2I0F

Lumazine synthase RibH1 from Brucella abortus (Gene BruAb1_0785, Swiss-Prot entry Q57DY1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and Kinetic Properties of Lumazine Synthase Isoenzymes in the Order Rhizobiales

Klinke, S.Zylberman, V.Bonomi, H.R.Haase, I.Guimaraes, B.G.Braden, B.C.Bacher, A.Fischer, M.Goldbaum, F.A.

(2007) J.Mol.Biol. 373: 664-680

  • DOI: 10.1016/j.jmb.2007.08.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 6,7-Dimethyl-8-ribityllumazine synthase (lumazine synthase; LS) catalyzes the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. This protein is known to exhibit different quaternary assemblies between species, existing ...

    6,7-Dimethyl-8-ribityllumazine synthase (lumazine synthase; LS) catalyzes the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. This protein is known to exhibit different quaternary assemblies between species, existing as free pentamers, decamers (dimers of pentamers) and icosahedrally arranged dodecamers of pentamers. A phylogenetic analysis on eubacterial, fungal and plant LSs allowed us to classify them into two categories: Type I LSs (pentameric or icosahedral) and Type II LSs (decameric). The Rhizobiales represent an order of alpha-proteobacteria that includes, among others, the genera Mesorhizobium, Agrobacterium and Brucella. Here, we present structural and kinetic studies on several LSs from Rhizobiales. Interestingly, Mesorhizobium and Brucella encode both a Type-I LS and a Type-II LS called RibH1 and RibH2, respectively. We show that Type II LSs appear to be almost inactive, whereas Type I LSs present a highly variable catalytic activity according to the genus. Additionally, we have solved four RibH1/RibH2 crystallographic structures from the genera Mesorhizobium and Brucella. The relationship between the active-site architecture and catalytic properties in these isoenzymes is discussed, and a model that describes the enzymatic behavior is proposed. Furthermore, sequence alignment studies allowed us to extend our results to the genus Agrobacterium. Our results suggest that the selective pressure controlling the riboflavin pathway favored the evolution of catalysts with low reaction rates, since the excess of flavins in the intracellular pool in Rhizobiales could act as a negative factor when these bacteria are exposed to oxidative or nitrosative stress.


    Organizational Affiliation

    FundaciĆ³n Instituto Leloir, IIBBA-CONICET, C1405BWE, Buenos Aires, Argentina. sklinke@leloir.org.ar




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6,7-dimethyl-8-ribityllumazine synthase 1
A, B, C, D, E
157Brucella abortus biovar 1 (strain 9-941)Mutation(s): 0 
Gene Names: ribH1 (ribH, ribH-1)
EC: 2.5.1.78
Find proteins for Q57DY1 (Brucella abortus biovar 1 (strain 9-941))
Go to UniProtKB:  Q57DY1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.242 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 124.101α = 90.00
b = 68.521β = 108.40
c = 90.649γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
SCALAdata scaling
CNSrefinement
AMoREphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-01-16
    Type: Structure summary
  • Version 1.3: 2017-10-18
    Type: Refinement description