5CJN

Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 3-(3-oxo-3,4-dihydroquinoxalin-2-yl)acrylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mycobacterium tuberculosis Malate Synthase Structures with Fragments Reveal a Portal for Substrate/Product Exchange.

Huang, H.L.Krieger, I.V.Parai, M.K.Gawandi, V.B.Sacchettini, J.C.

(2016) J. Biol. Chem. 291: 27421-27432

  • DOI: 10.1074/jbc.M116.750877
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fragment screening and high throughput screening are complementary approaches that combine with structural biology to explore the binding capabilities of an active site. We have used a fragment-based approach on malate synthase (GlcB) from Mycobacter ...

    Fragment screening and high throughput screening are complementary approaches that combine with structural biology to explore the binding capabilities of an active site. We have used a fragment-based approach on malate synthase (GlcB) from Mycobacterium tuberculosis and discovered several novel binding chemotypes. In addition, the crystal structures of GlcB in complex with these fragments indicated conformational changes in the active site that represent the enzyme conformations during catalysis. Additional structures of the complex with malate and of the apo form of GlcB supported that hypothesis. Comparative analysis of GlcB structures in complex with 18 fragments allowed us to characterize the preferred chemotypes and their binding modes. The fragment structures showed a hydrogen bond to the backbone carbonyl of Met-631. We successfully incorporated an indole group from a fragment into an existing phenyl-diketo acid series. The resulting indole-containing inhibitor was 100-fold more potent than the parent phenyl-diketo acid with an IC50 value of 20 nm.


    Related Citations: 
    • Structure-guided discovery of phenyl-diketo acids as potent inhibitors of M. tuberculosis malate synthase.
      Krieger, I.V.,Freundlich, J.S.,Gawandi, V.B.,Roberts, J.P.,Gawandi, V.B.,Sun, Q.,Owen, J.L.,Fraile, M.T.,Huss, S.I.,Lavandera, J.L.,Ioerger, T.R.,Sacchettini, J.C.
      (2012) Chem.Biol. 19: 1556
    • Biochemical and structural studies of malate synthase from Mycobacterium tuberculosis.
      Smith, C.V.,Huang, C.C.,Miczak, A.,Russell, D.G.,Sacchettini, J.C.,Honer zu Bentrup, K.
      (2003) J.Biol.Chem. 278: 1735


    Organizational Affiliation

    From the Departments of Chemistry and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Malate synthase G
A
741Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 1 
Gene Names: glcB
EC: 2.3.3.9
Find proteins for P9WK17 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WK17
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
52F
Query on 52F

Download SDF File 
Download CCD File 
A
3-(3-oxo-3,4-dihydroquinoxalin-2-yl)propanoic acid
C11 H10 N2 O3
HROJWOXFEZYMGL-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.171 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.807α = 90.00
b = 78.807β = 90.00
c = 223.823γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
SCALEPACKdata scaling
MOLREPphasing
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1024055

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-10-26
    Type: Database references
  • Version 1.2: 2017-01-11
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence