4G6I

Crystallographic structure of trimeric riboflavin synthase from Brucella abortus in complex with roseoflavin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic and kinetic study of riboflavin synthase from Brucella abortus, a chemotherapeutic target with an enhanced intrinsic flexibility.

Serer, M.I.Bonomi, H.R.Guimaraes, B.G.Rossi, R.C.Goldbaum, F.A.Klinke, S.

(2014) Acta Crystallogr.,Sect.D 70: 1419-1434

  • DOI: 10.1107/S1399004714005161
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Riboflavin synthase (RS) catalyzes the last step of riboflavin biosynthesis in microorganisms and plants, which corresponds to the dismutation of two molecules of 6,7-dimethyl-8-ribityllumazine to yield one molecule of riboflavin and one molecule of ...

    Riboflavin synthase (RS) catalyzes the last step of riboflavin biosynthesis in microorganisms and plants, which corresponds to the dismutation of two molecules of 6,7-dimethyl-8-ribityllumazine to yield one molecule of riboflavin and one molecule of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. Owing to the absence of this enzyme in animals and the fact that most pathogenic bacteria show a strict dependence on riboflavin biosynthesis, RS has been proposed as a potential target for antimicrobial drug development. Eubacterial, fungal and plant RSs assemble as homotrimers lacking C3 symmetry. Each monomer can bind two substrate molecules, yet there is only one active site for the whole enzyme, which is located at the interface between two neighbouring chains. This work reports the crystallographic structure of RS from the pathogenic bacterium Brucella abortus (the aetiological agent of the disease brucellosis) in its apo form, in complex with riboflavin and in complex with two different product analogues, being the first time that the structure of an intact RS trimer with bound ligands has been solved. These crystal models support the hypothesis of enhanced flexibility in the particle and also highlight the role of the ligands in assembling the unique active site. Kinetic and binding studies were also performed to complement these findings. The structural and biochemical information generated may be useful for the rational design of novel RS inhibitors with antimicrobial activity.


    Organizational Affiliation

    Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Riboflavin synthase subunit alpha
A, B, C
210N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RS3
Query on RS3

Download SDF File 
Download CCD File 
A, B, C
1-deoxy-1-[8-(dimethylamino)-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl]-D-ribitol
Roseoflavin
C18 H23 N5 O6
IGQLDUYTWDABFK-GUTXKFCHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.040α = 90.00
b = 92.570β = 90.00
c = 102.580γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
AMoREphasing
REFMACrefinement
MxCuBEdata collection
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2014-05-14
    Type: Database references
  • Version 1.2: 2014-05-28
    Type: Database references