PDBsum entry 3mk3

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Transferase PDB id
Protein chains
(+ 54 more) 154 a.a. *
SO4 ×79
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of lumazine synthase from salmonella typhi
Structure: 6,7-dimethyl-8-ribityllumazine synthase. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r v, w, x, y, z, 1, 2, 3, 4, 5, 6, 7, 8, 9, a, b, c, d, e, f, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y. Synonym: dmrl synthase, lumazine synthase, riboflavin synth chain. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 99287. Strain: lt2. Gene: ribh, stm0417. Expressed in: escherichia coli. Expression_system_taxid: 562.
3.57Å     R-factor:   0.226     R-free:   0.264
Authors: P.Kumar,M.Singh,S.Karthikeyan
Key ref: P.Kumar et al. (2011). Crystal structure analysis of icosahedral lumazine synthase from Salmonella typhimurium, an antibacterial drug target. Acta Crystallogr D Biol Crystallogr, 67, 131-139. PubMed id: 21245535 DOI: 10.1107/S0907444910053370
14-Apr-10     Release date:   02-Feb-11    
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Protein chains
Pfam   ArchSchema ?
P66038  (RISB_SALTY) -  6,7-dimethyl-8-ribityllumazine synthase
156 a.a.
154 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 6,7-dimethyl-8-ribityllumazine synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6- (D-ribitylamino)uracil = 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate
1-deoxy-L-glycero-tetrulose 4-phosphate
+ 5-amino-6- (D-ribitylamino)uracil
= 6,7-dimethyl-8-(D-ribityl)lumazine
+ 2 × H(2)O
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     riboflavin synthase complex   1 term 
  Biological process     riboflavin biosynthetic process   1 term 
  Biochemical function     transferase activity     2 terms  


DOI no: 10.1107/S0907444910053370 Acta Crystallogr D Biol Crystallogr 67:131-139 (2011)
PubMed id: 21245535  
Crystal structure analysis of icosahedral lumazine synthase from Salmonella typhimurium, an antibacterial drug target.
P.Kumar, M.Singh, S.Karthikeyan.
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.