Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Homo 60-mer - A60 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 968.92 kDa 
• Atom Count: 66544 
• Modelled Residue Count: 9240 
• Deposited Residue Count: 9360 
• Unique protein chains: 1

3MK3

Crystal structure of Lumazine synthase from Salmonella typhimurium LT2

• PDB DOI: 10.2210/pdb3MK3/pdb

• Classification: TRANSFERASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-04-14 Released: 2011-02-02 
• Deposition Author(s): Kumar, P., Singh, M., Karthikeyan, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.57 Å
• R-Value Free: 0.264 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 

Literature

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

Kumar, P., Singh, M., Karthikeyan, S.

(2011) Acta Crystallogr D Biol Crystallogr 67: 131-139

• PubMed: 21245535 
• DOI: 10.1107/S0907444910053370
• Primary Citation of Related Structures:  
  3MK3


• 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 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6,7-dimethyl-8-ribityllumazine synthase	AA [auth 1], BA [auth 2], CA [auth 3], DA [auth 4], EA [auth 5], FA [auth 6], GA [auth 7], HA [auth 8], IA [auth 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, Z, JA [auth a], KA [auth b], LA [auth c], MA [auth d], NA [auth e], OA [auth f], PA [auth g], QA [auth h], RA [auth i], SA [auth j], TA [auth k], UA [auth l], VA [auth m], WA [auth n], XA [auth o], YA [auth p], ZA [auth q], AB [auth r], BB [auth s], CB [auth t], DB [auth u], EB [auth v], FB [auth w], GB [auth x], HB [auth y]	156	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: ribH, STM0417 EC: 2.5.1.78
UniProt
Find proteins for P66038 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P66038  Go to UniProtKB:  P66038

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AC [auth M], AD [auth 7], AE [auth q], BC [auth M], BD [auth 8], BE [auth q], CC [auth M], CD [auth 9], CE [auth s], DC [auth O], DD [auth a], DE [auth s], EC [auth P], ED [auth b], EE [auth u], FC [auth P], FD [auth b], FE [auth v], GC [auth Q], GD [auth b], GE [auth x], HC [auth R], HD [auth d], HE [auth x], IB [auth A], IC [auth R], ID [auth d], IE [auth y], JB [auth B], JC [auth T], JD [auth e], KB [auth B], KC [auth U], KD [auth f], LB [auth B], LC [auth V], LD [auth g], MB [auth D], MC [auth W], MD [auth h], NB [auth D], NC [auth X], ND [auth h], OB [auth E], OC [auth Y], OD [auth h], PB [auth F], PC [auth Z], PD [auth i], QB [auth F], QC [auth Z], QD [auth k], RB [auth G], RC [auth 1], RD [auth k], SB [auth H], SC [auth 1], SD [auth l], TB [auth H], TC [auth 1], TD [auth m], UB [auth I], UC [auth 2], UD [auth n], VB [auth J], VC [auth 2], VD [auth o], WB [auth K], WC [auth 3], WD [auth o], XB [auth L], XC [auth 5], XD [auth p], YB [auth L], YC [auth 6], YD [auth p], ZB [auth L], ZC [auth 7], ZD [auth p]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.57 Å
• R-Value Free: 0.264 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.234	α = 90
b = 151.503	β = 97.08
c = 235.032	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
CCP4	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-04-14 
• Released Date: 2011-02-02 
Deposition Author(s): Kumar, P., Singh, M., Karthikeyan, S.

Revision History  

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