Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21.90 kDa 
• Atom Count: 1421 
• Modelled Residue Count: 174 
• Deposited Residue Count: 194 
• Unique protein chains: 1

1PKV

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

• PDB DOI: 10.2210/pdb1PKV/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-06-06 Released: 2004-06-08 
• Deposition Author(s): Meining, W., Eberhardt, S., Bacher, A., Ladenstein, R.

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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 

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: 12927541 
• 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. 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.

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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

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Organizational Affiliation: 

Södertörns Högskola, S-14189, Huddinge, Sweden. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Riboflavin synthase alpha chain	A, B	97	Escherichia coli	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RBF	C [auth A], D [auth B]	RIBOFLAVIN C17 H20 N4 O6 AUNGANRZJHBGPY-SCRDCRAPSA-N

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 = 50.161	α = 90
b = 104.383	β = 90
c = 85.113	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-06-06 
• Released Date: 2004-06-08 
Deposition Author(s): Meining, W., Eberhardt, S., Bacher, A., Ladenstein, R.

Revision History  

• 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