PDBsum entry 1n07

Transferase

PDB id: 1n07

Contents

Protein chains

154 a.a. *

Ligands

ADP ×2

FMN ×2

Waters ×82

* Residue conservation analysis

PDB id:

1n07

Name:

Transferase

Title:

Crystal structure of schizosaccharomyces pombe riboflavin kinase reveals a novel atp and riboflavin binding fold

Structure:

Putative riboflavin kinase. Chain: a, b. Engineered: yes

Source:

Schizosaccharomyces pombe. Fission yeast. Organism_taxid: 4896. Gene: spcc18.16c. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.45Å R-factor: 0.228 R-free: 0.285

Authors:

S.Bauer,K.Kemter,A.Bacher,R.Huber,M.Fischer,S.Steinbacher

Key ref:

S.Bauer et al. (2003). Crystal structure of Schizosaccharomyces pombe riboflavin kinase reveals a novel ATP and riboflavin-binding fold. J Mol Biol, 326, 1463-1473. PubMed id: 12595258 DOI: 10.1016/S0022-2836(03)00059-7

Date:

11-Oct-02 Release date: 25-Feb-03

Protein chains

O74866  (RIFK_SCHPO) -  Riboflavin kinase from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 163 a.a.

Struc: 154 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.1.26 - riboflavin kinase.
• Reaction: riboflavin + ATP = FMN + ADP + H⁺

riboflavin + ATP = FMN (Bound ligand (Het Group name = ADP) corresponds exactly) + ADP (Bound ligand (Het Group name = FMN) corresponds exactly) + H(+)

• Cofactor: Mg(2+) or Zn(2+) or Mn(2+)

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

reference

DOI no: 10.1016/S0022-2836(03)00059-7

J Mol Biol 326:1463-1473 (2003)

PubMed id: 12595258

Crystal structure of Schizosaccharomyces pombe riboflavin kinase reveals a novel ATP and riboflavin-binding fold.

S.Bauer, K.Kemter, A.Bacher, R.Huber, M.Fischer, S.Steinbacher.

ABSTRACT

The essential redox cofactors riboflavin monophosphate (FMN) and flavin adenine dinucleotide (FAD) are synthesised from their precursor, riboflavin, in sequential reactions by the metal-dependent riboflavin kinase and FAD synthetase. Here, we describe the 1.6A crystal structure of the Schizosaccharomyces pombe riboflavin kinase. The enzyme represents a novel family of phosphoryl transferring enzymes. It is a monomer comprising a central beta-barrel clasped on one side by two C-terminal helices that display an L-like shape. The opposite side of the beta-barrel serves as a platform for substrate binding as demonstrated by complexes with ADP and FMN. Formation of the ATP-binding site requires significant rearrangements in a short alpha-helix as compared to the substrate free form. The diphosphate moiety of ADP is covered by the glycine-rich flap I formed from parts of this alpha-helix. In contrast, no significant changes are observed upon binding of riboflavin. The ribityl side-chain might be covered by a rather flexible flap II. The unusual metal-binding site involves, in addition to the ADP phosphates, only the strictly conserved Thr45. This may explain the preference for zinc observed in vitro.

Selected figure(s)

Figure 1.
Figure 1. Reaction catalysed by riboflavin kinase and FAD synthetase. 1, Riboflavin; 2, FMN; 3, FAD.

Figure 5.
Figure 5. Proposed catalytic mechanism of riboflavin synthase. (a) Stereo drawings of the active site of the riboflavin kinase. Bound FMN and ADP are shown as ball-and-stick models. The position of the zinc ion was taken from ADP+Zn complex. Flap I covers the b and g phosphate-binding sites. (b) Residues involved in catalysis.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 326, 1463-1473) copyright 2003.

Figures were selected by an automated process.