5H8U

Crystal structure of mycobacterium tuberculosis wild-type malate synthase in complex with product malate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    5C7V, 5C9U, 5C9X, 5C9W, 5C9R, 5CAK, 5CAH, 5CBI, 5CBJ, 5CBB

  • 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 Mycobacterium tuberculosis and discovered several novel binding chemotypes ...

    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 IC 50 value of 20 nm.


    Related Citations: 
    • 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
    • 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

    Organizational Affiliation

    Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Malate synthase G AB741Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: glcBRv1837cMTCY1A11.06
EC: 2.3.3.9
Find proteins for P9WK17 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WK17 
Go to UniProtKB:  P9WK17
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMR
Query on LMR

Download Ideal Coordinates CCD File 
A
(2S)-2-hydroxybutanedioic acid
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
 Ligand Interaction
GLV
Query on GLV

Download Ideal Coordinates CCD File 
B
GLYOXYLIC ACID
C2 H2 O3
HHLFWLYXYJOTON-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.659α = 90
b = 120.659β = 90
c = 232.224γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1024055

Revision History  (Full details and data files)

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