3MK3

Crystal structure of Lumazine synthase from Salmonella typhimurium LT2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.569 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal structure analysis of icosahedral lumazine synthase from Salmonella typhimurium, an antibacterial drug target.

Kumar, P., Singh, M., Karthikeyan, S.

(2011) Acta Crystallogr.,Sect.D 67: 131-139

  • DOI: 10.1107/S0907444910053370

  • PubMed Abstract: 

    • Riboflavin biosynthesis is an essential pathway in bacteria, in contrast to animals, which obtain riboflavin from their diet. Therefore, the enzymes involved in the riboflavin-biosynthesis pathway are potential targets for the development of antibact ...

    Riboflavin biosynthesis is an essential pathway in bacteria, in contrast to animals, which obtain riboflavin from their diet. Therefore, the enzymes involved in the riboflavin-biosynthesis pathway are potential targets for the development of antibacterial drugs. Lumazine synthase, an enzyme that is involved in the penultimate step of riboflavin biosynthesis, catalyzes the formation of 6,7-dimethyl-8-ribityllumazine from 3,4-dihydroxy-2-butanone 4-phosphate and 5-amino-6-ribitylamino-2,4-(1H,3H)-pyrimidinedione. Lumazine synthase from Salmonella typhimurium (sLS) has been cloned, overexpressed, purified and was crystallized in three forms, each with different crystal packing. The crystal structure of sLS in the monoclinic space group P2(1) has been determined with 60 subunits per asymmetric unit, packed as an icosahedron, at 3.57 Å resolution. Interestingly, sLS contains an N-terminal proline residue (Pro11) which had previously been suggested to disrupt the formation of the icosohedral assembly. In addition, comparison of the structure of sLS with known orthologous lumazine synthase structures allowed identification of the amino-acid residues involved in substrate binding and catalysis. The sLS structure reported here could serve as a starting point for the development of species-specific antibacterial drugs.

    Organizational Affiliation: 

    Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh 160 036, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6,7-dimethyl-8-ribityllumazine synthase
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 1, 2, 3, 4, 5, 6, 7, 8, 9, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y
156Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: ribH
EC: 2.5.1.78
Find proteins for P66038 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P66038
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
1, 2, 3, 5, 6, 7, 8, 9, a, A, B, b, D, d, E, e, f, F, G, g, H, h, I, i, J, K, k, l, L, m, M, n, O, o, P, p, q, Q, R, s, T, U, u, v, V, W, X, x, Y, y, Z
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.569 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 154.234α = 90.00
b = 151.503β = 97.08
c = 235.032γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
CCP4model building
HKL-2000data scaling
MAR345dtbdata collection
CCP4phasing
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-01-23
    Type: Structure summary