coelicolor GlgEI-V279S.

Thanna, S.Lindenberger, J.J.Gaitonde, V.V.Ronning, D.R.Sucheck, S.J.

(2015) Org.Biomol.Chem. 13: 7542-7550

  • DOI: 10.1039/c5ob00867k

  • PubMed Abstract: 
  • Streptomyces coelicolor (Sco) GlgEI is a glycoside hydrolase involved in α-glucan biosynthesis and can be used as a model enzyme for structure-based inhibitor design targeting Mycobacterium tuberculosis (Mtb) GlgE. The latter is a genetically validat ...

    Streptomyces coelicolor (Sco) GlgEI is a glycoside hydrolase involved in α-glucan biosynthesis and can be used as a model enzyme for structure-based inhibitor design targeting Mycobacterium tuberculosis (Mtb) GlgE. The latter is a genetically validated drug target for the development of anti-Tuberculosis (TB) treatments. Inhibition of Mtb GlgE results in a lethal buildup of the GlgE substrate maltose-1-phosphate (M1P). However, Mtb GlgE is difficult to crystallize and affords lower resolution X-ray structures. Sco GlgEI-V279S on the other hand crystallizes readily, produces high resolution X-ray data, and has active site topology identical to Mtb GlgE. We report the X-ray structure of Sco GlgEI-V279S in complex with 2-deoxy-2,2-difluoro-α-maltosyl fluoride (α-MTF, 5) at 2.3 Å resolution. α-MTF was designed as a non-hydrolysable mimic of M1P to probe the active site of GlgE1 prior to covalent bond formation without disruption of catalytic residues. The α-MTF complex revealed hydrogen bonding between Glu423 and the C1F which provides evidence that Glu423 functions as proton donor during catalysis. Further, hydrogen bonding between Arg392 and the axial C2 difluoromethylene moiety of α-MTF was observed suggesting that the C2 position tolerates substitution with hydrogen bond acceptors. The key step in the synthesis of α-MDF was transformation of peracetylated 2-fluoro-maltal 1 into peracetylated 2,2-difluoro-α-maltosyl fluoride 2 in a single step via the use of Selectfluor®.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, The University of Toledo, 2801 W. Bancroft Street, MS602, Toledo, OH, USA 43606. donald.ronning@utoledo.edu steve.sucheck@utoledo.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
A, B
683Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)Mutation(s): 1 
Gene Names: glgE1 (pep1, pep1A, pep1I)
EC: 2.4.99.16
Find proteins for Q9L1K2 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Go to UniProtKB:  Q9L1K2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMO
Query on FMO

Download SDF File 
Download CCD File 
A, B
2-deoxy-2,2-difluoro-4-O-alpha-D-glucopyranosyl-alpha-D-arabino-hexopyranosyl fluoride
1,2,2-trifluoromaltose
C12 H19 F3 O9
XXSHXGUAEVMBMC-DEIBAFIGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.163 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 113.297α = 90.00
b = 113.297β = 90.00
c = 314.330γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-3000phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI105084

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-08-12
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Refinement description