1PKV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

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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

  • DOI: 10.1016/s0022-2836(03)00844-1
  • Primary Citation of Related Structures:  
    1PKV

  • 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-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 ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Riboflavin synthase alpha chainA, B97Escherichia coliMutation(s): 0 
Gene Names: RIBE OR RIBC OR B1662 OR SF1690
EC: 2.5.1.9
UniProt
Find proteins for P0AFU8 (Escherichia coli (strain K12))
Explore P0AFU8 
Go to UniProtKB:  P0AFU8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFU8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RBF
Query on RBF

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
RIBOFLAVIN
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.161α = 90
b = 104.383β = 90
c = 85.113γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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