1T13

Crystal Structure Of Lumazine Synthase From Brucella Abortus Bound To 5-nitro-6-(D-ribitylamino)-2,4(1H,3H) pyrimidinedione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Crystallographic studies on Decameric Brucella spp. Lumazine Synthase: A Novel Quaternary Arrangement Evolved for a New Function?

Klinke, S.Zylberman, V.Vega, D.R.Guimaraes, B.G.Braden, B.C.Goldbaum, F.A.

(2005) J.Mol.Biol. 353: 124-137

  • DOI: 10.1016/j.jmb.2005.08.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The enzyme lumazine synthase (LS) catalyzes the penultimate step of riboflavin biosynthesis in plants, fungi and bacteria. The quaternary structure of the polypeptide differs between species, existing as pentamers or as icosahedrally arranged dodecam ...

    The enzyme lumazine synthase (LS) catalyzes the penultimate step of riboflavin biosynthesis in plants, fungi and bacteria. The quaternary structure of the polypeptide differs between species, existing as pentamers or as icosahedrally arranged dodecamers of pentamers with 60 subunits. The pathogen Brucella spp. expresses two proteins that exhibit LS activity, RibH1 and RibH2. The latter enzyme belongs to a novel third category of quaternary arrangement for LS, that of a decameric structure assembled as a head-to-head oriented dimer of pentamers. In contrast, the RibH1 enzyme is assembled as a pentamer, as noted for several other LS enzymes. RibH1 appears to be the functional LS in Brucella spp., whereas RibH2, an enzyme of lower catalytic activity, is a virulence factor presumably acting in response to oxidative stress. The latter observation prompted us to further investigate the structural and catalytic properties of RibH2 in order to clarify the biological function of this enzyme. Here, we present a detailed analysis of two new crystallographic forms of RibH2 that explain the low catalytic activity of this enzyme in comparison with RibH1 and other LSs. Additionally, we analyze the effect of pH on the structure of this enzyme, and the binding of riboflavin and 6,7-dimethyl-8-ribityllumazine to its active site.


    Organizational Affiliation

    FundaciĆ³n Instituto Leloir, C1405BWE Buenos Aires, Argentina.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6,7-dimethyl-8-ribityllumazine synthase
A, B, C, D, E
158Brucella abortus biovar 1 (strain 9-941)Mutation(s): 0 
Gene Names: ribH2 (ribH, ribH-2)
EC: 2.5.1.78
Find proteins for P61711 (Brucella abortus biovar 1 (strain 9-941))
Go to UniProtKB:  P61711
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D, E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
INI
Query on INI

Download SDF File 
Download CCD File 
A, B, C, D, E
5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE
C9 H14 N4 O8
KSKGHNZSCSCHEQ-RPDRRWSUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
INIKd: 42 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.217 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 126.321α = 90.00
b = 126.321β = 90.00
c = 165.669γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
CCP4data scaling
CNSrefinement
AMoREphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2013-01-16
    Type: Structure summary
  • Version 1.4: 2019-07-24
    Type: Data collection, Refinement description
  • Version 1.5: 2019-08-14
    Type: Data collection