1W29

Lumazine Synthase from Mycobacterium tuberculosis bound to 3-(1,3,7- trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)butane 1-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of Lumazine Synthase from Mycobacterium Tuberculosis as a Target for Rational Drug Design: Binding Mode of a New Class of Purinetrione Inhibitors(,)

Morgunova, E.Meining, W.Illarionov, B.Haase, I.Jin, G.Bacher, A.Cushman, M.Fischer, M.Ladenstein, R.

(2005) Biochemistry 44: 2746

  • DOI: 10.1021/bi047848a
  • Primary Citation of Related Structures:  
    1W19, 1W29

  • PubMed Abstract: 
  • The enzymes involved in the biosynthesis of riboflavin represent attractive targets for the development of drugs against bacterial pathogens, because the inhibitors of these enzymes are not likely to interfere with enzymes of the mammalian metabolism. Lumazine synthase catalyzes the penultimate step in the riboflavin biosynthesis pathway ...

    The enzymes involved in the biosynthesis of riboflavin represent attractive targets for the development of drugs against bacterial pathogens, because the inhibitors of these enzymes are not likely to interfere with enzymes of the mammalian metabolism. Lumazine synthase catalyzes the penultimate step in the riboflavin biosynthesis pathway. A number of substituted purinetrione compounds represent a new class of highly specific inhibitors of lumazine synthase from Mycobacterium tuberculosis. To develop potent antibiotics for the treatment of tuberculosis, we have determined the structure of lumazine synthase from M. tuberculosis in complex with two purinetrione inhibitors and have studied binding via isothermal titration calorimetry. The structures were determined by molecular replacement using lumazine synthase from Saccharomyces cerevisiae as a search model and refined at 2 and 2.3 A resolution. The R-factors were 14.7 and 17.4%, respectively, and the R(free) values were 19.3 and 26.3%, respectively. The enzyme was found to be a pentamer consisting of five subunits related by 5-fold local symmetry. The comparison of the active site architecture with the active site of previously determined lumazine synthase structures reveals a largely conserved topology with the exception of residues Gln141 and Glu136, which participate in different charge-charge interactions in the core space of the active site. The impact of structural changes in the active site on the altered binding and catalytic properties of the enzyme is discussed. Isothermal titration calorimetry measurements indicate highly specific binding of the purinetrione inhibitors to the M. tuberculosis enzyme with dissociation constants in micromolar range.


    Organizational Affiliation

    Karolinska Institutet, NOVUM, Centre for Structural Biochemistry, S-14157 Huddinge, Sweden. katja.morgunova@biosci.ki.se



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASEA, B, C, D, E160Mycobacterium tuberculosisMutation(s): 0 
EC: 2.5.1.9 (PDB Primary Data), 2.5.1.78 (UniProt)
UniProt
Find proteins for P9WHE9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHE9 
Go to UniProtKB:  P9WHE9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TS0 (Subject of Investigation/LOI)
Query on TS0

Download Ideal Coordinates CCD File 
U [auth D]4-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL DIHYDROGEN PHOSPHATE
C14 H23 N4 O11 P
VBXZSBKAJFXURR-QXFUBDJGSA-N
 Ligand Interaction
TS1 (Subject of Investigation/LOI)
Query on TS1

Download Ideal Coordinates CCD File 
G [auth A], L [auth B], P [auth C], Y [auth E]4-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL DIHYDROGEN PHOSPHATE
C14 H23 N4 O11 P
VBXZSBKAJFXURR-MRTMQBJTSA-N
 Ligand Interaction
D1D (Subject of Investigation/LOI)
Query on D1D

Download Ideal Coordinates CCD File 
BA [auth E](4S,5S)-1,2-DITHIANE-4,5-DIOL
C4 H8 O2 S2
YPGMOWHXEQDBBV-QWWZWVQMSA-N
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
F [auth A], K [auth B], T [auth D], X [auth E]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
AA [auth E] , H [auth A] , I [auth A] , J [auth A] , M [auth B] , N [auth B] , O [auth B] , Q [auth C] , 
AA [auth E],  H [auth A],  I [auth A],  J [auth A],  M [auth B],  N [auth B],  O [auth B],  Q [auth C],  R [auth C],  S [auth C],  V [auth D],  W [auth D],  Z [auth E]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.37α = 90
b = 80.758β = 120.18
c = 85.965γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-04-10
    Changes: Data collection, Other, Source and taxonomy
  • Version 1.3: 2019-07-24
    Changes: Data collection