PDBsum entry: 1pkv

Transferase

PDB id: 1pkv

Contents

Protein chains

87 a.a. *

Ligands

RBF ×2

Waters ×37

* Residue conservation analysis

PDB id:

1pkv

Name:

Transferase

Title:

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

Structure:

Riboflavin synthase alpha chain. Chain: a, b. Fragment: n-terminal domain. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: ribe or ribc or b1662 or sf1690. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: xl1-blue cells.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.60Å R-factor: 0.177 R-free: 0.235

Authors:

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

Key ref:

W.Meining et al. (2003). The structure of the N-terminal domain of riboflavin synthase in complex with riboflavin at 2.6A resolution. J Mol Biol, 331, 1053-1063. PubMed id: 12927541 DOI: 10.1016/S0022-2836(03)00844-1

Date:

06-Jun-03 Release date: 08-Jun-04

Protein chains

P0AFU8  (RISA_ECOLI) -  Riboflavin synthase alpha chain

Seq: 213 a.a.

Struc: 87 a.a.

Enzyme reactions

• Enzyme class: E.C.2.5.1.9 - Riboflavin synthase.
• Reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D- ribitylamino)-5-amino-2,6-dihydroxypyrimidine

2 × 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin (Bound ligand (Het Group name = RBF) corresponds exactly) + 4-(1-D- ribitylamino)-5-amino-2,6-dihydroxypyrimidine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: oxidation-reduction process (2 terms)
• Biochemical function: oxidoreductase activity (2 terms)

Added reference

DOI no: 10.1016/S0022-2836(03)00844-1

J Mol Biol 331:1053-1063 (2003)

PubMed id: 12927541

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

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

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.

Selected figure(s)

Figure 3.
Figure 3. Refined electron density covering riboflavin (orange) and surrounding residues from subunit A (green) and B (red). The electron density was carved out using the programs MAMA and AVE. 35,36

Figure 4.
Figure 4. The structure of the N-terminal domain dimer of riboflavin synthase from E. coli with bound riboflavin viewed along the 2-fold non-crystallographic symmetry axis.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 331, 1053-1063) copyright 2003.

Figures were selected by the author.