PDBsum entry 5glg

Oxidoreductase

PDB id: 5glg

Contents

Protein chain

471 a.a.

Ligands

SIN

FAD

Waters ×110

PDB id:

5glg

Name:

Oxidoreductase

Title:

The novel function of osm1 under anaerobic condition in the er was revealed by crystal structure of osm1, a soluble fumarate reductase in yeast

Structure:

Fumarate reductase 2. Chain: a. Synonym: frds2,nadh-dependent fumarate reductase,osmotic sensitivity protein 1,soluble fumarate reductase,mitochondrial isozyme. Engineered: yes

Source:

Saccharomyces cerevisiae s288c. Baker's yeast. Organism_taxid: 559292. Strain: s288c. Gene: osm1. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.80Å R-factor: 0.181 R-free: 0.214

Authors:

H.H.Park,J.Y.Choi

Key ref:

S.Kim et al. (2018). Molecular basis of maintaining an oxidizing environment under anaerobiosis by soluble fumarate reductase. Nat Commun, 9, 4867. PubMed id: 30451826 DOI: 10.1038/s41467-018-07285-9

Date:

11-Jul-16 Release date: 12-Jul-17

Protein chain

P21375  (OSM1_YEAST) -  Fumarate reductase 2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 501 a.a.

Struc: 471 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.3.1.6 - fumarate reductase (NADH).
• Reaction: succinate + NAD⁺ = fumarate + NADH + H⁺

succinate (Bound ligand (Het Group name = FAD) matches with 76.36% similarity) + NAD(+) (Bound ligand (Het Group name = SIN) corresponds exactly) = fumarate + NADH + H(+)

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

reference

DOI no: 10.1038/s41467-018-07285-9

Nat Commun 9:4867 (2018)

PubMed id: 30451826

Molecular basis of maintaining an oxidizing environment under anaerobiosis by soluble fumarate reductase.

S.Kim, C.M.Kim, Y.J.Son, J.Y.Choi, R.K.Siegenthaler, Y.Lee, T.H.Jang, J.Song, H.Kang, C.A.Kaiser, H.H.Park.

ABSTRACT

Osm1 and Frd1 are soluble fumarate reductases from yeast that are critical for allowing survival under anaerobic conditions. Although they maintain redox balance during anaerobiosis, the underlying mechanism is not understood. Here, we report the crystal structure of a eukaryotic soluble fumarate reductase, which is unique among soluble fumarate reductases as it lacks a heme domain. Structural and enzymatic analyses indicate that Osm1 has a specific binding pocket for flavin molecules, including FAD, FMN, and riboflavin, catalyzing their oxidation while reducing fumarate to succinate. Moreover, ER-resident Osm1 can transfer electrons from the Ero1 FAD cofactor to fumarate either by free FAD or by a direct interaction, allowing de novo disulfide bond formation in the absence of oxygen. We conclude that soluble eukaryotic fumarate reductases can maintain an oxidizing environment under anaerobic conditions, either by oxidizing cellular flavin cofactors or by a direct interaction with flavoenzymes such as Ero1.