2JFB

3D Structure of Lumazine Synthase from Candida albicans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Lumazine Synthase from Candida Albicans as an Anti- Fungal Target Enzyme: Structural and Biochemical Basis for Drug Design.

Morgunova, E.Saller, S.Haase, I.Cushman, M.Bacher, A.Fischer, M.Ladenstein, R.

(2007) J Biol Chem 282: 17231

  • DOI: https://doi.org/10.1074/jbc.M701724200
  • Primary Citation of Related Structures:  
    2JFB

  • PubMed Abstract: 

    Lumazine synthase is an enzyme involved in riboflavin biosynthesis in many plants and microorganisms, including numerous human pathogens. The fact that the enzymes of the riboflavin biosynthesis pathway are not present in the human or animal host makes them potential targets for anti-infective agents. The crystal structure of lumazine synthase from Candida albicans was solved by molecular replacement and refined at 2.5-Angstrom resolution. The results of crystallographic investigations and sedimentation equilibrium experiments clearly indicated the presence of pentameric assemblies of the enzyme either in crystals or in solution. Isothermal titration calorimetry measurements of the binding reactions of four different inhibitors revealed high affinity for all four compounds with binding constants in the micromolar range. Structural comparison with previously determined structures of the enzyme.ligand complexes of other orthologue allowed modeling of the binding of four different inhibitors into the active site of lumazine synthase from Candida albicans.


  • Organizational Affiliation

    Karolinska Institutet, NOVUM, Centre for Structural Biochemistry, Halsovagen 7-9, S-14157 Huddinge, Sweden. katja.morgunova@biosci.ki.se


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
164Candida albicansMutation(s): 0 
EC: 2.5.1.9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
CA [auth K],
T [auth D],
Y [auth H]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AA [auth J]
BA [auth K]
DA [auth L]
EA [auth M]
FA [auth N]
AA [auth J],
BA [auth K],
DA [auth L],
EA [auth M],
FA [auth N],
GA [auth O],
P [auth A],
Q [auth B],
R [auth C],
S [auth D],
U [auth E],
V [auth F],
W [auth G],
X [auth H],
Z [auth I]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.648α = 90
b = 128.648β = 90
c = 284.965γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-01
    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
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description