PDBsum entry 4ha9

Oxidoreductase

PDB id: 4ha9

Contents

Protein chains

219 a.a.

204 a.a.

Ligands

NDP

Waters ×70

PDB id:

4ha9

Name:

Oxidoreductase

Title:

Structural insights into the reduction mechanism of saccharomyces cerevisia riboflavin biosynthesis reductase rib7

Structure:

2,5-diamino-6-ribosylamino-4(3h)-pyrimidinone 5'-phosphate reductase. Chain: a, b. Synonym: daropp reductase, darp reductase, 2,5-diamino-6-(5-phospho- d-ribosylamino)pyrimidin-4(3h)-one reductase, 2,5-diamino-6- ribitylamino-4(3h)-pyrimidinone 5'-phosphate synthase, daripp synthase. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: rib7, ybr153w, ybr1203. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.35Å R-factor: 0.208 R-free: 0.265

Authors:

Z.Lv,J.Sun,Y.Liu

Key ref:

Z.Lv et al. (2013). Structural and functional insights into Saccharomyces cerevisiae riboflavin biosynthesis reductase RIB7. Plos One, 8, e61249. PubMed id: 23620735 DOI: 10.1371/journal.pone.0061249

Date:

25-Sep-12 Release date: 04-Sep-13

Protein chain

P33312  (RIB7_YEAST) -  2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 244 a.a.

Struc: 219 a.a.

Protein chain

P33312  (RIB7_YEAST) -  2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 244 a.a.

Struc: 204 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: E.C.1.1.1.302 - 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase.
• Reaction:
  1. 2,5-diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphate + NAD⁺ = 2,5-diamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + NADH + H⁺
  2. 2,5-diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphate + NADP⁺ = 2,5-diamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + NADPH + H⁺

2,5-diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphate + NAD(+) (Bound ligand (Het Group name = NDP) matches with 91.67% similarity) = 2,5-diamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + NADH + H(+)

2,5-diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphate + NADP(+) (Bound ligand (Het Group name = NDP) corresponds exactly) = 2,5-diamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + NADPH + H(+)

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

reference

DOI no: 10.1371/journal.pone.0061249

Plos One 8:e61249 (2013)

PubMed id: 23620735

Structural and functional insights into Saccharomyces cerevisiae riboflavin biosynthesis reductase RIB7.

Z.Lv, J.Sun, Y.Liu.

ABSTRACT

Saccharomyces cerevisiae RIB7 (ScRIB7) is a potent target for anti-fungal agents because of its involvement in the riboflavin biosynthesis pathway as a NADPH-dependent reductase. However, the catalytic mechanism of riboflavin biosynthesis reductase (RBSRs) is controversial, and enzyme structure information is still lacking in eukaryotes. Here we report the crystal structure of Saccharomyces cerevisiae RIB7 at 2.10 Å resolution and its complex with NADPH at 2.35 Å resolution. ScRIB7 exists as a stable homodimer, and each subunit consists of nine central β-sheets flanked by five helices, resembling the structure of RIB7 homologues. A conserved G(76)-X-G(78)-Xn-G(181)-G(182) motif is present at the NADPH pyrophosphate group binding site. Activity assays confirmed the necessity of Thr79, Asp83, Glu180 and Gly182 for the activity of ScRIB7. Substrate preference of ScRIB7 was altered by mutating one residue (Thr35) to a Lysine, implying that ScRIB7 Thr35 and its corresponding residue, a lysine in bacteria, are important in substrate-specific recognition.