4U2Y

Sco GlgEI-V279S in Complex with Reaction Intermediate Azasugar


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.483 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of Mycobacterium tuberculosis GlgE and complexes with non-covalent inhibitors.

Lindenberger, J.J.Kumar Veleti, S.Wilson, B.N.Sucheck, S.J.Ronning, D.R.

(2015) Sci Rep 5: 12830-12830

  • DOI: 10.1038/srep12830
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • GlgE is a bacterial maltosyltransferase that catalyzes the elongation of a cytosolic, branched α-glucan. In Mycobacterium tuberculosis (M. tb), inactivation of GlgE (Mtb GlgE) results in the rapid death of the organism due to a toxic accumulation of ...

    GlgE is a bacterial maltosyltransferase that catalyzes the elongation of a cytosolic, branched α-glucan. In Mycobacterium tuberculosis (M. tb), inactivation of GlgE (Mtb GlgE) results in the rapid death of the organism due to a toxic accumulation of the maltosyl donor, maltose-1-phosphate (M1P), suggesting that GlgE is an intriguing target for inhibitor design. In this study, the crystal structures of the Mtb GlgE in a binary complex with maltose and a ternary complex with maltose and a maltosyl-acceptor molecule, maltohexaose, were solved to 3.3 Å and 4.0 Å, respectively. The maltohexaose structure reveals a dominant site for α-glucan binding. To obtain more detailed interactions between first generation, non-covalent inhibitors and GlgE, a variant Streptomyces coelicolor GlgEI (Sco GlgEI-V279S) was made to better emulate the Mtb GlgE M1P binding site. The structure of Sco GlgEI-V279S complexed with α-maltose-C-phosphonate (MCP), a non-hydrolyzable substrate analogue, was solved to 1.9 Å resolution, and the structure of Sco GlgEI-V279S complexed with 2,5-dideoxy-3-O-α-D-glucopyranosyl-2,5-imino-D-mannitol (DDGIM), an oxocarbenium mimic, was solved to 2.5 Å resolution. These structures detail important interactions that contribute to the inhibitory activity of these compounds, and provide information on future designs that may be exploited to improve upon these first generation GlgE inhibitors.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, The University of Toledo, 2801 W. Bancroft St. Ms602, Toledo, OH, United States.




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
RZM
Query on RZM

Download SDF File 
Download CCD File 
A, B
(2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl alpha-D-glucopyranoside
C12 H23 N O9
AZDBETUGBOOBRU-BBFNFCGLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.483 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.175 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 113.829α = 90.00
b = 113.829β = 90.00
c = 314.070γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

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: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-08-19
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations