1KZL

Riboflavin Synthase from S.pombe bound to Carboxyethyllumazine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Studies on the Reaction Mechanism of Riboflavin Synthase; X-Ray Crystal Structure of a Complex with 6-Carboxyethyl-7-Oxo-8-Ribityllumazine

Gerhardt, S.Schott, A.K.Kairies, N.Cushman, M.Illarionov, B.Eisenreich, W.Bacher, A.Huber, R.Steinbacher, S.Fischer, M.

(2002) STRUCTURE 10: 1371-1381


  • PubMed Abstract: 
  • Riboflavin synthase catalyzes the disproportionation of 6,7-dimethyl-8-ribityllumazine affording riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. We have determined the structure of riboflavin synthase from Schizosaccharomyces pombe ...

    Riboflavin synthase catalyzes the disproportionation of 6,7-dimethyl-8-ribityllumazine affording riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. We have determined the structure of riboflavin synthase from Schizosaccharomyces pombe in complex with the substrate analog, 6-carboxyethyl-7-oxo-8-ribityllumazine at 2.1 A resolution. In contrast to the homotrimeric solution state of native riboflavin synthase, we found the enzyme to be monomeric in the crystal structure. Structural comparison of the riboflavin synthases of S. pombe and Escherichia coli suggests oligomer contact sites and delineates the catalytic site for dimerization of the substrate and subsequent fragmentation of the pentacyclic intermediate. The pentacyclic substrate dimer was modeled into the proposed active site, and its stereochemical features were determined. The model suggests that the substrate molecule at the C-terminal domain donates a four-carbon unit to the substrate molecule bound at the N-terminal domain of an adjacent subunit in the oligomer.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried, Germany. gerhardt@biochem.mpg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Riboflavin Synthase
A
208Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rib5
EC: 2.5.1.9
Find proteins for Q9Y7P0 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9Y7P0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CRM
Query on CRM

Download SDF File 
Download CCD File 
A
3-[8-((2S,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL)-2,4,7-TRIOXO-1,3,8-TRIHYDROPTERIDIN-6-YL]PROPANOIC ACID
CARBOXYETHYLLUMAZINE
C14 H18 N4 O9
PTYCEIBBGGLADD-PJKMHFRUSA-N
 Ligand Interaction
HG
Query on HG

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Download CCD File 
A
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 70.485α = 90.00
b = 70.485β = 90.00
c = 92.952γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-06
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance