1PKV

The N-terminal domain of riboflavin synthase in complex with riboflavin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of the N-terminal domain of riboflavin synthase in complex with riboflavin at 2.6A resolution.

Meining, W.Eberhardt, S.Bacher, A.Ladenstein, R.

(2003) J.Mol.Biol. 331: 1053-1063


  • PubMed Abstract: 
  • Riboflavin synthase of Escherichia coli is a homotrimer with a molecular mass of 70 kDa. The enzyme catalyzes the dismutation of 6,7-dimethyl-8-(1'-D-ribityl)-lumazine, affording riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. The N ...

    Riboflavin synthase of Escherichia coli is a homotrimer with a molecular mass of 70 kDa. The enzyme catalyzes the dismutation of 6,7-dimethyl-8-(1'-D-ribityl)-lumazine, affording riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. The N-terminal segment (residues 1-87) and the C-terminal segment (residues 98-187) form beta-barrels with similar fold and a high degree of sequence similarity. A recombinant peptide comprising amino acid residues 1-97 forms a dimer, which binds riboflavin with high affinity. Here, we report the structure of this construct in complex with riboflavin at 2.6A resolution. It is demonstrated that the complex can serve as a model for ligand-binding in the native enzyme. The structure and riboflavin-binding mode is in excellent agreement with structural information obtained from the native enzyme from Escherichia coli and riboflavin synthase from Schizosaccharomyces pombe. The implications for the binding specificity and the regiospecificity of the catalyzed reaction are discussed.


    Related Citations: 
    • Domain structure of riboflavin synthase
      Eberhardt, S.,Zingler, N.,Kemter, K.,Richter, G.,Cushman, M.,Bacher, A.
      (2001) Eur.J.Biochem. 268: 4315
    • Riboflavin Synthase of Escherichia coli. Effect of single amino acid substitutions on reaction rate and ligand binding properties
      Illarionov, B.,Kemter, K.,Eberhardt, S.,Richter, G.,Cushman, M.,Bacher, A.
      (2001) J.Biol.Chem. 276: 11524


    Organizational Affiliation

    Södertörns Högskola, S-14189, Huddinge, Sweden. winfried.meining@csb.ki.se




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Riboflavin synthase alpha chain
A, B
97Escherichia coli (strain K12)Gene Names: ribC (ribE)
EC: 2.5.1.9
Find proteins for P0AFU8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AFU8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RBF
Query on RBF

Download SDF File 
Download CCD File 
A, B
RIBOFLAVIN
RIBOFLAVINE; VITAMIN B2
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.174 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 50.161α = 90.00
b = 104.383β = 90.00
c = 85.113γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-08
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance